diff --git a/configs/005_trust_align_test/env.yml b/configs/005_trust_align_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7269a235a90bf200ab897dadb084044fe93a1643
--- /dev/null
+++ b/configs/005_trust_align_test/env.yml
@@ -0,0 +1,97 @@
+name: 005_trust_align_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - blas=2.136
+  - blas-devel=3.9.0
+  - brotli-python=1.1.0
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - certifi=2024.2.2
+  - charset-normalizer=3.3.2
+  - colorama=0.4.6
+  - cycler=0.12.1
+  - freetype=2.14.1
+  - idna=3.10
+  - joblib=1.4.2
+  - kiwisolver=1.4.4
+  - lcms2=2.17
+  - ld_impl_linux-64=2.44
+  - lerc=4.0.0
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libdeflate=1.24
+  - libffi=3.4.6
+  - libfreetype=2.14.1
+  - libfreetype6=2.14.1
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgomp=15.1.0
+  - libjpeg-turbo=3.1.0
+  - liblapack=3.9.0
+  - liblapacke=3.9.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.30
+  - libpng=1.6.50
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.7.1
+  - libuuid=2.41.2
+  - libwebp-base=1.6.0
+  - libxcb=1.17.0
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - matplotlib-base=3.4.3
+  - ncurses=6.5
+  - networkx=2.8.8
+  - numpy=1.24.4
+  - openblas=0.3.30
+  - openjpeg=2.5.4
+  - openssl=3.5.4
+  - packaging=25.0
+  - pandas=2.0.3
+  - patsy=0.5.6
+  - pillow=10.4.0
+  - pip=22.1.2
+  - plotly=5.24.1
+  - pthread-stubs=0.4
+  - pyparsing=3.1.4
+  - pysocks=1.7.1
+  - python=3.8.20
+  - python-dateutil=2.8.2
+  - python-tzdata=2025.2
+  - python_abi=3.8
+  - pytz=2024.2
+  - readline=8.2
+  - requests=2.32.3
+  - scikit-learn=1.3.2
+  - scipy=1.9.3
+  - seaborn=0.13.2
+  - seaborn-base=0.13.2
+  - setuptools=70.3.0
+  - statsmodels=0.13.5
+  - tenacity=8.5.0
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - tornado=6.2
+  - tqdm=4.67.1
+  - urllib3=2.2.1
+  - wheel=0.45.1
+  - xorg-libxau=1.0.12
+  - xorg-libxdmcp=1.1.5
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - zstd=1.5.7
+  - pip:
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/005_trust_align_test
diff --git a/configs/005_trust_align_test/explicit.txt b/configs/005_trust_align_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b3c660a068b88b956abacead2624b4ba1bc988d
--- /dev/null
+++ b/configs/005_trust_align_test/explicit.txt
@@ -0,0 +1,94 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8
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+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba
+https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda#9fa334557db9f63da6c9285fd2a48638
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+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
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+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb9d3cd8_0.conda#f6ebe2cb3f82ba6c057dde5d9debe4f7
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480
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diff --git a/configs/005_trust_align_test/meta.json b/configs/005_trust_align_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0dde47f264b4001eda5ce42facc4c9e9e629a405
--- /dev/null
+++ b/configs/005_trust_align_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "005_trust_align_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/005_trust_align_test",
+  "exported_at": "2026-05-17T04:03:09Z"
+}
diff --git a/configs/005_trust_align_test/pip-clean.txt b/configs/005_trust_align_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f271a23de93dc8c8129983d777110b01acb7fe5c
--- /dev/null
+++ b/configs/005_trust_align_test/pip-clean.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
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+fbpca==1.0
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+ffmpy==0.3.2
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+ftfy==6.0.3
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+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
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+gitdb==4.0.11
+GitPython==3.1.43
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+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
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+hf_transfer==0.1.9
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+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
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+importlib-metadata==7.0.0
+importlib_resources==6.4.5
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+iniconfig==1.1.1
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+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
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+jsonpath-python==1.0.6
+jsonpickle==2.0.0
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+kaggle==1.7.4.5
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+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
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+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
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+litellm==1.77.4
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+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
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+MarkupSafe==2.1.5
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+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
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+monotonic==1.6
+mrcfile==1.5.4
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+multidict==6.0.5
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+murmurhash==1.0.10
+mypy-extensions==1.0.0
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+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.9.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/009_brain_bandit_test/editable.txt b/configs/009_brain_bandit_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/009_brain_bandit_test/env.yml b/configs/009_brain_bandit_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bfb283f99f9a29a067fc495a2692cbe4abd338bb
--- /dev/null
+++ b/configs/009_brain_bandit_test/env.yml
@@ -0,0 +1,117 @@
+name: 009_brain_bandit_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - blas=2.136
+  - blas-devel=3.9.0
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - certifi=2024.2.2
+  - colorama=0.4.6
+  - cycler=0.12.1
+  - freetype=2.14.1
+  - joblib=1.4.2
+  - kiwisolver=1.4.4
+  - lcms2=2.17
+  - ld_impl_linux-64=2.44
+  - lerc=4.0.0
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libdeflate=1.24
+  - libffi=3.4.6
+  - libfreetype=2.14.1
+  - libfreetype6=2.14.1
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgomp=15.1.0
+  - libjpeg-turbo=3.1.0
+  - liblapack=3.9.0
+  - liblapacke=3.9.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.30
+  - libpng=1.6.50
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.7.1
+  - libuuid=2.41.2
+  - libwebp-base=1.6.0
+  - libxcb=1.17.0
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - matplotlib-base=3.4.3
+  - ncurses=6.5
+  - openblas=0.3.30
+  - openjpeg=2.5.4
+  - openssl=3.5.4
+  - packaging=25.0
+  - pandas=2.0.3
+  - patsy=0.5.6
+  - pillow=10.4.0
+  - pip=22.1.2
+  - plotly=5.24.1
+  - pthread-stubs=0.4
+  - pyparsing=3.1.4
+  - python=3.8.20
+  - python-dateutil=2.8.2
+  - python-tzdata=2025.2
+  - python_abi=3.8
+  - pytz=2024.2
+  - readline=8.2
+  - scikit-learn=1.3.2
+  - scipy=1.9.3
+  - seaborn=0.13.2
+  - seaborn-base=0.13.2
+  - setuptools=70.3.0
+  - statsmodels=0.13.5
+  - tenacity=8.5.0
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - tornado=6.2
+  - tqdm=4.67.1
+  - wheel=0.45.1
+  - xorg-libxau=1.0.12
+  - xorg-libxdmcp=1.1.5
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - zstd=1.5.7
+  - pip:
+    - filelock==3.16.1
+    - flatbuffers==25.9.23
+    - fsspec==2025.3.0
+    - google-auth==2.41.1
+    - google-auth-oauthlib==1.0.0
+    - idna==3.10
+    - jinja2==3.1.6
+    - keras==2.13.1
+    - libclang==18.1.1
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.3
+    - nvidia-cudnn-cu12==8.9.2.26
+    - nvidia-nccl-cu12==2.18.1
+    - protobuf==4.25.8
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - six==1.17.0
+    - sympy==1.13.3
+    - tensorboard==2.13.0
+    - tensorboard-data-server==0.7.2
+    - tensorflow==2.13.1
+    - tensorflow-estimator==2.13.0
+    - tensorflow-io-gcs-filesystem==0.34.0
+    - torch==2.1.2
+    - triton==2.1.0
+    - typing-extensions==4.5.0
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/009_brain_bandit_test
diff --git a/configs/009_brain_bandit_test/explicit.txt b/configs/009_brain_bandit_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c089cb55b9d0e48bdd237d8135af9db270ac677
--- /dev/null
+++ b/configs/009_brain_bandit_test/explicit.txt
@@ -0,0 +1,87 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba
+https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda#9fa334557db9f63da6c9285fd2a48638
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
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diff --git a/configs/009_brain_bandit_test/meta.json b/configs/009_brain_bandit_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0d5474525d0160bd9018ddd7ad6abb7587fd2813
--- /dev/null
+++ b/configs/009_brain_bandit_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "009_brain_bandit_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/009_brain_bandit_test",
+  "exported_at": "2026-05-17T04:03:14Z"
+}
diff --git a/configs/009_brain_bandit_test/pip-clean.txt b/configs/009_brain_bandit_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79411482ee6b05f843beca0c8483ab58d2255d51
--- /dev/null
+++ b/configs/009_brain_bandit_test/pip-clean.txt
@@ -0,0 +1,467 @@
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diff --git a/configs/009_brain_bandit_test/pip-freeze.txt b/configs/009_brain_bandit_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0728bb90dae94a4002caacafb8080564078f5466
--- /dev/null
+++ b/configs/009_brain_bandit_test/pip-freeze.txt
@@ -0,0 +1,475 @@
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+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/013_attention_as_hypernetwork_test/editable.txt b/configs/013_attention_as_hypernetwork_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/013_attention_as_hypernetwork_test/env.yml b/configs/013_attention_as_hypernetwork_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0bf04b8500d9cd5e3c5c450593dfc6cc55a871e1
--- /dev/null
+++ b/configs/013_attention_as_hypernetwork_test/env.yml
@@ -0,0 +1,47 @@
+name: 013_attention_as_hypernetwork_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - cached-property==2.0.1
+    - contextlib2==21.6.0
+    - etils==1.3.0
+    - flax==0.7.2
+    - markdown-it-py==3.0.0
+    - ml-collections==0.1.1
+    - numpy==1.24.4
+    - orbax-checkpoint==0.2.3
+    - packaging==25.0
+    - pyyaml==6.0.3
+    - six==1.17.0
+    - tensorstore==0.1.45
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/013_attention_as_hypernetwork_test
diff --git a/configs/013_attention_as_hypernetwork_test/explicit.txt b/configs/013_attention_as_hypernetwork_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/013_attention_as_hypernetwork_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/013_attention_as_hypernetwork_test/meta.json b/configs/013_attention_as_hypernetwork_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2123c89af5c1974298469f1f0958cbd398fdb169
--- /dev/null
+++ b/configs/013_attention_as_hypernetwork_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "013_attention_as_hypernetwork_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/013_attention_as_hypernetwork_test",
+  "exported_at": "2026-05-17T04:03:16Z"
+}
diff --git a/configs/013_attention_as_hypernetwork_test/pip-clean.txt b/configs/013_attention_as_hypernetwork_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..356667b47994492a227f7fec94563a8f7c5693a9
--- /dev/null
+++ b/configs/013_attention_as_hypernetwork_test/pip-clean.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
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+bs4==0.0.2
+cached-property==2.0.1
+cachetools==4.2.4
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+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contextlib2==21.6.0
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
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+einops==0.7.0
+email-validator==2.3.0
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+equinox==0.10.4
+et-xmlfile==1.1.0
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+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
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+graphlib_backport==1.1.0
+greenlet==1.1.2
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+h11==0.14.0
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+httpx==0.28.1
+httpx-sse==0.4.0
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+icetk==0.0.4
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
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+kubernetes==29.0.0
+langchain==0.1.16
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+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+tensorstore==0.1.45
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/013_attention_as_hypernetwork_test/pip-freeze.txt b/configs/013_attention_as_hypernetwork_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..356667b47994492a227f7fec94563a8f7c5693a9
--- /dev/null
+++ b/configs/013_attention_as_hypernetwork_test/pip-freeze.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cached-property==2.0.1
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contextlib2==21.6.0
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+etils==1.3.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+flax==0.7.2
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+ml_collections==0.1.1
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+orbax-checkpoint==0.2.3
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+tensorstore==0.1.45
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/017_test/editable.txt b/configs/017_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/017_test/env.yml b/configs/017_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7f198098b02041d0d5b4aec87dd0a5f431db035e
--- /dev/null
+++ b/configs/017_test/env.yml
@@ -0,0 +1,49 @@
+name: 017_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - beartype==0.13.1
+    - cached-property==2.0.1
+    - cloudpickle==3.1.1
+    - decorator==5.2.1
+    - etils==1.3.0
+    - gpjax==0.6.9
+    - numpy==1.24.4
+    - orbax-checkpoint==0.2.3
+    - packaging==25.0
+    - plum-dispatch==2.2.1
+    - scipy==1.10.1
+    - simple-pytree==0.1.7
+    - six==1.17.0
+    - tensorflow-probability==0.19.0
+    - tensorstore==0.1.45
+prefix: /home/lily/yz979/anaconda3/envs/017_test
diff --git a/configs/017_test/explicit.txt b/configs/017_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/017_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
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diff --git a/configs/017_test/meta.json b/configs/017_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d2c611535459b38786fef77421e618be4fbe2776
--- /dev/null
+++ b/configs/017_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "017_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/017_test",
+  "exported_at": "2026-05-17T04:03:20Z"
+}
diff --git a/configs/017_test/pip-clean.txt b/configs/017_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ec45729e1a892e0fd479867702d2f3ed93a5dda
--- /dev/null
+++ b/configs/017_test/pip-clean.txt
@@ -0,0 +1,454 @@
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diff --git a/configs/017_test/pip-freeze.txt b/configs/017_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ec45729e1a892e0fd479867702d2f3ed93a5dda
--- /dev/null
+++ b/configs/017_test/pip-freeze.txt
@@ -0,0 +1,454 @@
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+cloudpickle==3.1.1
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+decorator==5.2.1
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+etils==1.3.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpjax==0.6.9
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+orbax-checkpoint==0.2.3
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+plum-dispatch==2.2.1
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+simple-pytree==0.1.7
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+tensorflow-probability==0.19.0
+tensorstore==0.1.45
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/018_test/editable.txt b/configs/018_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/018_test/env.yml b/configs/018_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..538a4932f674206a38bd4b19312e2b539635cb6a
--- /dev/null
+++ b/configs/018_test/env.yml
@@ -0,0 +1,72 @@
+name: 018_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - charset-normalizer==3.4.3
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - filelock==3.16.1
+    - fonttools==4.57.0
+    - idna==3.10
+    - importlib-resources==6.4.5
+    - jinja2==3.1.6
+    - kiwisolver==1.4.7
+    - lpips==0.1.4
+    - markupsafe==2.1.5
+    - matplotlib==3.7.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-cusparse-cu12==12.1.0.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - torchvision==0.19.1
+    - triton==3.0.0
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/018_test
diff --git a/configs/018_test/explicit.txt b/configs/018_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/018_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/018_test/meta.json b/configs/018_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..bc021f79924e89c5f3b35e89dcea36d5662d413b
--- /dev/null
+++ b/configs/018_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "018_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/018_test",
+  "exported_at": "2026-05-17T04:03:23Z"
+}
diff --git a/configs/018_test/pip-clean.txt b/configs/018_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad8bd83c921680ba9e7cb6721be751a01e331047
--- /dev/null
+++ b/configs/018_test/pip-clean.txt
@@ -0,0 +1,472 @@
+absl-py==2.3.1
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+vllm==0.2.7
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diff --git a/configs/018_test/pip-freeze.txt b/configs/018_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad8bd83c921680ba9e7cb6721be751a01e331047
--- /dev/null
+++ b/configs/018_test/pip-freeze.txt
@@ -0,0 +1,472 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
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+azure-storage-blob==12.26.0
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+chaospy==3.3.9
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+Deprecated==1.2.14
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+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lpips==0.1.4
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/019_test/editable.txt b/configs/019_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/019_test/env.yml b/configs/019_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7bf5eee132a1a65c613152a4d74797e93c342b19
--- /dev/null
+++ b/configs/019_test/env.yml
@@ -0,0 +1,179 @@
+name: 019_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2026.4.22
+  - ld_impl_linux-64=2.45.1
+  - libexpat=2.7.5
+  - libffi=3.5.2
+  - libgcc=15.2.0
+  - libgcc-ng=15.2.0
+  - libgomp=15.2.0
+  - liblzma=5.8.3
+  - libnsl=2.0.1
+  - libsqlite=3.53.0
+  - libuuid=2.42
+  - libxcrypt=4.4.36
+  - libzlib=1.3.2
+  - ncurses=6.6
+  - openssl=3.6.2
+  - packaging=26.2
+  - pip=26.0.1
+  - python=3.10.20
+  - readline=8.3
+  - tk=8.6.13
+  - wheel=0.47.0
+  - zstd=1.5.7
+  - pip:
+    - accelerate==1.13.0
+    - adjusttext==1.3.0
+    - aiohappyeyeballs==2.6.1
+    - aiohttp==3.13.5
+    - aiosignal==1.4.0
+    - annotated-doc==0.0.4
+    - annotated-types==0.7.0
+    - anyio==4.13.0
+    - asttokens==3.0.1
+    - async-timeout==5.0.1
+    - attrs==26.1.0
+    - babe==0.0.7
+    - beartype==0.22.9
+    - better-abc==0.0.3
+    - bitsandbytes==0.49.2
+    - certifi==2026.4.22
+    - charset-normalizer==3.4.7
+    - click==8.3.3
+    - colorama==0.4.6
+    - config2py==0.1.47
+    - contourpy==1.3.2
+    - cuda-bindings==13.2.0
+    - cuda-pathfinder==1.5.4
+    - cuda-toolkit==13.0.2
+    - cycler==0.12.1
+    - datasets==4.8.5
+    - decorator==5.2.1
+    - dill==0.4.1
+    - docstring-parser==0.18.0
+    - dol==0.3.41
+    - einops==0.8.2
+    - exceptiongroup==1.3.1
+    - executing==2.2.1
+    - fancy-einsum==0.0.3
+    - filelock==3.29.0
+    - fonttools==4.62.1
+    - frozenlist==1.8.0
+    - fsspec==2026.2.0
+    - gitdb==4.0.12
+    - gitpython==3.1.49
+    - graze==0.1.39
+    - h11==0.16.0
+    - hf-xet==1.4.3
+    - httpcore==1.0.9
+    - httpx==0.28.1
+    - huggingface-hub==1.12.2
+    - i2==0.1.63
+    - idna==3.13
+    - importlib-resources==7.1.0
+    - ipython==8.39.0
+    - jaxtyping==0.3.7
+    - jedi==0.19.2
+    - jinja2==3.1.6
+    - joblib==1.5.3
+    - kiwisolver==1.5.0
+    - markdown-it-py==4.0.0
+    - markupsafe==3.0.3
+    - matplotlib==3.10.9
+    - matplotlib-inline==0.2.1
+    - mdurl==0.1.2
+    - mpmath==1.3.0
+    - multidict==6.7.1
+    - multiprocess==0.70.19
+    - narwhals==2.20.0
+    - neel-plotly==0.0.0
+    - networkx==3.4.2
+    - nltk==3.9.4
+    - numpy==2.2.6
+    - nvidia-cublas==13.1.0.3
+    - nvidia-cuda-cupti==13.0.85
+    - nvidia-cuda-nvrtc==13.0.88
+    - nvidia-cuda-runtime==13.0.96
+    - nvidia-cudnn-cu13==9.19.0.56
+    - nvidia-cufft==12.0.0.61
+    - nvidia-cufile==1.15.1.6
+    - nvidia-curand==10.4.0.35
+    - nvidia-cusolver==12.0.4.66
+    - nvidia-cusparse==12.6.3.3
+    - nvidia-cusparselt-cu13==0.8.0
+    - nvidia-nccl-cu13==2.28.9
+    - nvidia-nvjitlink==13.0.88
+    - nvidia-nvshmem-cu13==3.4.5
+    - nvidia-nvtx==13.0.85
+    - pandas==2.3.3
+    - parso==0.8.6
+    - patsy==1.0.2
+    - pexpect==4.9.0
+    - pillow==12.2.0
+    - platformdirs==4.9.6
+    - plotly==6.7.0
+    - plotly-express==0.4.1
+    - prompt-toolkit==3.0.52
+    - propcache==0.4.1
+    - protobuf==7.34.1
+    - psutil==7.2.2
+    - ptyprocess==0.7.0
+    - pure-eval==0.2.3
+    - py2store==0.1.22
+    - pyarrow==24.0.0
+    - pydantic==2.13.3
+    - pydantic-core==2.46.3
+    - pygments==2.20.0
+    - pyparsing==3.3.2
+    - python-dateutil==2.9.0.post0
+    - python-dotenv==1.2.2
+    - pytz==2026.1.post1
+    - pyyaml==6.0.3
+    - rapidfuzz==3.14.5
+    - regex==2026.4.4
+    - requests==2.33.1
+    - rich==15.0.0
+    - sae-lens==6.42.0
+    - safetensors==0.7.0
+    - scikit-learn==1.7.2
+    - scipy==1.15.3
+    - seaborn==0.13.2
+    - sentencepiece==0.2.1
+    - sentry-sdk==2.58.0
+    - setuptools==81.0.0
+    - shellingham==1.5.4
+    - simple-parsing==0.1.8
+    - six==1.17.0
+    - smmap==5.0.3
+    - stack-data==0.6.3
+    - statsmodels==0.14.6
+    - sympy==1.14.0
+    - tenacity==9.1.4
+    - thefuzz==0.22.1
+    - threadpoolctl==3.6.0
+    - tokenizers==0.22.2
+    - torch==2.11.0
+    - tqdm==4.67.3
+    - traitlets==5.14.3
+    - transformer-lens==3.0.0
+    - transformers==5.7.0
+    - transformers-stream-generator==0.0.5
+    - triton==3.6.0
+    - typeguard==4.5.1
+    - typer==0.25.0
+    - typing-extensions==4.15.0
+    - typing-inspection==0.4.2
+    - tzdata==2026.2
+    - urllib3==2.6.3
+    - wadler-lindig==0.1.7
+    - wandb==0.26.1
+    - wcwidth==0.6.0
+    - xxhash==3.7.0
+    - yarl==1.23.0
+prefix: /home/lily/yz979/anaconda3/envs/019_test
diff --git a/configs/019_test/explicit.txt b/configs/019_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49231f8372a4e98cb167a8e993eb3e11dfe74864
--- /dev/null
+++ b/configs/019_test/explicit.txt
@@ -0,0 +1,29 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda#49f570f3bc4c874a06ea69b7225753af
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a360c33a5abe61c07959e449fa1453eb
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda#d5e96b1ed75ca01906b3d2469b4ce493
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.0-h0c1763c_0.conda#393c8b31bd128e3d979e7ec17e9507c6
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda#38ffe67b78c9d4de527be8315e5ada2c
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda#fc21868a1a5aacc937e7a18747acb8a5
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
+https://conda.anaconda.org/conda-forge/linux-64/python-3.10.20-h3c07f61_0_cpython.conda#5d4e2b00d99feacd026859b7fa239dc0
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.2-pyhc364b38_0.conda#4c06a92e74452cfa53623a81592e8934
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.47.0-pyhd8ed1ab_0.conda#d0e3b2f0030cf4fca58bde71d246e94c
+https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh8b19718_0.conda#67bdec43082fd8a9cffb9484420b39a2
diff --git a/configs/019_test/meta.json b/configs/019_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..abfc51dc0af6301f5c6b86abf60d622010f46e0e
--- /dev/null
+++ b/configs/019_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "019_test",
+  "python_version": "3.10.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/019_test",
+  "exported_at": "2026-05-17T04:03:36Z"
+}
diff --git a/configs/019_test/pip-clean.txt b/configs/019_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67b08ff31bedfb996efa6262b750499ce6fb9d26
--- /dev/null
+++ b/configs/019_test/pip-clean.txt
@@ -0,0 +1,147 @@
+accelerate==1.13.0
+adjustText==1.3.0
+aiohappyeyeballs==2.6.1
+aiohttp==3.13.5
+aiosignal==1.4.0
+annotated-doc==0.0.4
+annotated-types==0.7.0
+anyio==4.13.0
+asttokens==3.0.1
+async-timeout==5.0.1
+attrs==26.1.0
+babe==0.0.7
+beartype==0.22.9
+better-abc==0.0.3
+bitsandbytes==0.49.2
+certifi==2026.4.22
+charset-normalizer==3.4.7
+click==8.3.3
+colorama==0.4.6
+config2py==0.1.47
+contourpy==1.3.2
+cuda-bindings==13.2.0
+cuda-pathfinder==1.5.4
+cuda-toolkit==13.0.2
+cycler==0.12.1
+datasets==4.8.5
+decorator==5.2.1
+dill==0.4.1
+docstring_parser==0.18.0
+dol==0.3.41
+einops==0.8.2
+exceptiongroup==1.3.1
+executing==2.2.1
+fancy-einsum==0.0.3
+filelock==3.29.0
+fonttools==4.62.1
+frozenlist==1.8.0
+fsspec==2026.2.0
+gitdb==4.0.12
+GitPython==3.1.49
+graze==0.1.39
+h11==0.16.0
+hf-xet==1.4.3
+httpcore==1.0.9
+httpx==0.28.1
+huggingface_hub==1.12.2
+i2==0.1.63
+idna==3.13
+importlib_resources==7.1.0
+ipython==8.39.0
+jaxtyping==0.3.7
+jedi==0.19.2
+Jinja2==3.1.6
+joblib==1.5.3
+kiwisolver==1.5.0
+markdown-it-py==4.0.0
+MarkupSafe==3.0.3
+matplotlib==3.10.9
+matplotlib-inline==0.2.1
+mdurl==0.1.2
+mpmath==1.3.0
+multidict==6.7.1
+multiprocess==0.70.19
+narwhals==2.20.0
+neel_plotly @ git+https://github.com/neelnanda-io/neel-plotly.git@6dc24b26f8dec991908479d7445dae496b3430b7
+networkx==3.4.2
+nltk==3.9.4
+numpy==2.2.6
+nvidia-cublas==13.1.0.3
+nvidia-cuda-cupti==13.0.85
+nvidia-cuda-nvrtc==13.0.88
+nvidia-cuda-runtime==13.0.96
+nvidia-cudnn-cu13==9.19.0.56
+nvidia-cufft==12.0.0.61
+nvidia-cufile==1.15.1.6
+nvidia-curand==10.4.0.35
+nvidia-cusolver==12.0.4.66
+nvidia-cusparse==12.6.3.3
+nvidia-cusparselt-cu13==0.8.0
+nvidia-nccl-cu13==2.28.9
+nvidia-nvjitlink==13.0.88
+nvidia-nvshmem-cu13==3.4.5
+nvidia-nvtx==13.0.85
+pandas==2.3.3
+parso==0.8.6
+patsy==1.0.2
+pexpect==4.9.0
+pillow==12.2.0
+platformdirs==4.9.6
+plotly==6.7.0
+plotly-express==0.4.1
+prompt_toolkit==3.0.52
+propcache==0.4.1
+protobuf==7.34.1
+psutil==7.2.2
+ptyprocess==0.7.0
+pure_eval==0.2.3
+py2store==0.1.22
+pyarrow==24.0.0
+pydantic==2.13.3
+pydantic_core==2.46.3
+Pygments==2.20.0
+pyparsing==3.3.2
+python-dateutil==2.9.0.post0
+python-dotenv==1.2.2
+pytz==2026.1.post1
+PyYAML==6.0.3
+RapidFuzz==3.14.5
+regex==2026.4.4
+requests==2.33.1
+rich==15.0.0
+sae-lens==6.42.0
+safetensors==0.7.0
+scikit-learn==1.7.2
+scipy==1.15.3
+seaborn==0.13.2
+sentencepiece==0.2.1
+sentry-sdk==2.58.0
+shellingham==1.5.4
+simple-parsing==0.1.8
+six==1.17.0
+smmap==5.0.3
+stack-data==0.6.3
+statsmodels==0.14.6
+sympy==1.14.0
+tenacity==9.1.4
+thefuzz==0.22.1
+threadpoolctl==3.6.0
+tokenizers==0.22.2
+torch==2.11.0
+tqdm==4.67.3
+traitlets==5.14.3
+transformer-lens==3.0.0
+transformers==5.7.0
+transformers-stream-generator==0.0.5
+triton==3.6.0
+typeguard==4.5.1
+typer==0.25.0
+typing-inspection==0.4.2
+typing_extensions==4.15.0
+tzdata==2026.2
+urllib3==2.6.3
+wadler_lindig==0.1.7
+wandb==0.26.1
+wcwidth==0.6.0
+xxhash==3.7.0
+yarl==1.23.0
diff --git a/configs/019_test/pip-freeze.txt b/configs/019_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c9901499b59a4c7bdab4b82e87b76a554228bd0
--- /dev/null
+++ b/configs/019_test/pip-freeze.txt
@@ -0,0 +1,148 @@
+accelerate==1.13.0
+adjustText==1.3.0
+aiohappyeyeballs==2.6.1
+aiohttp==3.13.5
+aiosignal==1.4.0
+annotated-doc==0.0.4
+annotated-types==0.7.0
+anyio==4.13.0
+asttokens==3.0.1
+async-timeout==5.0.1
+attrs==26.1.0
+babe==0.0.7
+beartype==0.22.9
+better-abc==0.0.3
+bitsandbytes==0.49.2
+certifi==2026.4.22
+charset-normalizer==3.4.7
+click==8.3.3
+colorama==0.4.6
+config2py==0.1.47
+contourpy==1.3.2
+cuda-bindings==13.2.0
+cuda-pathfinder==1.5.4
+cuda-toolkit==13.0.2
+cycler==0.12.1
+datasets==4.8.5
+decorator==5.2.1
+dill==0.4.1
+docstring_parser==0.18.0
+dol==0.3.41
+einops==0.8.2
+exceptiongroup==1.3.1
+executing==2.2.1
+fancy-einsum==0.0.3
+filelock==3.29.0
+fonttools==4.62.1
+frozenlist==1.8.0
+fsspec==2026.2.0
+gitdb==4.0.12
+GitPython==3.1.49
+graze==0.1.39
+h11==0.16.0
+hf-xet==1.4.3
+httpcore==1.0.9
+httpx==0.28.1
+huggingface_hub==1.12.2
+i2==0.1.63
+idna==3.13
+importlib_resources==7.1.0
+ipython==8.39.0
+jaxtyping==0.3.7
+jedi==0.19.2
+Jinja2==3.1.6
+joblib==1.5.3
+kiwisolver==1.5.0
+markdown-it-py==4.0.0
+MarkupSafe==3.0.3
+matplotlib==3.10.9
+matplotlib-inline==0.2.1
+mdurl==0.1.2
+mpmath==1.3.0
+multidict==6.7.1
+multiprocess==0.70.19
+narwhals==2.20.0
+neel_plotly @ git+https://github.com/neelnanda-io/neel-plotly.git@6dc24b26f8dec991908479d7445dae496b3430b7
+networkx==3.4.2
+nltk==3.9.4
+numpy==2.2.6
+nvidia-cublas==13.1.0.3
+nvidia-cuda-cupti==13.0.85
+nvidia-cuda-nvrtc==13.0.88
+nvidia-cuda-runtime==13.0.96
+nvidia-cudnn-cu13==9.19.0.56
+nvidia-cufft==12.0.0.61
+nvidia-cufile==1.15.1.6
+nvidia-curand==10.4.0.35
+nvidia-cusolver==12.0.4.66
+nvidia-cusparse==12.6.3.3
+nvidia-cusparselt-cu13==0.8.0
+nvidia-nccl-cu13==2.28.9
+nvidia-nvjitlink==13.0.88
+nvidia-nvshmem-cu13==3.4.5
+nvidia-nvtx==13.0.85
+packaging @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_packaging_1777103621/work
+pandas==2.3.3
+parso==0.8.6
+patsy==1.0.2
+pexpect==4.9.0
+pillow==12.2.0
+platformdirs==4.9.6
+plotly==6.7.0
+plotly-express==0.4.1
+prompt_toolkit==3.0.52
+propcache==0.4.1
+protobuf==7.34.1
+psutil==7.2.2
+ptyprocess==0.7.0
+pure_eval==0.2.3
+py2store==0.1.22
+pyarrow==24.0.0
+pydantic==2.13.3
+pydantic_core==2.46.3
+Pygments==2.20.0
+pyparsing==3.3.2
+python-dateutil==2.9.0.post0
+python-dotenv==1.2.2
+pytz==2026.1.post1
+PyYAML==6.0.3
+RapidFuzz==3.14.5
+regex==2026.4.4
+requests==2.33.1
+rich==15.0.0
+sae-lens==6.42.0
+safetensors==0.7.0
+scikit-learn==1.7.2
+scipy==1.15.3
+seaborn==0.13.2
+sentencepiece==0.2.1
+sentry-sdk==2.58.0
+shellingham==1.5.4
+simple-parsing==0.1.8
+six==1.17.0
+smmap==5.0.3
+stack-data==0.6.3
+statsmodels==0.14.6
+sympy==1.14.0
+tenacity==9.1.4
+thefuzz==0.22.1
+threadpoolctl==3.6.0
+tokenizers==0.22.2
+torch==2.11.0
+tqdm==4.67.3
+traitlets==5.14.3
+transformer-lens==3.0.0
+transformers==5.7.0
+transformers-stream-generator==0.0.5
+triton==3.6.0
+typeguard==4.5.1
+typer==0.25.0
+typing-inspection==0.4.2
+typing_extensions==4.15.0
+tzdata==2026.2
+urllib3==2.6.3
+wadler_lindig==0.1.7
+wandb==0.26.1
+wcwidth==0.6.0
+xxhash==3.7.0
+yarl==1.23.0
diff --git a/configs/022_test/editable.txt b/configs/022_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/022_test/env.yml b/configs/022_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a0088fb5687b1c02ea0e0ab513ea0a08f7aa6b42
--- /dev/null
+++ b/configs/022_test/env.yml
@@ -0,0 +1,49 @@
+name: 022_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.2.25
+    - filelock==3.13.1
+    - fsspec==2024.6.1
+    - httpx==0.28.1
+    - idna==3.10
+    - jinja2==3.1.4
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - typing-extensions==4.12.2
+prefix: /home/lily/yz979/anaconda3/envs/022_test
diff --git a/configs/022_test/explicit.txt b/configs/022_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/022_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/022_test/meta.json b/configs/022_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a10e663d8d744308fd85dc1d651a0f5f183ef9d9
--- /dev/null
+++ b/configs/022_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "022_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/022_test",
+  "exported_at": "2026-05-17T04:03:29Z"
+}
diff --git a/configs/022_test/pip-clean.txt b/configs/022_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89195ebdf3a23b68d8d8be1d3c5324c922f990d6
--- /dev/null
+++ b/configs/022_test/pip-clean.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.2.25
+cffi==1.15.0
+cftime==1.6.4.post1
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+confection==0.1.4
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+torch==2.4.1+cpu
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+torchaudio==2.1.2+cu118
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+typing-inspect==0.9.0
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+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
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+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
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+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
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+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/022_test/pip-freeze.txt b/configs/022_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89195ebdf3a23b68d8d8be1d3c5324c922f990d6
--- /dev/null
+++ b/configs/022_test/pip-freeze.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
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+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.2.25
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+chaospy==3.3.9
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+cobra==0.29.1
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+coloredlogs==15.0.1
+confection==0.1.4
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+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
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+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
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+Deprecated==1.2.14
+deprecation==2.1.0
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+dnspython==2.6.1
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+fastavro==1.9.4
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+fbpca==1.0
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+ffmpy==0.3.2
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+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/033_test/editable.txt b/configs/033_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/033_test/env.yml b/configs/033_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d7269fe4bbd69cc2c00987f7fe52d2720ad1236d
--- /dev/null
+++ b/configs/033_test/env.yml
@@ -0,0 +1,53 @@
+name: 033_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.2.25
+    - filelock==3.13.1
+    - fsspec==2024.6.1
+    - idna==3.10
+    - jinja2==3.1.4
+    - jsonlines==4.0.0
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - typing-extensions==4.12.2
+    - urllib3==2.2.3
+    - zstandard==0.23.0
+prefix: /home/lily/yz979/anaconda3/envs/033_test
diff --git a/configs/033_test/explicit.txt b/configs/033_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/033_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/033_test/meta.json b/configs/033_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..117f83f8a78669c3985dd51ec20f09ad878f8457
--- /dev/null
+++ b/configs/033_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "033_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/033_test",
+  "exported_at": "2026-05-17T04:03:41Z"
+}
diff --git a/configs/033_test/pip-clean.txt b/configs/033_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7849afc4d2a25f1763640bf54be07a404f35ab95
--- /dev/null
+++ b/configs/033_test/pip-clean.txt
@@ -0,0 +1,452 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.2.25
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.13.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonlines==4.0.0
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
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+torchaudio==2.1.2+cu118
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+tzdata==2024.1
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+umap-learn==0.5.7
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+wandb==0.22.0
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+weasel==0.3.4
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+xxhash==2.0.2
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+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
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diff --git a/configs/033_test/pip-freeze.txt b/configs/033_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7849afc4d2a25f1763640bf54be07a404f35ab95
--- /dev/null
+++ b/configs/033_test/pip-freeze.txt
@@ -0,0 +1,452 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+alabaster==0.7.12
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+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
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+attrs==25.3.0
+autograd==1.7.0
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+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
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+backoff==2.2.1
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+beartype==0.14.1
+better-abc==0.0.3
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+bitsandbytes==0.43.1
+blessed==1.20.0
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+chaospy==3.3.9
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+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/036_test/editable.txt b/configs/036_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/036_test/env.yml b/configs/036_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..792482ddee24e34cc946bb1a10dd563608462ead
--- /dev/null
+++ b/configs/036_test/env.yml
@@ -0,0 +1,48 @@
+name: 036_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.13.1
+    - fsspec==2024.6.1
+    - idna==3.10
+    - jinja2==3.1.4
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - peft==0.13.2
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - typing-extensions==4.12.2
+prefix: /home/lily/yz979/anaconda3/envs/036_test
diff --git a/configs/036_test/explicit.txt b/configs/036_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/036_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/036_test/meta.json b/configs/036_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7c970f78ae87138f2fdb6ad04ec7a479a8963d36
--- /dev/null
+++ b/configs/036_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "036_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/036_test",
+  "exported_at": "2026-05-17T04:03:44Z"
+}
diff --git a/configs/036_test/pip-clean.txt b/configs/036_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d4ce294b9f93d37039cf11f077cfdf9d5384f28
--- /dev/null
+++ b/configs/036_test/pip-clean.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.13.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.0
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
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+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
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+overrides==7.7.0
+packaging==26.2
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+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+peft==0.13.2
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
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+pycocotools==2.0.7
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+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
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+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
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+referencing==0.35.1
+regex==2022.4.24
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+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/036_test/pip-freeze.txt b/configs/036_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d4ce294b9f93d37039cf11f077cfdf9d5384f28
--- /dev/null
+++ b/configs/036_test/pip-freeze.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.13.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.0
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+peft==0.13.2
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/039_test/editable.txt b/configs/039_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/039_test/env.yml b/configs/039_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..31654c6f9a3e51a5faf39594def6b5f49fdb5d44
--- /dev/null
+++ b/configs/039_test/env.yml
@@ -0,0 +1,52 @@
+name: 039_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.24.4
+    - nvidia-cublas-cu11==11.10.3.66
+    - nvidia-cuda-nvrtc-cu11==11.7.99
+    - nvidia-cuda-runtime-cu11==11.7.99
+    - nvidia-cudnn-cu11==8.5.0.96
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - torch==1.13.1
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/039_test
diff --git a/configs/039_test/explicit.txt b/configs/039_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/039_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
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diff --git a/configs/039_test/meta.json b/configs/039_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9d9db3a073fa5981b8d9c4407144d8a8c91d806a
--- /dev/null
+++ b/configs/039_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "039_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/039_test",
+  "exported_at": "2026-05-17T04:03:44Z"
+}
diff --git a/configs/039_test/pip-clean.txt b/configs/039_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd8e330dcf05629740bed4de095b6bb9f6245677
--- /dev/null
+++ b/configs/039_test/pip-clean.txt
@@ -0,0 +1,456 @@
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diff --git a/configs/039_test/pip-freeze.txt b/configs/039_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd8e330dcf05629740bed4de095b6bb9f6245677
--- /dev/null
+++ b/configs/039_test/pip-freeze.txt
@@ -0,0 +1,456 @@
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+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu11==11.10.3.66
+nvidia-cuda-nvrtc-cu11==11.7.99
+nvidia-cuda-runtime-cu11==11.7.99
+nvidia-cudnn-cu11==8.5.0.96
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==1.13.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/042_test/editable.txt b/configs/042_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/042_test/env.yml b/configs/042_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b36aef3faeee365a50d1f8325fbd62fa2c2a06a5
--- /dev/null
+++ b/configs/042_test/env.yml
@@ -0,0 +1,75 @@
+name: 042_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.2.25
+    - cycler==0.12.1
+    - filelock==3.16.1
+    - fonttools==4.57.0
+    - fsspec==2025.3.0
+    - idna==3.10
+    - importlib-resources==6.4.5
+    - jinja2==3.1.6
+    - kiwisolver==1.4.7
+    - markupsafe==2.1.5
+    - matplotlib==3.7.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.9.2.10
+    - nvidia-cuda-cupti-cu12==12.9.79
+    - nvidia-cuda-nvrtc-cu12==12.9.86
+    - nvidia-cuda-runtime-cu12==12.9.79
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.4.1.4
+    - nvidia-curand-cu12==10.3.10.19
+    - nvidia-cusparse-cu12==12.5.10.65
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.9.79
+    - packaging==25.0
+    - pillow==10.4.0
+    - psutil==7.2.2
+    - pyparsing==3.1.4
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - torch-scatter==2.1.2
+    - torch-sparse==0.6.18
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/042_test
diff --git a/configs/042_test/explicit.txt b/configs/042_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/042_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/042_test/meta.json b/configs/042_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5878351a93a41e81fde780590125f702b1a1383f
--- /dev/null
+++ b/configs/042_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "042_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/042_test",
+  "exported_at": "2026-05-17T04:03:51Z"
+}
diff --git a/configs/042_test/pip-clean.txt b/configs/042_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1556cc5e401c3eb9f28e69174d140d000009336c
--- /dev/null
+++ b/configs/042_test/pip-clean.txt
@@ -0,0 +1,474 @@
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diff --git a/configs/042_test/pip-freeze.txt b/configs/042_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1556cc5e401c3eb9f28e69174d140d000009336c
--- /dev/null
+++ b/configs/042_test/pip-freeze.txt
@@ -0,0 +1,474 @@
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+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.9.2.10
+nvidia-cuda-cupti-cu12==12.9.79
+nvidia-cuda-nvrtc-cu12==12.9.86
+nvidia-cuda-runtime-cu12==12.9.79
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.4.1.4
+nvidia-curand-cu12==10.3.10.19
+nvidia-cusparse-cu12==12.5.10.65
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.9.79
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+psutil==7.2.2
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torch_scatter==2.1.2
+torch_sparse==0.6.18
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/048_test/editable.txt b/configs/048_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/048_test/env.yml b/configs/048_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..42d89a65323bcda840b2ecf353c3054e20000248
--- /dev/null
+++ b/configs/048_test/env.yml
@@ -0,0 +1,64 @@
+name: 048_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.4.22
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - idna==3.10
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.3
+    - nvidia-cublas-cu12==12.9.2.10
+    - nvidia-cuda-cupti-cu12==12.9.79
+    - nvidia-cuda-nvrtc-cu12==12.9.86
+    - nvidia-cuda-runtime-cu12==12.9.79
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.4.1.4
+    - nvidia-curand-cu12==10.3.10.19
+    - nvidia-cusparse-cu12==12.5.10.65
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.9.79
+    - packaging==25.0
+    - psutil==7.2.2
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/048_test
diff --git a/configs/048_test/explicit.txt b/configs/048_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/048_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/048_test/meta.json b/configs/048_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2b1c34a6dc2a1986a1bd158377a5466de0b7be37
--- /dev/null
+++ b/configs/048_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "048_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/048_test",
+  "exported_at": "2026-05-17T04:03:55Z"
+}
diff --git a/configs/048_test/pip-clean.txt b/configs/048_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77f41b0a4fb91f93b99473753600049d42dd36dc
--- /dev/null
+++ b/configs/048_test/pip-clean.txt
@@ -0,0 +1,465 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
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+torchaudio==2.1.2+cu118
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
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+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
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+word2number==1.1
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+xxhash==2.0.2
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+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
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diff --git a/configs/048_test/pip-freeze.txt b/configs/048_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77f41b0a4fb91f93b99473753600049d42dd36dc
--- /dev/null
+++ b/configs/048_test/pip-freeze.txt
@@ -0,0 +1,465 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
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+chaospy==3.3.9
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+Cython==0.29.30
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+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.3
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.9.2.10
+nvidia-cuda-cupti-cu12==12.9.79
+nvidia-cuda-nvrtc-cu12==12.9.86
+nvidia-cuda-runtime-cu12==12.9.79
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.4.1.4
+nvidia-curand-cu12==10.3.10.19
+nvidia-cusparse-cu12==12.5.10.65
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.9.79
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+psutil==7.2.2
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/050_test/editable.txt b/configs/050_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/050_test/env.yml b/configs/050_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c260d9b708cb6516ff5531fdc4b603004db68241
--- /dev/null
+++ b/configs/050_test/env.yml
@@ -0,0 +1,58 @@
+name: 050_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.9.2.10
+    - nvidia-cuda-cupti-cu12==12.9.79
+    - nvidia-cuda-nvrtc-cu12==12.9.86
+    - nvidia-cuda-runtime-cu12==12.9.79
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.4.1.4
+    - nvidia-curand-cu12==10.3.10.19
+    - nvidia-cusparse-cu12==12.5.10.65
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.9.79
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/050_test
diff --git a/configs/050_test/explicit.txt b/configs/050_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/050_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/050_test/meta.json b/configs/050_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d74fa3e1c5c3fd4a0278fd9e392942f170913e14
--- /dev/null
+++ b/configs/050_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "050_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/050_test",
+  "exported_at": "2026-05-17T04:03:58Z"
+}
diff --git a/configs/050_test/pip-clean.txt b/configs/050_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fc1e4e508ca31d9f244ccef325fcbc3573b99dd
--- /dev/null
+++ b/configs/050_test/pip-clean.txt
@@ -0,0 +1,460 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
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+nvidia-cublas-cu12==12.9.2.10
+nvidia-cuda-cupti-cu12==12.9.79
+nvidia-cuda-nvrtc-cu12==12.9.86
+nvidia-cuda-runtime-cu12==12.9.79
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.4.1.4
+nvidia-curand-cu12==10.3.10.19
+nvidia-cusparse-cu12==12.5.10.65
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.9.79
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+opentelemetry-sdk==1.24.0
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+opt-einsum==3.3.0
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+pathlib==1.0.1
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+pyfaidx==0.9.0.1
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+pymodbus==3.6.9
+PyMuPDF==1.23.16
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+pypdfium2==4.29.0
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+pyro-ppl==1.9.1
+pysam==0.23.3
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+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
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+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
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+PyYAML==6.0.3
+quantile-python==1.1
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+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
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+regex==2022.4.24
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+rouge-score==0.1.2
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+sacrebleu==2.1.0
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+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
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+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tifffile==2023.7.10
+tiktoken==0.7.0
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+toml==0.10.2
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+toolz==0.12.1
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+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+transformer-lens==2.16.1
+transformers==4.46.3
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+typeguard==4.4.0
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+typing-inspect==0.9.0
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+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/050_test/pip-freeze.txt b/configs/050_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fc1e4e508ca31d9f244ccef325fcbc3573b99dd
--- /dev/null
+++ b/configs/050_test/pip-freeze.txt
@@ -0,0 +1,460 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
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+fbpca==1.0
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+filelock==3.16.1
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+future==0.18.2
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+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
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+h11==0.14.0
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+httpx-sse==0.4.0
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+icetk==0.0.4
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
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+kubernetes==29.0.0
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+madoka==0.7.1
+marisa-trie==1.1.0
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+nvidia-cusparse-cu12==12.5.10.65
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
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+nvidia-nvtx-cu12==12.9.79
+nvitop==1.3.2
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+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
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+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/062_test/editable.txt b/configs/062_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/062_test/env.yml b/configs/062_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..31593c110d2c93a98e2e1d2c933fa000038d43f4
--- /dev/null
+++ b/configs/062_test/env.yml
@@ -0,0 +1,52 @@
+name: 062_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.4.22
+    - filelock==3.16.1
+    - fsspec==2024.6.1
+    - idna==3.10
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.1.2+cpu
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/062_test
diff --git a/configs/062_test/explicit.txt b/configs/062_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/062_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/062_test/meta.json b/configs/062_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..925dd9142e78b81a320979fc11c22df8a99e7d63
--- /dev/null
+++ b/configs/062_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "062_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/062_test",
+  "exported_at": "2026-05-17T04:04:13Z"
+}
diff --git a/configs/062_test/pip-clean.txt b/configs/062_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b836e62fd18dddf32452c1e0e7dfce5189ad4968
--- /dev/null
+++ b/configs/062_test/pip-clean.txt
@@ -0,0 +1,452 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
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+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
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+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
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+overrides==7.7.0
+packaging==26.2
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+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
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+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.1.2+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/062_test/pip-freeze.txt b/configs/062_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b836e62fd18dddf32452c1e0e7dfce5189ad4968
--- /dev/null
+++ b/configs/062_test/pip-freeze.txt
@@ -0,0 +1,452 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.1.2+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/068_test/editable.txt b/configs/068_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/068_test/env.yml b/configs/068_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e4e4739c287a8bbf587599ded64e3c32e7e17d70
--- /dev/null
+++ b/configs/068_test/env.yml
@@ -0,0 +1,68 @@
+name: 068_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.4.22
+    - filelock==3.16.1
+    - idna==3.10
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-cusparse-cu12==12.1.0.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - open-clip-torch==2.32.0
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scikit-image==0.21.0
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - torchvision==0.19.1
+    - triton==3.0.0
+    - urllib3==2.2.3
+    - wcwidth==0.2.14
+prefix: /home/lily/yz979/anaconda3/envs/068_test
diff --git a/configs/068_test/explicit.txt b/configs/068_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/068_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/068_test/meta.json b/configs/068_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6afade937224362c0e29a0329cf3d2600edb171c
--- /dev/null
+++ b/configs/068_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "068_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/068_test",
+  "exported_at": "2026-05-17T04:04:17Z"
+}
diff --git a/configs/068_test/pip-clean.txt b/configs/068_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02521cd84cf832b9167f95f0621c9a3456d70190
--- /dev/null
+++ b/configs/068_test/pip-clean.txt
@@ -0,0 +1,470 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+open_clip_torch==2.32.0
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-image==0.21.0
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+wcwidth==0.2.14
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/068_test/pip-freeze.txt b/configs/068_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02521cd84cf832b9167f95f0621c9a3456d70190
--- /dev/null
+++ b/configs/068_test/pip-freeze.txt
@@ -0,0 +1,470 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+open_clip_torch==2.32.0
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-image==0.21.0
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+wcwidth==0.2.14
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/070_test/editable.txt b/configs/070_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/070_test/env.yml b/configs/070_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a9a73efb68d422c7ca0b8995d53b7791eeb88016
--- /dev/null
+++ b/configs/070_test/env.yml
@@ -0,0 +1,42 @@
+name: 070_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.4.22
+    - httpx==0.28.1
+    - idna==3.13
+    - numpy==1.24.4
+    - ollama==0.6.1
+    - packaging==25.0
+    - six==1.17.0
+    - zhipuai==2.1.5.20250825
+prefix: /home/lily/yz979/anaconda3/envs/070_test
diff --git a/configs/070_test/explicit.txt b/configs/070_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/070_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
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diff --git a/configs/070_test/meta.json b/configs/070_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..059bbf8995d241219af5a197d4f5bf7aad74e8c9
--- /dev/null
+++ b/configs/070_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "070_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/070_test",
+  "exported_at": "2026-05-17T04:04:13Z"
+}
diff --git a/configs/070_test/pip-clean.txt b/configs/070_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e423ba35d5ea02e6998a1ae003a08963eeb5f35
--- /dev/null
+++ b/configs/070_test/pip-clean.txt
@@ -0,0 +1,447 @@
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diff --git a/configs/070_test/pip-freeze.txt b/configs/070_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e423ba35d5ea02e6998a1ae003a08963eeb5f35
--- /dev/null
+++ b/configs/070_test/pip-freeze.txt
@@ -0,0 +1,447 @@
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+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.13
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+ollama==0.6.1
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zhipuai==2.1.5.20250825
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/071_test/env.yml b/configs/071_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..82991c6416be1b33815e32054aedabb69647db91
--- /dev/null
+++ b/configs/071_test/env.yml
@@ -0,0 +1,64 @@
+name: 071_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.2.25
+    - filelock==3.16.1
+    - fsspec==2024.3.1
+    - idna==3.10
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.9.2.10
+    - nvidia-cuda-cupti-cu12==12.9.79
+    - nvidia-cuda-nvrtc-cu12==12.9.86
+    - nvidia-cuda-runtime-cu12==12.9.79
+    - nvidia-cudnn-cu12==8.9.2.26
+    - nvidia-cufft-cu12==11.4.1.4
+    - nvidia-curand-cu12==10.3.10.19
+    - nvidia-cusparse-cu12==12.5.10.65
+    - nvidia-nccl-cu12==2.18.1
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.9.79
+    - packaging==25.0
+    - python-dateutil==2.9.0.post0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.1.2
+    - triton==2.1.0
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/071_test
diff --git a/configs/075_test/editable.txt b/configs/075_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/075_test/env.yml b/configs/075_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..32edcd98cb5e0b0fa24beddb477b313fcc26f96c
--- /dev/null
+++ b/configs/075_test/env.yml
@@ -0,0 +1,69 @@
+name: 075_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - boto3==1.37.38
+    - botocore==1.37.38
+    - certifi==2026.2.25
+    - easydict==1.13
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - idna==3.10
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-cusparse-cu12==12.1.0.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - pillow==10.4.0
+    - pytest==8.3.5
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - s3transfer==0.11.5
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - torchvision==0.19.1
+    - triton==3.0.0
+    - urllib3==1.26.20
+prefix: /home/lily/yz979/anaconda3/envs/075_test
diff --git a/configs/075_test/explicit.txt b/configs/075_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/075_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
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diff --git a/configs/075_test/meta.json b/configs/075_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..797491f0611b7c65566b6b54ca3be28855c44016
--- /dev/null
+++ b/configs/075_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "075_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/075_test",
+  "exported_at": "2026-05-17T04:04:24Z"
+}
diff --git a/configs/075_test/pip-clean.txt b/configs/075_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c37cddec34d76fced276c1543fa1a4192dff56fd
--- /dev/null
+++ b/configs/075_test/pip-clean.txt
@@ -0,0 +1,467 @@
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diff --git a/configs/075_test/pip-freeze.txt b/configs/075_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c37cddec34d76fced276c1543fa1a4192dff56fd
--- /dev/null
+++ b/configs/075_test/pip-freeze.txt
@@ -0,0 +1,467 @@
+absl-py==2.3.1
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+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+easydict==1.13
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest==8.3.5
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==1.26.20
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_44757_7_test/editable.txt b/configs/s41467_024_44757_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bc990ddfe884ec5cfc34ca9bb19fcad7d9ab3d3
--- /dev/null
+++ b/configs/s41467_024_44757_7_test/editable.txt
@@ -0,0 +1 @@
+sift_sc-0.1.0.egg-link	/data/lily/yz979/xx/Python/s41467-024-44757-7/sift-sc
diff --git a/configs/s41467_024_44757_7_test/env.yml b/configs/s41467_024_44757_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f128da46b78df038fca790f1e1cab597d9e3b225
--- /dev/null
+++ b/configs/s41467_024_44757_7_test/env.yml
@@ -0,0 +1,149 @@
+name: s41467_024_44757_7_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - blas=1.1
+  - brotli-python=1.1.0
+  - bzip2=1.0.8
+  - ca-certificates=2026.4.22
+  - certifi=2024.2.2
+  - cffi=1.16.0
+  - filelock=3.16.1
+  - freetype=2.14.1
+  - fsspec=2024.10.0
+  - future=1.0.0
+  - jinja2=3.1.3
+  - joblib=1.4.2
+  - jpeg=9e
+  - lcms2=2.16
+  - ld_impl_linux-64=2.44
+  - lerc=4.0.0
+  - libabseil=20240116.2
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libdeflate=1.22
+  - libffi=3.4.6
+  - libfreetype=2.14.1
+  - libfreetype6=2.14.1
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgomp=15.1.0
+  - liblapack=3.9.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.25
+  - libpng=1.6.50
+  - libprotobuf=3.20.3
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.5.1
+  - libuuid=2.38.1
+  - libuv=1.51.0
+  - libwebp-base=1.6.0
+  - libxcb=1.13
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - markupsafe=2.1.5
+  - mpmath=1.3.0
+  - ncurses=6.5
+  - networkx=2.8.8
+  - ninja=1.13.1
+  - nomkl=1.0
+  - numpy=1.24.4
+  - openblas=0.3.25
+  - openjpeg=2.5.2
+  - openssl=3.6.2
+  - pillow=9.4.0
+  - pip=22.1.2
+  - pthread-stubs=0.4
+  - pycparser=2.22
+  - pysocks=1.7.1
+  - python=3.8.20
+  - python_abi=3.8
+  - pytorch=1.12.1
+  - pyyaml=6.0.2
+  - readline=8.2
+  - scikit-learn=1.3.2
+  - setuptools=70.3.0
+  - sleef=3.9.0
+  - sympy=1.13.0
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - torchvision=0.14.1
+  - typing-extensions=3.7.4.1
+  - typing_extensions=3.7.4.1
+  - wheel=0.45.1
+  - xorg-libxau=1.0.12
+  - xorg-libxdmcp=1.1.5
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - yaml=0.2.5
+  - zlib=1.3.1
+  - zstd=1.5.7
+  - pip:
+    - anndata==0.9.2
+    - asttokens==3.0.0
+    - backcall==0.2.0
+    - charset-normalizer==3.4.3
+    - contourpy==1.1.1
+    - coverage==7.6.1
+    - cycler==0.12.1
+    - decorator==5.2.1
+    - executing==2.2.0
+    - get-annotations==0.1.2
+    - h5py==3.11.0
+    - idna==3.10
+    - importlib-resources==6.4.5
+    - ipython==8.12.3
+    - jedi==0.19.2
+    - keopscore==2.3
+    - kiwisolver==1.4.7
+    - latexcodec==3.0.0
+    - llvmlite==0.41.1
+    - markdown-it-py==3.0.0
+    - matplotlib==3.7.5
+    - matplotlib-inline==0.1.7
+    - natsort==8.4.0
+    - numba==0.58.1
+    - packaging==25.0
+    - pandas==2.0.3
+    - parso==0.8.4
+    - patsy==1.0.1
+    - pexpect==4.9.0
+    - pickleshare==0.7.5
+    - ptyprocess==0.7.0
+    - pure-eval==0.2.3
+    - pybind11==3.0.0
+    - pybtex==0.25.1
+    - pybtex-docutils==1.0.3
+    - pykeops==2.3
+    - pynndescent==0.5.13
+    - pyparsing==3.1.4
+    - pytest-cov==5.0.0
+    - python-dateutil==2.9.0.post0
+    - requests==2.32.4
+    - scanpy==1.9.8
+    - scipy==1.10.1
+    - seaborn==0.13.2
+    - session-info==1.0.1
+    - sift-sc==0.1.0
+    - six==1.16.0
+    - sphinxcontrib-bibtex==2.6.3
+    - stack-data==0.6.3
+    - statsmodels==0.14.1
+    - stdlib-list==0.10.0
+    - traitlets==5.14.3
+    - umap-learn==0.5.7
+    - unittest-xml-reporting==3.2.0
+    - urllib3==2.2.3
+    - wcwidth==0.2.13
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_44757_7_test
diff --git a/configs/s41467_024_44757_7_test/explicit.txt b/configs/s41467_024_44757_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f77be84bd79cfd2ba23008cdf6579bef820d3d7
--- /dev/null
+++ b/configs/s41467_024_44757_7_test/explicit.txt
@@ -0,0 +1,95 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/noarch/nomkl-1.0-h5ca1d4c_0.tar.bz2#9a66894dfd07c4510beb6b3f9672ccc0
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
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diff --git a/configs/s41467_024_44757_7_test/meta.json b/configs/s41467_024_44757_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..b62d44114bedc6158914d7feb991dc92c23fda67
--- /dev/null
+++ b/configs/s41467_024_44757_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_44757_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 1,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_44757_7_test",
+  "exported_at": "2026-05-17T04:04:30Z"
+}
diff --git a/configs/s41467_024_44757_7_test/pip-clean.txt b/configs/s41467_024_44757_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..759ca1d5ef7cf12780eafc7e7e5857628619b2d2
--- /dev/null
+++ b/configs/s41467_024_44757_7_test/pip-clean.txt
@@ -0,0 +1,476 @@
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diff --git a/configs/s41467_024_44757_7_test/pip-freeze.txt b/configs/s41467_024_44757_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b91466b921b86e69e200502210bc78a014453f43
--- /dev/null
+++ b/configs/s41467_024_44757_7_test/pip-freeze.txt
@@ -0,0 +1,486 @@
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+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scanpy==1.9.8
+scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+-e git+https://github.com/nitzanlab/sift-sc.git@fa4e5615879abd3ddb108ec07c51a8217fe31035#egg=sift_sc
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-bibtex==2.6.3
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+stack-data==0.6.3
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy @ file:///home/conda/feedstock_root/build_artifacts/sympy_1721004795885/work
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==1.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision @ file:///home/conda/feedstock_root/build_artifacts/torchvision-split_1674349377586/work
+tornado==6.4
+tqdm==4.67.1
+traitlets==5.14.3
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1708239446578/work
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+wcwidth==0.2.13
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_44803_4_test/editable.txt b/configs/s41467_024_44803_4_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_44803_4_test/env.yml b/configs/s41467_024_44803_4_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6c2a10aa881d63c32e410f98cd85fd444b423298
--- /dev/null
+++ b/configs/s41467_024_44803_4_test/env.yml
@@ -0,0 +1,84 @@
+name: s41467_024_44803_4_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - attrs==25.3.0
+    - charset-normalizer==3.4.3
+    - comet-ml==3.51.0
+    - configobj==5.0.9
+    - coverage==7.6.1
+    - dill==0.3.8
+    - dulwich==0.22.4
+    - everett==3.1.0
+    - hf-xet==1.1.8
+    - huggingface-hub==0.34.4
+    - idna==3.10
+    - jsonschema==4.23.0
+    - jsonschema-specifications==2023.12.1
+    - markdown-it-py==3.0.0
+    - mpmath==1.3.0
+    - multiprocess==0.70.16
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - pandas==2.0.3
+    - pkgutil-resolve-name==1.3.10
+    - protobuf==5.29.5
+    - pyarrow==17.0.0
+    - pytest-cov==5.0.0
+    - python-box==6.1.0
+    - referencing==0.35.1
+    - requests==2.32.4
+    - requests-toolbelt==1.0.0
+    - rpds-py==0.20.1
+    - scipy==1.10.1
+    - sentry-sdk==2.35.0
+    - simplejson==3.20.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - tokenizers==0.20.3
+    - transformers==4.46.3
+    - typing-extensions==4.13.2
+    - unittest-xml-reporting==3.2.0
+    - urllib3==2.2.3
+    - wrapt==1.17.3
+    - wurlitzer==3.1.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_44803_4_test
diff --git a/configs/s41467_024_44803_4_test/explicit.txt b/configs/s41467_024_44803_4_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_44803_4_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_44803_4_test/meta.json b/configs/s41467_024_44803_4_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5aee5fe2248c47fd4350082648738a817520eaeb
--- /dev/null
+++ b/configs/s41467_024_44803_4_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_44803_4_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_44803_4_test",
+  "exported_at": "2026-05-17T04:04:28Z"
+}
diff --git a/configs/s41467_024_44803_4_test/pip-clean.txt b/configs/s41467_024_44803_4_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c661043b3d5da42ffcbf6eb657eb17faedf8a7f
--- /dev/null
+++ b/configs/s41467_024_44803_4_test/pip-clean.txt
@@ -0,0 +1,468 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+comet_ml==3.51.0
+confection==0.1.4
+ConfigArgParse==1.5.3
+configobj==5.0.9
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+dulwich==0.22.4
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+everett==3.1.0
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
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+nvidia-cuda-runtime-cu12==12.1.105
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+nvidia-ml-py==12.535.133
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+nvidia-nvtx-cu12==12.1.105
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+tzdata==2024.1
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+umap-learn==0.5.7
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
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+watchdog==3.0.0
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+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
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+Werkzeug==2.0.2
+word2number==1.1
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+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_44803_4_test/pip-freeze.txt b/configs/s41467_024_44803_4_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c661043b3d5da42ffcbf6eb657eb17faedf8a7f
--- /dev/null
+++ b/configs/s41467_024_44803_4_test/pip-freeze.txt
@@ -0,0 +1,468 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
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+chaospy==3.3.9
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+chromadb==0.4.15
+click==8.1.7
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+coloredlogs==15.0.1
+comet_ml==3.51.0
+confection==0.1.4
+ConfigArgParse==1.5.3
+configobj==5.0.9
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+coverage==7.6.1
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+cryptography==42.0.5
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+Deprecated==1.2.14
+deprecation==2.1.0
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+dulwich==0.22.4
+editdistance==0.6.0
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+fairseq==0.10.2
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+fancy-einsum==0.0.3
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+google-pasta==0.2.0
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+nvidia-cuda-runtime-cu12==12.1.105
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+nvidia-nvjitlink-cu12==12.9.86
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+nvitop==1.3.2
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+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+wrapt==1.17.3
+wurlitzer==3.1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_45674_5_test/editable.txt b/configs/s41467_024_45674_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_45674_5_test/env.yml b/configs/s41467_024_45674_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bac1b9155a39f8a06519cb59adb51bcff36b89a7
--- /dev/null
+++ b/configs/s41467_024_45674_5_test/env.yml
@@ -0,0 +1,179 @@
+name: s41467_024_45674_5_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - alsa-lib=1.2.14
+  - binutils_impl_linux-64=2.44
+  - binutils_linux-64=2.44
+  - brotli=1.1.0
+  - brotli-bin=1.1.0
+  - bzip2=1.0.8
+  - c-ares=1.34.5
+  - ca-certificates=2025.8.3
+  - cairo=1.18.4
+  - cmake=3.25.3
+  - contourpy=1.3.3
+  - cycler=0.12.1
+  - cyrus-sasl=2.1.28
+  - dbus=1.16.2
+  - double-conversion=3.3.1
+  - expat=2.7.1
+  - fftw=3.3.10
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=3.000
+  - font-ttf-source-code-pro=2.038
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.15.0
+  - fonts-conda-ecosystem=1
+  - fonts-conda-forge=1
+  - fonttools=4.60.1
+  - freetype=2.14.1
+  - gcc_impl_linux-64=13.4.0
+  - gcc_linux-64=13.4.0
+  - graphite2=1.3.14
+  - gtest=1.17.0
+  - gxx_impl_linux-64=13.4.0
+  - gxx_linux-64=13.4.0
+  - harfbuzz=12.1.0
+  - icu=75.1
+  - joblib=1.5.2
+  - kernel-headers_linux-64=4.18.0
+  - keyutils=1.6.3
+  - kiwisolver=1.4.9
+  - krb5=1.21.3
+  - lcms2=2.17
+  - ld_impl_linux-64=2.44
+  - lerc=4.0.0
+  - libblas=3.9.0
+  - libbrotlicommon=1.1.0
+  - libbrotlidec=1.1.0
+  - libbrotlienc=1.1.0
+  - libcblas=3.9.0
+  - libclang-cpp21.1=21.1.2
+  - libclang13=21.1.2
+  - libcups=2.3.3
+  - libcurl=8.14.1
+  - libdeflate=1.24
+  - libdrm=2.4.125
+  - libedit=3.1.20250104
+  - libegl=1.7.0
+  - libev=4.33
+  - libexpat=2.7.1
+  - libffi=3.4.6
+  - libfreetype=2.14.1
+  - libfreetype6=2.14.1
+  - libgcc=15.1.0
+  - libgcc-devel_linux-64=13.4.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgl=1.7.0
+  - libglib=2.86.0
+  - libglvnd=1.7.0
+  - libglx=1.7.0
+  - libgomp=15.1.0
+  - libiconv=1.18
+  - libjpeg-turbo=3.1.0
+  - liblapack=3.9.0
+  - libllvm21=21.1.2
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libmpdec=4.0.0
+  - libnghttp2=1.67.0
+  - libntlm=1.8
+  - libopenblas=0.3.30
+  - libopengl=1.7.0
+  - libpciaccess=0.18
+  - libpng=1.6.50
+  - libpq=18.0
+  - libsanitizer=13.4.0
+  - libsqlite=3.50.4
+  - libssh2=1.11.1
+  - libstdcxx=15.1.0
+  - libstdcxx-devel_linux-64=13.4.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.7.1
+  - libuuid=2.41.2
+  - libuv=1.51.0
+  - libvulkan-loader=1.4.313.0
+  - libwebp-base=1.6.0
+  - libxcb=1.17.0
+  - libxcrypt=4.4.36
+  - libxkbcommon=1.11.0
+  - libxml2=2.15.0
+  - libxml2-16=2.15.0
+  - libxslt=1.1.43
+  - libzlib=1.3.1
+  - matplotlib=3.10.6
+  - matplotlib-base=3.10.6
+  - munkres=1.1.4
+  - ncurses=6.5
+  - networkx=2.8.8
+  - numpy=2.3.3
+  - openjpeg=2.5.4
+  - openldap=2.6.10
+  - openssl=3.5.4
+  - packaging=25.0
+  - pandas=2.3.3
+  - patsy=1.0.1
+  - pcre2=10.46
+  - pillow=11.3.0
+  - pip=25.2
+  - pixman=0.46.4
+  - pthread-stubs=0.4
+  - pyparsing=3.2.5
+  - pyside6=6.9.3
+  - python=3.13.7
+  - python-dateutil=2.9.0.post0
+  - python-tzdata=2025.2
+  - python_abi=3.13
+  - pytz=2025.2
+  - qhull=2020.2
+  - qt6-main=6.9.3
+  - readline=8.2
+  - rhash=1.4.3
+  - scikit-learn=1.7.2
+  - scipy=1.16.2
+  - seaborn=0.13.2
+  - seaborn-base=0.13.2
+  - setuptools=80.9.0
+  - six=1.17.0
+  - statsmodels=0.14.5
+  - sysroot_linux-64=2.28
+  - threadpoolctl=3.6.0
+  - tk=8.6.13
+  - tornado=6.5.2
+  - tzdata=2025b
+  - wayland=1.24.0
+  - xcb-util=0.4.1
+  - xcb-util-cursor=0.1.5
+  - xcb-util-image=0.4.0
+  - xcb-util-keysyms=0.4.1
+  - xcb-util-renderutil=0.3.10
+  - xcb-util-wm=0.4.2
+  - xkeyboard-config=2.45
+  - xorg-libice=1.1.2
+  - xorg-libsm=1.2.6
+  - xorg-libx11=1.8.12
+  - xorg-libxau=1.0.12
+  - xorg-libxcomposite=0.4.6
+  - xorg-libxcursor=1.2.3
+  - xorg-libxdamage=1.1.6
+  - xorg-libxdmcp=1.1.5
+  - xorg-libxext=1.3.6
+  - xorg-libxfixes=6.0.2
+  - xorg-libxi=1.8.2
+  - xorg-libxrandr=1.5.4
+  - xorg-libxrender=0.9.12
+  - xorg-libxtst=1.2.5
+  - xorg-libxxf86vm=1.1.6
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - zlib=1.3.1
+  - zstd=1.5.7
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45674_5_test
diff --git a/configs/s41467_024_45674_5_test/explicit.txt b/configs/s41467_024_45674_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b887078db121350700981d76a829324c0fd41930
--- /dev/null
+++ b/configs/s41467_024_45674_5_test/explicit.txt
@@ -0,0 +1,177 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_8.conda#ff007ab0f0fdc53d245972bba8a6d40c
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.4.0-hba01cd7_105.conda#b4ce93bd1b4247ffc2f093170206c4b4
+https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda#434ca7e50e40f4918ab701e3facd59a0
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.4.0-hba01cd7_105.conda#bdd8348a594d12b3acc3351ee80197db
+https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda#94305520c52a4aa3f6c2b1ff6008d9f8
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
+https://conda.anaconda.org/conda-forge/linux-64/libegl-1.7.0-ha4b6fd6_2.conda#c151d5eb730e9b7480e6d48c0fc44048
+https://conda.anaconda.org/conda-forge/linux-64/libopengl-1.7.0-ha4b6fd6_2.conda#7df50d44d4a14d6c31a2c54f2cd92157
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_8.conda#1bad93f0aa428d618875ef3a588a889e
+https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.44-h4bf12b8_1.conda#e45cfedc8ca5630e02c106ea36d2c5c6
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda#76df83c2a9035c54df5d04ff81bcc02d
+https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.44-h4852527_1.conda#38e0be090e3af56e44a9cac46101f6cd
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda#f7f0d6cc2dc986d42ac2689ec88192be
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3
+https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hb03c661_4.conda#1d29d2e33fe59954af82ef54a8af3fe1
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.1-hecca717_0.conda#4211416ecba1866fab0c6470986c22d6
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba
+https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda#915f5995e94f60e9a4826e0b0920ee88
+https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda#9fa334557db9f63da6c9285fd2a48638
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb9d3cd8_0.conda#c7e925f37e3b40d893459e625f6a53f1
+https://conda.anaconda.org/conda-forge/linux-64/libntlm-1.8-hb9d3cd8_0.conda#7c7927b404672409d9917d49bff5f2d6
+https://conda.anaconda.org/conda-forge/linux-64/libpciaccess-0.18-hb9d3cd8_0.conda#70e3400cbbfa03e96dcde7fc13e38c7b
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_5.conda#4e02a49aaa9d5190cb630fa43528fbe6
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libuv-1.51.0-hb03c661_1.conda#0f03292cc56bf91a077a134ea8747118
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda#aea31d2e5b1091feca96fcfe945c3cf9
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
+https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda#b3c17d95b5a10c6e64a21fa17573e70e
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda#fb901ff28063514abb6046c9ec2c4a45
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb9d3cd8_0.conda#f6ebe2cb3f82ba6c057dde5d9debe4f7
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480
+https://conda.anaconda.org/conda-forge/linux-64/double-conversion-3.3.1-h5888daf_0.conda#bfd56492d8346d669010eccafe0ba058
+https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.1-hecca717_0.conda#6033d8c2bb9b460929d00ba54154614c
+https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda#2cd94587f3a401ae05e03a6caf09539d
+https://conda.anaconda.org/conda-forge/linux-64/gtest-1.17.0-h84d6215_1.conda#55e29b72a71339bc651f9975492db71f
+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
+https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.1.0-hb03c661_4.conda#5cb5a1c9a94a78f5b23684bcb845338d
+https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hb03c661_4.conda#2e55011fa483edb8bfe3fd92e860cd79
+https://conda.anaconda.org/conda-forge/linux-64/libdrm-2.4.125-hb03c661_1.conda#9314bc5a1fe7d1044dc9dfd3ef400535
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
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diff --git a/configs/s41467_024_45674_5_test/meta.json b/configs/s41467_024_45674_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..946ea60c395d2719feec0a294ac13fb375cb46ae
--- /dev/null
+++ b/configs/s41467_024_45674_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_45674_5_test",
+  "python_version": "3.13.7",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_45674_5_test",
+  "exported_at": "2026-05-17T04:04:46Z"
+}
diff --git a/configs/s41467_024_45674_5_test/pip-clean.txt b/configs/s41467_024_45674_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b17c9323de741736a60cf6520a0d72769a784d5
--- /dev/null
+++ b/configs/s41467_024_45674_5_test/pip-clean.txt
@@ -0,0 +1,5 @@
+matplotlib==3.10.6
+munkres==1.1.4
+PySide6==6.9.3
+setuptools==80.9.0
+shiboken6==6.9.3
diff --git a/configs/s41467_024_45674_5_test/pip-freeze.txt b/configs/s41467_024_45674_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80c8f96eb93f082279db1d11964fdbbd954c6929
--- /dev/null
+++ b/configs/s41467_024_45674_5_test/pip-freeze.txt
@@ -0,0 +1,27 @@
+contourpy @ file:///home/conda/feedstock_root/build_artifacts/contourpy_1756544611453/work
+cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1733332471406/work
+fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1759187078489/work
+joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1756321760188/work
+kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_kiwisolver_1756467528/work
+matplotlib==3.10.6
+munkres==1.1.4
+networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work
+numpy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_numpy_1757505485/work/dist/numpy-2.3.3-cp313-cp313-linux_x86_64.whl#sha256=b852fc611d6e291ec5e5b3479e5d0aa2fdf63fd264ebf89ebd2c62649a91b3ce
+packaging @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_packaging_1745345660/work
+pandas @ file:///home/conda/feedstock_root/build_artifacts/pandas_1759265556233/work
+patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1733792384640/work
+pillow @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pillow_1758208668/work
+pyparsing @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pyparsing_1758436411/work
+PySide6==6.9.3
+python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_python-dateutil_1751104122/work
+pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1742920838005/work
+scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1757406014136/work/dist/scikit_learn-1.7.2-cp313-cp313-linux_x86_64.whl#sha256=57a01e14089134138162e1d97e88306d884f79ffcdb68a7ec41d3c3eb56ae97a
+scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1757681044632/work/dist/scipy-1.16.2-cp313-cp313-linux_x86_64.whl#sha256=0a1104325b56a664a1c608c286d76f7d19815da3f0a5fbd29472eab99b3879d3
+seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1733730015268/work
+setuptools==80.9.0
+shiboken6==6.9.3
+six @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_six_1753199211/work
+statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1759296941273/work
+threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1741878222898/work
+tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1756854903354/work
+tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1742745135198/work
diff --git a/configs/s41467_024_46000_9_test/editable.txt b/configs/s41467_024_46000_9_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46000_9_test/env.yml b/configs/s41467_024_46000_9_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1a6f32a34e8e06a5af648ee7db5da5133c1db63f
--- /dev/null
+++ b/configs/s41467_024_46000_9_test/env.yml
@@ -0,0 +1,99 @@
+name: s41467_024_46000_9_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2026.4.22
+  - joblib=1.4.2
+  - ld_impl_linux-64=2.44
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgomp=15.1.0
+  - liblapack=3.9.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.25
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - networkx=2.8.8
+  - numpy=1.24.4
+  - openssl=3.6.2
+  - pip=22.1.2
+  - python=3.8.20
+  - python_abi=3.8
+  - readline=8.2
+  - scikit-learn=1.3.2
+  - setuptools=70.3.0
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - charset-normalizer==3.4.3
+    - contourpy==1.1.1
+    - coverage==7.6.1
+    - cycler==0.12.1
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - google-auth==2.40.3
+    - google-auth-oauthlib==1.0.0
+    - idna==3.10
+    - imbalanced-learn==0.12.4
+    - importlib-resources==6.4.5
+    - jinja2==3.1.6
+    - kiwisolver==1.4.7
+    - markupsafe==2.1.5
+    - matplotlib==3.7.5
+    - mpmath==1.3.0
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - pandas==2.0.3
+    - pillow==10.4.0
+    - protobuf==5.29.5
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - pyparsing==3.1.4
+    - pytest-cov==5.0.0
+    - python-dateutil==2.9.0.post0
+    - pytz==2025.2
+    - requests==2.32.4
+    - scipy==1.10.1
+    - seaborn==0.13.2
+    - six==1.17.0
+    - sympy==1.13.3
+    - tensorboard==2.14.0
+    - tensorboard-data-server==0.7.2
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - unittest-xml-reporting==3.2.0
+    - urllib3==2.2.3
+    - xgboost==2.1.4
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46000_9_test
diff --git a/configs/s41467_024_46000_9_test/explicit.txt b/configs/s41467_024_46000_9_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf595b9ad834bbad62b2489f55af6188f11b96fd
--- /dev/null
+++ b/configs/s41467_024_46000_9_test/explicit.txt
@@ -0,0 +1,47 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda#0c91408b3dec0b97e8a3c694845bd63b
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_4.conda#2d34729cbc1da0ec988e57b13b712067
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.1.0-h69a702a_5.conda#41a5893c957ffed7f82b4005bc24866c
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.25-pthreads_h413a1c8_0.conda#d172b34a443b95f86089e8229ddc9a17
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-20_linux64_openblas.conda#2b7bb4f7562c8cf334fc2e20c2d28abc
+https://conda.anaconda.org/conda-forge/noarch/networkx-2.8.8-pyhd8ed1ab_0.tar.bz2#bb45ff9deddb045331fd039949f39650
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.3.0-pyhc1e730c_0.conda#698d2d2b621640bddb9191f132967c9f
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/joblib-1.4.2-pyhd8ed1ab_0.conda#25df261d4523d9f9783bcdb7208d872f
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-20_linux64_openblas.conda#36d486d72ab64ffea932329a1d3729a3
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-20_linux64_openblas.conda#6fabc51f5e647d09cc010c40061557e0
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.24.4-py38h59b608b_0.conda#8c3e050afeeb2b32575bdb8955cc67b2
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.8.0-py38h56a6a73_1.tar.bz2#86073932d9e675c5929376f6f8b79b97
+https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.3.2-py38ha25d942_2.conda#1f09a56de42f4661aa45922f88f8beb8
diff --git a/configs/s41467_024_46000_9_test/meta.json b/configs/s41467_024_46000_9_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..29470112026415b560d8475b18414975f3ba0f89
--- /dev/null
+++ b/configs/s41467_024_46000_9_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46000_9_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46000_9_test",
+  "exported_at": "2026-05-17T04:04:49Z"
+}
diff --git a/configs/s41467_024_46000_9_test/pip-clean.txt b/configs/s41467_024_46000_9_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de5df54b486af7491f619d8706a2145a47994292
--- /dev/null
+++ b/configs/s41467_024_46000_9_test/pip-clean.txt
@@ -0,0 +1,476 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-auth==2.40.3
+google-auth-oauthlib==1.0.0
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imbalanced-learn==0.12.4
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
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+litellm-enterprise==0.1.20
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diff --git a/configs/s41467_024_46000_9_test/pip-freeze.txt b/configs/s41467_024_46000_9_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b6b25820e5913fa78b927c1c25a7a51510c30fb
--- /dev/null
+++ b/configs/s41467_024_46000_9_test/pip-freeze.txt
@@ -0,0 +1,479 @@
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+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard==2.14.0
+tensorboard-data-server==0.7.2
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1+cpu
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xgboost==2.1.4
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46089_y_test/editable.txt b/configs/s41467_024_46089_y_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46089_y_test/env.yml b/configs/s41467_024_46089_y_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..36144cca21b5f3ff7bd8f2740216476ebc6c50a7
--- /dev/null
+++ b/configs/s41467_024_46089_y_test/env.yml
@@ -0,0 +1,68 @@
+name: s41467_024_46089_y_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.4.22
+    - charset-normalizer==3.4.3
+    - coverage==7.6.1
+    - flatbuffers==25.2.10
+    - gast==0.7.0
+    - google-auth==2.40.3
+    - google-auth-oauthlib==1.0.0
+    - h5py==3.11.0
+    - idna==3.10
+    - keras==2.13.1
+    - libclang==18.1.1
+    - numpy==1.24.3
+    - packaging==25.0
+    - pandas==1.3.5
+    - protobuf==4.25.8
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - pytest-cov==5.0.0
+    - python-dateutil==2.9.0.post0
+    - pytz==2025.2
+    - requests==2.32.4
+    - scikit-learn==1.3.2
+    - scipy==1.7.3
+    - six==1.17.0
+    - tensorboard==2.13.0
+    - tensorboard-data-server==0.7.2
+    - tensorflow==2.13.1
+    - tensorflow-estimator==2.13.0
+    - tensorflow-io-gcs-filesystem==0.34.0
+    - termcolor==2.4.0
+    - typing-extensions==4.5.0
+    - unittest-xml-reporting==3.2.0
+    - urllib3==2.2.3
+    - wrapt==1.17.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46089_y_test
diff --git a/configs/s41467_024_46089_y_test/explicit.txt b/configs/s41467_024_46089_y_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_46089_y_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_46089_y_test/meta.json b/configs/s41467_024_46089_y_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..8fabd241cf73f7589cd131c61bfc1fd4e94c02fe
--- /dev/null
+++ b/configs/s41467_024_46089_y_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46089_y_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46089_y_test",
+  "exported_at": "2026-05-17T04:04:51Z"
+}
diff --git a/configs/s41467_024_46089_y_test/pip-clean.txt b/configs/s41467_024_46089_y_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..765b7909f28f17b55d2c54065981bb299405fd44
--- /dev/null
+++ b/configs/s41467_024_46089_y_test/pip-clean.txt
@@ -0,0 +1,465 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+flatbuffers==25.2.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gast==0.7.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-auth==2.40.3
+google-auth-oauthlib==1.0.0
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+h5py==3.11.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+keras==2.13.1
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+libclang==18.1.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
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+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
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+nltk==3.8.1
+numba==0.58.1
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+numpoly==1.0.6
+numpy==1.24.3
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
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+tzdata==2024.1
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+wandb==0.22.0
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+xxhash==2.0.2
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+youtube-search==2.1.2
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+zope.event==4.5.0
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diff --git a/configs/s41467_024_46089_y_test/pip-freeze.txt b/configs/s41467_024_46089_y_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..765b7909f28f17b55d2c54065981bb299405fd44
--- /dev/null
+++ b/configs/s41467_024_46089_y_test/pip-freeze.txt
@@ -0,0 +1,465 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
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+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
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+async-timeout==4.0.3
+attrs==25.3.0
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+autoray==0.6.12
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+azure-core==1.33.0
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+azure-storage-blob==12.26.0
+Babel==2.9.1
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+backports.zoneinfo==0.2.1
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+beartype==0.14.1
+better-abc==0.0.3
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+blessed==1.20.0
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+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+wrapt==1.17.3
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46413_6_test/editable.txt b/configs/s41467_024_46413_6_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46413_6_test/env.yml b/configs/s41467_024_46413_6_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6300ce6d3bbcb8814a72e1968043cdb948cf7a6c
--- /dev/null
+++ b/configs/s41467_024_46413_6_test/env.yml
@@ -0,0 +1,70 @@
+name: s41467_024_46413_6_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - anndata==0.9.2
+    - asciitree==0.3.3
+    - fasteners==0.20
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - idna==3.11
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numcodecs==0.12.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-cusolver-cu12==11.4.5.107
+    - nvidia-cusparse-cu12==12.1.0.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - pillow==10.4.0
+    - pytest==8.3.5
+    - scanpy==1.9.8
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - torchvision==0.19.1
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+    - zarr==2.16.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46413_6_test
diff --git a/configs/s41467_024_46413_6_test/explicit.txt b/configs/s41467_024_46413_6_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_46413_6_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_46413_6_test/meta.json b/configs/s41467_024_46413_6_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..641b47239ff7d9cdca07ce52b55ba4ba81528372
--- /dev/null
+++ b/configs/s41467_024_46413_6_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46413_6_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46413_6_test",
+  "exported_at": "2026-05-17T04:04:57Z"
+}
diff --git a/configs/s41467_024_46413_6_test/pip-clean.txt b/configs/s41467_024_46413_6_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07fa5409c09e56782d726056d2b84e6061a82614
--- /dev/null
+++ b/configs/s41467_024_46413_6_test/pip-clean.txt
@@ -0,0 +1,472 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+anndata==0.9.2
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+asciitree==0.3.3
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fasteners==0.20
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.11
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numcodecs==0.12.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusolver-cu12==11.4.5.107
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
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+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest==8.3.5
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scanpy==1.9.8
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zarr==2.16.1
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46413_6_test/pip-freeze.txt b/configs/s41467_024_46413_6_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07fa5409c09e56782d726056d2b84e6061a82614
--- /dev/null
+++ b/configs/s41467_024_46413_6_test/pip-freeze.txt
@@ -0,0 +1,472 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+anndata==0.9.2
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+asciitree==0.3.3
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fasteners==0.20
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
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+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.11
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numcodecs==0.12.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusolver-cu12==11.4.5.107
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest==8.3.5
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scanpy==1.9.8
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zarr==2.16.1
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46523_1_test/editable.txt b/configs/s41467_024_46523_1_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46523_1_test/pip-clean.txt b/configs/s41467_024_46523_1_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c99e608869aee722f181038aca65fc6f371c3864
--- /dev/null
+++ b/configs/s41467_024_46523_1_test/pip-clean.txt
@@ -0,0 +1,442 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
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+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
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+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
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+monotonic==1.6
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+msal-extensions==1.3.0
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+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46523_1_test/pip-freeze.txt b/configs/s41467_024_46523_1_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f08c0b49f781c964c6aedec9e210f61880604df
--- /dev/null
+++ b/configs/s41467_024_46523_1_test/pip-freeze.txt
@@ -0,0 +1,445 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1687808301083/work
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work
+scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1644357257999/work
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46614_z_test/editable.txt b/configs/s41467_024_46614_z_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46614_z_test/env.yml b/configs/s41467_024_46614_z_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..3935fa2bd239352924fb98aa4251daaeba7b4309
--- /dev/null
+++ b/configs/s41467_024_46614_z_test/env.yml
@@ -0,0 +1,46 @@
+name: s41467_024_46614_z_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46614_z_test
diff --git a/configs/s41467_024_46614_z_test/explicit.txt b/configs/s41467_024_46614_z_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_46614_z_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_46614_z_test/meta.json b/configs/s41467_024_46614_z_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7cb95fad3598759a4782a47454f3fb7ef06cfaca
--- /dev/null
+++ b/configs/s41467_024_46614_z_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46614_z_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46614_z_test",
+  "exported_at": "2026-05-17T04:04:54Z"
+}
diff --git a/configs/s41467_024_46614_z_test/pip-clean.txt b/configs/s41467_024_46614_z_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5a0b7e783f4ccb2d346fb977dcdaa1f28fd0bf8
--- /dev/null
+++ b/configs/s41467_024_46614_z_test/pip-clean.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
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+nvidia-ml-py==12.535.133
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+python-iso639==2024.4.27
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+python-multipart==0.0.18
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+torchaudio==2.1.2+cu118
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+typing-inspect==0.9.0
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+tzdata==2024.1
+tzlocal==5.2
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
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+unstructured-inference==0.7.15
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+validators==0.28.1
+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46614_z_test/pip-freeze.txt b/configs/s41467_024_46614_z_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5a0b7e783f4ccb2d346fb977dcdaa1f28fd0bf8
--- /dev/null
+++ b/configs/s41467_024_46614_z_test/pip-freeze.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
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+botocore==1.36.26
+botorch==0.8.5
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+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+fschat==0.2.35
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+gevent==21.12.0
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+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
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+isodate==0.7.2
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+jax==0.4.13
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+jmespath==0.10.0
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+jsonnet==0.17.0
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
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+kubernetes==29.0.0
+langchain==0.1.16
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+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
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+madoka==0.7.1
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+overrides==7.7.0
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+parsimonious==0.8.1
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+PICOS==2.6.1
+pikepdf==8.4.1
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+regex==2022.4.24
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+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46945_x_test/editable.txt b/configs/s41467_024_46945_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46945_x_test/env.yml b/configs/s41467_024_46945_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c0f63d8d82ff4dcd8745ada7ceca324acf47c4a7
--- /dev/null
+++ b/configs/s41467_024_46945_x_test/env.yml
@@ -0,0 +1,37 @@
+name: s41467_024_46945_x_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - numpy==1.24.4
+    - packaging==25.0
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46945_x_test
diff --git a/configs/s41467_024_46945_x_test/explicit.txt b/configs/s41467_024_46945_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_46945_x_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_46945_x_test/meta.json b/configs/s41467_024_46945_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..1fa0debb38f80631c544c92ddac6f48b62602d3d
--- /dev/null
+++ b/configs/s41467_024_46945_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46945_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46945_x_test",
+  "exported_at": "2026-05-17T04:04:59Z"
+}
diff --git a/configs/s41467_024_46945_x_test/pip-clean.txt b/configs/s41467_024_46945_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_46945_x_test/pip-clean.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
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+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
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+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
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+nh3==0.2.17
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+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46945_x_test/pip-freeze.txt b/configs/s41467_024_46945_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_46945_x_test/pip-freeze.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46976_4_test/editable.txt b/configs/s41467_024_46976_4_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46976_4_test/env.yml b/configs/s41467_024_46976_4_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a3c323ff5e301efc270c3d1cd6597310bb9e9bef
--- /dev/null
+++ b/configs/s41467_024_46976_4_test/env.yml
@@ -0,0 +1,57 @@
+name: s41467_024_46976_4_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46976_4_test
diff --git a/configs/s41467_024_46976_4_test/explicit.txt b/configs/s41467_024_46976_4_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_46976_4_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_46976_4_test/meta.json b/configs/s41467_024_46976_4_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..97a258f9e534658d2bb6e3b78e05269055d17267
--- /dev/null
+++ b/configs/s41467_024_46976_4_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46976_4_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46976_4_test",
+  "exported_at": "2026-05-17T04:05:05Z"
+}
diff --git a/configs/s41467_024_46976_4_test/pip-clean.txt b/configs/s41467_024_46976_4_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7b2a7c6319c079b872a26715e90b38f1c31ed4c
--- /dev/null
+++ b/configs/s41467_024_46976_4_test/pip-clean.txt
@@ -0,0 +1,459 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
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+snowballstemmer==2.2.0
+sobol-seq==0.2.0
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+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
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+starlette==0.44.0
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+stdlib-list==0.10.0
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+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+toml==0.10.2
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+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
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+transformer-lens==2.16.1
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+typed-argument-parser==1.10.1
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+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_46976_4_test/pip-freeze.txt b/configs/s41467_024_46976_4_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7b2a7c6319c079b872a26715e90b38f1c31ed4c
--- /dev/null
+++ b/configs/s41467_024_46976_4_test/pip-freeze.txt
@@ -0,0 +1,459 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_47831_2_test/editable.txt b/configs/s41467_024_47831_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_47831_2_test/env.yml b/configs/s41467_024_47831_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..3c398104db05203621c66811f3164aa3608a2b12
--- /dev/null
+++ b/configs/s41467_024_47831_2_test/env.yml
@@ -0,0 +1,52 @@
+name: s41467_024_47831_2_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - charset-normalizer==3.4.3
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - idna==3.10
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.23.5
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - urllib3==2.2.3
+    - zipp==3.20.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_47831_2_test
diff --git a/configs/s41467_024_47831_2_test/explicit.txt b/configs/s41467_024_47831_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_47831_2_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
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diff --git a/configs/s41467_024_47831_2_test/meta.json b/configs/s41467_024_47831_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f25182a61b50c0b9be021eba942739cefe190539
--- /dev/null
+++ b/configs/s41467_024_47831_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_47831_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_47831_2_test",
+  "exported_at": "2026-05-17T04:05:13Z"
+}
diff --git a/configs/s41467_024_47831_2_test/pip-clean.txt b/configs/s41467_024_47831_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..352f845d2f2423d1044735886114b535df5e2830
--- /dev/null
+++ b/configs/s41467_024_47831_2_test/pip-clean.txt
@@ -0,0 +1,453 @@
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diff --git a/configs/s41467_024_47831_2_test/pip-freeze.txt b/configs/s41467_024_47831_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..352f845d2f2423d1044735886114b535df5e2830
--- /dev/null
+++ b/configs/s41467_024_47831_2_test/pip-freeze.txt
@@ -0,0 +1,453 @@
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+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.23.5
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_48107_5_test/editable.txt b/configs/s41467_024_48107_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_48107_5_test/env.yml b/configs/s41467_024_48107_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4edb3ddd29a0463b754b1496dd0eef9867910e59
--- /dev/null
+++ b/configs/s41467_024_48107_5_test/env.yml
@@ -0,0 +1,50 @@
+name: s41467_024_48107_5_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - networkx==3.1
+    - numpy==1.24.4
+    - opencv-python==4.13.0.92
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - scikit-image==0.21.0
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_48107_5_test
diff --git a/configs/s41467_024_48107_5_test/explicit.txt b/configs/s41467_024_48107_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_48107_5_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_48107_5_test/meta.json b/configs/s41467_024_48107_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..71c10fa8bd58e196885e64644e8b182ff88d8e44
--- /dev/null
+++ b/configs/s41467_024_48107_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_48107_5_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_48107_5_test",
+  "exported_at": "2026-05-17T04:05:13Z"
+}
diff --git a/configs/s41467_024_48107_5_test/pip-clean.txt b/configs/s41467_024_48107_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39150fbdf9804aff9b0b15c741b1e03f720e74bc
--- /dev/null
+++ b/configs/s41467_024_48107_5_test/pip-clean.txt
@@ -0,0 +1,455 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
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+streamlit-antd-components==0.3.1
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+timm==0.9.16
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+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
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+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
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+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_48107_5_test/pip-freeze.txt b/configs/s41467_024_48107_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39150fbdf9804aff9b0b15c741b1e03f720e74bc
--- /dev/null
+++ b/configs/s41467_024_48107_5_test/pip-freeze.txt
@@ -0,0 +1,455 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
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+cachetools==4.2.4
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+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
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+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
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+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
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+fastuuid==0.13.5
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+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+get-annotations==0.1.2
+gevent==21.12.0
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+GitPython==3.1.43
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+googleapis-common-protos==1.63.0
+gpustat==1.1.1
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+kaggle==1.7.4.5
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+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+opencv-python==4.13.0.92
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-image==0.21.0
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_48446_3_test/editable.txt b/configs/s41467_024_48446_3_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_48446_3_test/env.yml b/configs/s41467_024_48446_3_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1e7c59f9de58270b694cc78c80c948cb1031adf9
--- /dev/null
+++ b/configs/s41467_024_48446_3_test/env.yml
@@ -0,0 +1,59 @@
+name: s41467_024_48446_3_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - h5py==3.11.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - psutil==7.2.2
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_48446_3_test
diff --git a/configs/s41467_024_48446_3_test/explicit.txt b/configs/s41467_024_48446_3_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_48446_3_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_48446_3_test/meta.json b/configs/s41467_024_48446_3_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..257d349ba6e291ddca789372b45af36acaa1cad5
--- /dev/null
+++ b/configs/s41467_024_48446_3_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_48446_3_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_48446_3_test",
+  "exported_at": "2026-05-17T04:05:19Z"
+}
diff --git a/configs/s41467_024_48446_3_test/pip-clean.txt b/configs/s41467_024_48446_3_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3717e922eeff8cd5f4a8c23798dcb66a063be8e1
--- /dev/null
+++ b/configs/s41467_024_48446_3_test/pip-clean.txt
@@ -0,0 +1,461 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+h5py==3.11.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
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+nvidia-cudnn-cu12==9.1.0.70
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+nvidia-ml-py==12.535.133
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+nvidia-nvtx-cu12==12.1.105
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+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
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+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
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+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
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+regex==2022.4.24
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+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
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+sentry-sdk==2.39.0
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+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tifffile==2023.7.10
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+torch==2.4.1+cpu
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+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+transformers==4.46.3
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+typeguard==4.4.0
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+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_48446_3_test/pip-freeze.txt b/configs/s41467_024_48446_3_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3717e922eeff8cd5f4a8c23798dcb66a063be8e1
--- /dev/null
+++ b/configs/s41467_024_48446_3_test/pip-freeze.txt
@@ -0,0 +1,461 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+geosketch==1.3
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+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
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+h11==0.14.0
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+icetk==0.0.4
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+jmespath==0.10.0
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
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+nvidia-cuda-runtime-cu12==12.1.105
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+nvidia-ml-py==12.535.133
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+nvidia-nvtx-cu12==12.1.105
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+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_49163_7_test/editable.txt b/configs/s41467_024_49163_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_49163_7_test/env.yml b/configs/s41467_024_49163_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f115c0de0d703b0989c01c3f652af90d491d5b6b
--- /dev/null
+++ b/configs/s41467_024_49163_7_test/env.yml
@@ -0,0 +1,41 @@
+name: s41467_024_49163_7_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - fonttools==4.57.0
+    - kiwisolver==1.4.7
+    - numpy==1.24.4
+    - packaging==25.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_49163_7_test
diff --git a/configs/s41467_024_49163_7_test/explicit.txt b/configs/s41467_024_49163_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_49163_7_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_49163_7_test/meta.json b/configs/s41467_024_49163_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6068b5bcbbb6a1e30d2b4d5652a34b664b61d893
--- /dev/null
+++ b/configs/s41467_024_49163_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_49163_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_49163_7_test",
+  "exported_at": "2026-05-17T04:05:19Z"
+}
diff --git a/configs/s41467_024_49163_7_test/pip-clean.txt b/configs/s41467_024_49163_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d1a50684a62da5297853b2b76d27cce33b22b8e
--- /dev/null
+++ b/configs/s41467_024_49163_7_test/pip-clean.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
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+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
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+oauthlib==3.2.2
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+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
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+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
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+opentelemetry-semantic-conventions==0.45b0
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+optax==0.1.5
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+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
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+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
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+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
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+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_49163_7_test/pip-freeze.txt b/configs/s41467_024_49163_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d1a50684a62da5297853b2b76d27cce33b22b8e
--- /dev/null
+++ b/configs/s41467_024_49163_7_test/pip-freeze.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
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+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
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+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_49516_2_test/env.yml b/configs/s41467_024_49516_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b40091298dbe8816797cefd1a1a7993a379f8c5e
--- /dev/null
+++ b/configs/s41467_024_49516_2_test/env.yml
@@ -0,0 +1,53 @@
+name: s41467_024_49516_2_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.2.25
+    - filelock==3.13.1
+    - fsspec==2024.6.1
+    - idna==3.11
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - psutil==7.2.2
+    - pyparsing==3.1.4
+    - requests==2.32.4
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torch-scatter==2.1.2
+    - typing-extensions==4.12.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_49516_2_test
diff --git a/configs/s41467_024_50505_8_test/editable.txt b/configs/s41467_024_50505_8_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_50505_8_test/explicit.txt b/configs/s41467_024_50505_8_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_50505_8_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_50505_8_test/meta.json b/configs/s41467_024_50505_8_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3d0342de18492c8736c363866706801b1b7382ed
--- /dev/null
+++ b/configs/s41467_024_50505_8_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_50505_8_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_50505_8_test",
+  "exported_at": "2026-05-17T04:05:29Z"
+}
diff --git a/configs/s41467_024_50505_8_test/pip-clean.txt b/configs/s41467_024_50505_8_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_50505_8_test/pip-clean.txt
@@ -0,0 +1,451 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
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+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
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+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
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+parsimonious==0.8.1
+pathlib==1.0.1
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+pikepdf==8.4.1
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+rouge-score==0.1.2
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+scipy==1.10.1
+scooby==0.10.1
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+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_50505_8_test/pip-freeze.txt b/configs/s41467_024_50505_8_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_50505_8_test/pip-freeze.txt
@@ -0,0 +1,451 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_51491_7_test/editable.txt b/configs/s41467_024_51491_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_51491_7_test/env.yml b/configs/s41467_024_51491_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..046e4e80bc6099def58c6d30754d743eae9e0ef7
--- /dev/null
+++ b/configs/s41467_024_51491_7_test/env.yml
@@ -0,0 +1,64 @@
+name: s41467_024_51491_7_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - asttokens==3.0.1
+    - backcall==0.2.0
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - decorator==5.2.1
+    - executing==2.2.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - ipython==8.12.3
+    - jedi==0.19.2
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - matplotlib-inline==0.1.7
+    - numpy==1.24.4
+    - packaging==25.0
+    - parso==0.8.6
+    - pexpect==4.9.0
+    - pickleshare==0.7.5
+    - pillow==10.4.0
+    - ptyprocess==0.7.0
+    - pure-eval==0.2.3
+    - pydantic==2.10.6
+    - pyparsing==3.1.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - stack-data==0.6.3
+    - traitlets==5.14.3
+    - typing-extensions==4.13.2
+    - wcwidth==0.6.0
+    - weac==2.0.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_51491_7_test
diff --git a/configs/s41467_024_51491_7_test/explicit.txt b/configs/s41467_024_51491_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_51491_7_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
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diff --git a/configs/s41467_024_51491_7_test/meta.json b/configs/s41467_024_51491_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..fb8c557fc1384571ef904afa2d93d598f846089c
--- /dev/null
+++ b/configs/s41467_024_51491_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_51491_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_51491_7_test",
+  "exported_at": "2026-05-17T04:05:38Z"
+}
diff --git a/configs/s41467_024_51491_7_test/pip-clean.txt b/configs/s41467_024_51491_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35fc8453b67e940ec0105e72bf52c9e3381f235d
--- /dev/null
+++ b/configs/s41467_024_51491_7_test/pip-clean.txt
@@ -0,0 +1,467 @@
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diff --git a/configs/s41467_024_51491_7_test/pip-freeze.txt b/configs/s41467_024_51491_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35fc8453b67e940ec0105e72bf52c9e3381f235d
--- /dev/null
+++ b/configs/s41467_024_51491_7_test/pip-freeze.txt
@@ -0,0 +1,467 @@
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+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+decorator==5.2.1
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
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+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+executing==2.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
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+fastapi-sso==0.16.0
+fastavro==1.9.4
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+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
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+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
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+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
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+hf_transfer==0.1.9
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+humanfriendly==10.0
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+jaxtyping==0.2.19
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+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
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+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
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+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+matplotlib-inline==0.1.7
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
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+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+parso==0.8.6
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pexpect==4.9.0
+pfzy==0.3.4
+pickleshare==0.7.5
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+ptyprocess==0.7.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pure_eval==0.2.3
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
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+sacrebleu==2.1.0
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+scipy==1.10.1
+scooby==0.10.1
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+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+stack-data==0.6.3
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
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+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
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+tokenizers==0.20.3
+toml==0.10.2
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+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+traitlets==5.14.3
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
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+typing_extensions==4.13.2
+tzdata==2024.1
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+unittest-xml-reporting==3.2.0
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+watchdog==3.0.0
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+wavedrom==2.0.3.post3
+wcwidth==0.6.0
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+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_51555_8_test/editable.txt b/configs/s41467_024_51555_8_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_51555_8_test/env.yml b/configs/s41467_024_51555_8_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..25464533da8f314cbd16196e6cacfafb81fe1b4f
--- /dev/null
+++ b/configs/s41467_024_51555_8_test/env.yml
@@ -0,0 +1,41 @@
+name: s41467_024_51555_8_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - numpy==1.24.4
+    - packaging==25.0
+    - pandas==2.0.3
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+    - xarray==2023.1.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_51555_8_test
diff --git a/configs/s41467_024_51555_8_test/explicit.txt b/configs/s41467_024_51555_8_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_51555_8_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_51555_8_test/meta.json b/configs/s41467_024_51555_8_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..31ec3f12e2616d4b6bf80309d2693f849b0bebbd
--- /dev/null
+++ b/configs/s41467_024_51555_8_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_51555_8_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_51555_8_test",
+  "exported_at": "2026-05-17T04:05:37Z"
+}
diff --git a/configs/s41467_024_51555_8_test/pip-clean.txt b/configs/s41467_024_51555_8_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2c13ca0dedcea4872b83afd4b52852ee1104e31
--- /dev/null
+++ b/configs/s41467_024_51555_8_test/pip-clean.txt
@@ -0,0 +1,445 @@
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diff --git a/configs/s41467_024_51555_8_test/pip-freeze.txt b/configs/s41467_024_51555_8_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2c13ca0dedcea4872b83afd4b52852ee1104e31
--- /dev/null
+++ b/configs/s41467_024_51555_8_test/pip-freeze.txt
@@ -0,0 +1,445 @@
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+marisa-trie==1.1.0
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+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
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+unstructured==0.11.0
+unstructured-client==0.22.0
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+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xarray==2023.1.0
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_51864_y_test/editable.txt b/configs/s41467_024_51864_y_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_51864_y_test/env.yml b/configs/s41467_024_51864_y_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..45ec95b4100a8ef248e7aa0b9ab1e2eb762204c2
--- /dev/null
+++ b/configs/s41467_024_51864_y_test/env.yml
@@ -0,0 +1,37 @@
+name: s41467_024_51864_y_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - numpy==1.24.4
+    - packaging==25.0
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_51864_y_test
diff --git a/configs/s41467_024_51864_y_test/explicit.txt b/configs/s41467_024_51864_y_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_51864_y_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_51864_y_test/meta.json b/configs/s41467_024_51864_y_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f9fcceb23bbe43ca23b8d586014a28a46409712d
--- /dev/null
+++ b/configs/s41467_024_51864_y_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_51864_y_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_51864_y_test",
+  "exported_at": "2026-05-17T04:05:40Z"
+}
diff --git a/configs/s41467_024_51864_y_test/pip-clean.txt b/configs/s41467_024_51864_y_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_51864_y_test/pip-clean.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+typing-inspect==0.9.0
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+tzdata==2024.1
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
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+unstructured.pytesseract==0.3.12
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+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
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+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_51864_y_test/pip-freeze.txt b/configs/s41467_024_51864_y_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_51864_y_test/pip-freeze.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
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+bitsandbytes==0.43.1
+blessed==1.20.0
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+botorch==0.8.5
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+Brotli==1.1.0
+bs4==0.0.2
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+chaospy==3.3.9
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+chroma-hnswlib==0.7.3
+chromadb==0.4.15
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+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
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+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
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+datasets==2.19.0
+deepdiff==7.0.1
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+email-validator==2.3.0
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_52081_3_test/editable.txt b/configs/s41467_024_52081_3_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_52081_3_test/env.yml b/configs/s41467_024_52081_3_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..54ef3d25eeb276725384c1d0f18d98bf194fbca1
--- /dev/null
+++ b/configs/s41467_024_52081_3_test/env.yml
@@ -0,0 +1,47 @@
+name: s41467_024_52081_3_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_52081_3_test
diff --git a/configs/s41467_024_52081_3_test/meta.json b/configs/s41467_024_52081_3_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..00b85073f5b2c02187493c4d7d07315a24f51c91
--- /dev/null
+++ b/configs/s41467_024_52081_3_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_52081_3_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_52081_3_test",
+  "exported_at": "2026-05-17T04:05:46Z"
+}
diff --git a/configs/s41467_024_52081_3_test/pip-clean.txt b/configs/s41467_024_52081_3_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_52081_3_test/pip-clean.txt
@@ -0,0 +1,451 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+allennlp==0.8.4
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+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
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+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
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+blessed==1.20.0
+blis==0.7.11
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+botocore==1.36.26
+botorch==0.8.5
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+Brotli==1.1.0
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+chaospy==3.3.9
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+click==8.1.7
+cloudpathlib==0.16.0
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+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
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+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
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+dm-tree==0.1.8
+dnspython==2.6.1
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+dotenv==0.9.9
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+editdistance==0.6.0
+effdet==0.4.1
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+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
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+fairseq==0.10.2
+faiss-cpu==1.7.4
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+fancy-einsum==0.0.3
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+geosketch==1.3
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+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
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+gpytorch==1.10
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+icetk==0.0.4
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+jaxlib==0.4.13
+jaxtyping==0.2.19
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+jiter==0.9.1
+jmespath==0.10.0
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+jsonnet==0.17.0
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+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
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+lmdb==1.7.3
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+madoka==0.7.1
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+markdown-it-py==3.0.0
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+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
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+mdtex2html==1.3.0
+mdurl==0.1.2
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+ml-dtypes==0.2.0
+monotonic==1.6
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+msal-extensions==1.3.0
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+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
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+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
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+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
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+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
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+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
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+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
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+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
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+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
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+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
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+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
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+tomlkit==0.12.0
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+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
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+typeguard==4.4.0
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+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
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+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
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+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_52081_3_test/pip-freeze.txt b/configs/s41467_024_52081_3_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_52081_3_test/pip-freeze.txt
@@ -0,0 +1,451 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_53146_z_test/editable.txt b/configs/s41467_024_53146_z_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_53146_z_test/env.yml b/configs/s41467_024_53146_z_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ec66ff83bf480220d0b92fc5626905336032b828
--- /dev/null
+++ b/configs/s41467_024_53146_z_test/env.yml
@@ -0,0 +1,48 @@
+name: s41467_024_53146_z_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+    - tqdm==4.67.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_53146_z_test
diff --git a/configs/s41467_024_53146_z_test/explicit.txt b/configs/s41467_024_53146_z_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_53146_z_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
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+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
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diff --git a/configs/s41467_024_53146_z_test/meta.json b/configs/s41467_024_53146_z_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5603bdfd61a7eaca5a1345f658603bd2e4081391
--- /dev/null
+++ b/configs/s41467_024_53146_z_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_53146_z_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_53146_z_test",
+  "exported_at": "2026-05-17T04:05:50Z"
+}
diff --git a/configs/s41467_024_53146_z_test/pip-clean.txt b/configs/s41467_024_53146_z_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_53146_z_test/pip-clean.txt
@@ -0,0 +1,451 @@
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diff --git a/configs/s41467_024_53146_z_test/pip-freeze.txt b/configs/s41467_024_53146_z_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_53146_z_test/pip-freeze.txt
@@ -0,0 +1,451 @@
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+hyperframe==6.0.1
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+imagesize==1.3.0
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+importlib-metadata==7.0.0
+importlib_resources==6.4.5
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+jsonnet==0.17.0
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+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
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+kubernetes==29.0.0
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+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
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+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
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+tzdata==2024.1
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+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
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+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
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+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_53455_3_test/editable.txt b/configs/s41467_024_53455_3_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_53455_3_test/env.yml b/configs/s41467_024_53455_3_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9caa6c9a8936b7e1cb53e754350a725c945a125e
--- /dev/null
+++ b/configs/s41467_024_53455_3_test/env.yml
@@ -0,0 +1,40 @@
+name: s41467_024_53455_3_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - numpy==1.24.4
+    - packaging==25.0
+    - reedsolo==1.7.0
+    - scipy==1.10.1
+    - six==1.17.0
+    - tqdm==4.67.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_53455_3_test
diff --git a/configs/s41467_024_53455_3_test/explicit.txt b/configs/s41467_024_53455_3_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_53455_3_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_53455_3_test/meta.json b/configs/s41467_024_53455_3_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5f8f0e839066ac68bd98546f4c2e1ca815f6ec89
--- /dev/null
+++ b/configs/s41467_024_53455_3_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_53455_3_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_53455_3_test",
+  "exported_at": "2026-05-17T04:05:51Z"
+}
diff --git a/configs/s41467_024_53455_3_test/pip-clean.txt b/configs/s41467_024_53455_3_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aab63cad84d69dd16df0592159892b37c4394e8b
--- /dev/null
+++ b/configs/s41467_024_53455_3_test/pip-clean.txt
@@ -0,0 +1,445 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
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+python-iso639==2024.4.27
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+tzdata==2024.1
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
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+vllm==0.2.7
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+wandb==0.22.0
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+watchfiles==0.21.0
+wavedrom==2.0.3.post3
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+websocket-client==1.8.0
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+Werkzeug==2.0.2
+word2number==1.1
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+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_53455_3_test/pip-freeze.txt b/configs/s41467_024_53455_3_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aab63cad84d69dd16df0592159892b37c4394e8b
--- /dev/null
+++ b/configs/s41467_024_53455_3_test/pip-freeze.txt
@@ -0,0 +1,445 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
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+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+blessed==1.20.0
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+chaospy==3.3.9
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+confection==0.1.4
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+cvxopt==1.3.2
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+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
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+Deprecated==1.2.14
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+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
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+fairseq==0.10.2
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+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+reedsolo==1.7.0
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_53818_w_test/env.yml b/configs/s41467_024_53818_w_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..10e558d591b536448e34acca00af6c6890d2b09a
--- /dev/null
+++ b/configs/s41467_024_53818_w_test/env.yml
@@ -0,0 +1,39 @@
+name: s41467_024_53818_w_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - numpy==1.24.4
+    - packaging==25.0
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_53818_w_test
diff --git a/configs/s41467_024_54067_7_test/editable.txt b/configs/s41467_024_54067_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_54067_7_test/env.yml b/configs/s41467_024_54067_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b5d3c8c1cb187330cd9f12bbceacb77ee1b4a7e3
--- /dev/null
+++ b/configs/s41467_024_54067_7_test/env.yml
@@ -0,0 +1,44 @@
+name: s41467_024_54067_7_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.2.25
+    - httpx==0.28.1
+    - idna==3.11
+    - numpy==1.24.4
+    - packaging==25.0
+    - pydantic==2.10.6
+    - six==1.17.0
+    - tqdm==4.67.1
+    - typing-extensions==4.13.2
+    - wcwidth==0.2.14
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_54067_7_test
diff --git a/configs/s41467_024_54067_7_test/explicit.txt b/configs/s41467_024_54067_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_54067_7_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_54067_7_test/meta.json b/configs/s41467_024_54067_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..054aae44dd6e0dc96a3360afe9aafa6923f9ff46
--- /dev/null
+++ b/configs/s41467_024_54067_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_54067_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_54067_7_test",
+  "exported_at": "2026-05-17T04:05:55Z"
+}
diff --git a/configs/s41467_024_54067_7_test/pip-clean.txt b/configs/s41467_024_54067_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7277b8cca283f8e9beb5e4b9d15ddd9a0281979b
--- /dev/null
+++ b/configs/s41467_024_54067_7_test/pip-clean.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.2.25
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.11
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tzdata==2024.1
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+vllm==0.2.7
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+watchdog==3.0.0
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+wavedrom==2.0.3.post3
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+XlsxWriter==3.0.2
+xxhash==2.0.2
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+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_54067_7_test/pip-freeze.txt b/configs/s41467_024_54067_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7277b8cca283f8e9beb5e4b9d15ddd9a0281979b
--- /dev/null
+++ b/configs/s41467_024_54067_7_test/pip-freeze.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+alabaster==0.7.12
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+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
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+async-timeout==4.0.3
+attrs==25.3.0
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+autoray==0.6.12
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+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
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+chaospy==3.3.9
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+confection==0.1.4
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+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+wcwidth==0.2.14
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_54375_y_test/editable.txt b/configs/s41467_024_54375_y_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_54375_y_test/env.yml b/configs/s41467_024_54375_y_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..44d7e2caf8d7ad080f2410b4d439b78130bd6975
--- /dev/null
+++ b/configs/s41467_024_54375_y_test/env.yml
@@ -0,0 +1,76 @@
+name: s41467_024_54375_y_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - joblib=1.4.2
+  - ld_impl_linux-64=2.44
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgomp=15.1.0
+  - liblapack=3.9.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.25
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - numpy=1.24.4
+  - openssl=3.5.2
+  - pandas=2.0.3
+  - pip=22.1.2
+  - python=3.8.20
+  - python-dateutil=2.8.2
+  - python-tzdata=2025.2
+  - python_abi=3.8
+  - pytz=2024.2
+  - readline=8.2
+  - scikit-learn=1.3.2
+  - scipy=1.8.0
+  - setuptools=70.3.0
+  - six=1.16.0
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_54375_y_test
diff --git a/configs/s41467_024_54375_y_test/explicit.txt b/configs/s41467_024_54375_y_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94c8d02862b3f33b829a80350b4f123de9398b69
--- /dev/null
+++ b/configs/s41467_024_54375_y_test/explicit.txt
@@ -0,0 +1,51 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda#0c91408b3dec0b97e8a3c694845bd63b
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_4.conda#2d34729cbc1da0ec988e57b13b712067
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.1.0-h69a702a_5.conda#41a5893c957ffed7f82b4005bc24866c
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.25-pthreads_h413a1c8_0.conda#d172b34a443b95f86089e8229ddc9a17
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-20_linux64_openblas.conda#2b7bb4f7562c8cf334fc2e20c2d28abc
+https://repo.anaconda.com/pkgs/main/noarch/python-tzdata-2025.2-pyhd3eb1b0_0.conda#5ac858f05dbf9d3cdb04d53516901247
+https://conda.anaconda.org/conda-forge/noarch/pytz-2024.2-pyhd8ed1ab_0.conda#260009d03c9d5c0f111904d851f053dc
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2
+https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.3.0-pyhc1e730c_0.conda#698d2d2b621640bddb9191f132967c9f
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/joblib-1.4.2-pyhd8ed1ab_0.conda#25df261d4523d9f9783bcdb7208d872f
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-20_linux64_openblas.conda#36d486d72ab64ffea932329a1d3729a3
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-20_linux64_openblas.conda#6fabc51f5e647d09cc010c40061557e0
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
+https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.24.4-py38h59b608b_0.conda#8c3e050afeeb2b32575bdb8955cc67b2
+https://conda.anaconda.org/conda-forge/linux-64/pandas-2.0.3-py38h01efb38_1.conda#01a2b6144e65631e2fe24e569d0738ee
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.8.0-py38h56a6a73_1.tar.bz2#86073932d9e675c5929376f6f8b79b97
+https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.3.2-py38ha25d942_2.conda#1f09a56de42f4661aa45922f88f8beb8
diff --git a/configs/s41467_024_54375_y_test/meta.json b/configs/s41467_024_54375_y_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..281c3bec4fb60bcead941169ab85cb11deb2f1ad
--- /dev/null
+++ b/configs/s41467_024_54375_y_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_54375_y_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_54375_y_test",
+  "exported_at": "2026-05-17T04:06:00Z"
+}
diff --git a/configs/s41467_024_54375_y_test/pip-clean.txt b/configs/s41467_024_54375_y_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16e83390f46da25e7dc30cb93c7f5f0651452bda
--- /dev/null
+++ b/configs/s41467_024_54375_y_test/pip-clean.txt
@@ -0,0 +1,459 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
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diff --git a/configs/s41467_024_54375_y_test/pip-freeze.txt b/configs/s41467_024_54375_y_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11f832b5c12f7ffd3cc933cdcb39e451a66298ec
--- /dev/null
+++ b/configs/s41467_024_54375_y_test/pip-freeze.txt
@@ -0,0 +1,462 @@
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+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1+cpu
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_54639_7_test/editable.txt b/configs/s41467_024_54639_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_54639_7_test/env.yml b/configs/s41467_024_54639_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4ce4bf444953ca9ef6021092b3894b131eac8a34
--- /dev/null
+++ b/configs/s41467_024_54639_7_test/env.yml
@@ -0,0 +1,58 @@
+name: s41467_024_54639_7_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_54639_7_test
diff --git a/configs/s41467_024_54639_7_test/explicit.txt b/configs/s41467_024_54639_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_54639_7_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_54639_7_test/meta.json b/configs/s41467_024_54639_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..b4633096db8acaa886e573e3ee27ecc06ff33051
--- /dev/null
+++ b/configs/s41467_024_54639_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_54639_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_54639_7_test",
+  "exported_at": "2026-05-17T04:05:58Z"
+}
diff --git a/configs/s41467_024_54639_7_test/pip-clean.txt b/configs/s41467_024_54639_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cb97759d3d8610433b1907f3311948b9f94ed5f
--- /dev/null
+++ b/configs/s41467_024_54639_7_test/pip-clean.txt
@@ -0,0 +1,460 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
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+monotonic==1.6
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+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
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+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
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+pulsar-client==3.5.0
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+pyarrow-hotfix==0.6
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+pycocotools==2.0.7
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+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
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+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1+cpu
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_54639_7_test/pip-freeze.txt b/configs/s41467_024_54639_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cb97759d3d8610433b1907f3311948b9f94ed5f
--- /dev/null
+++ b/configs/s41467_024_54639_7_test/pip-freeze.txt
@@ -0,0 +1,460 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
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+ffmpy==0.3.2
+filelock==3.16.1
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+fschat==0.2.35
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+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
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+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
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+gpustat==1.1.1
+gpytorch==1.10
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+h11==0.14.0
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+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
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+icetk==0.0.4
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+jax==0.4.13
+jaxlib==0.4.13
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+jiter==0.9.1
+jmespath==0.10.0
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+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
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+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
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+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
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+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
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+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
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+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
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+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
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+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
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+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1+cpu
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_54696_y_test/editable.txt b/configs/s41467_024_54696_y_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_54696_y_test/env.yml b/configs/s41467_024_54696_y_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..8376a35a4b5356e524d199d3bbd8231664b19ee0
--- /dev/null
+++ b/configs/s41467_024_54696_y_test/env.yml
@@ -0,0 +1,42 @@
+name: s41467_024_54696_y_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - fonttools==4.57.0
+    - kiwisolver==1.4.7
+    - numpy==1.24.4
+    - packaging==25.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - six==1.17.0
+    - tqdm==4.67.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_54696_y_test
diff --git a/configs/s41467_024_54696_y_test/explicit.txt b/configs/s41467_024_54696_y_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_54696_y_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_54696_y_test/meta.json b/configs/s41467_024_54696_y_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..919ca51f643502e9d703bb6d044e1fc36a1eca63
--- /dev/null
+++ b/configs/s41467_024_54696_y_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_54696_y_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_54696_y_test",
+  "exported_at": "2026-05-17T04:05:57Z"
+}
diff --git a/configs/s41467_024_54696_y_test/pip-clean.txt b/configs/s41467_024_54696_y_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d1a50684a62da5297853b2b76d27cce33b22b8e
--- /dev/null
+++ b/configs/s41467_024_54696_y_test/pip-clean.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
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+mrcfile==1.5.4
+msal==1.36.0
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+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
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+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
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+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
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+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
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+pyarrow-hotfix==0.6
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+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
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+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
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+PyMuPDFb==1.23.9
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+pystan==2.19.1.1
+pytesseract==0.3.10
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+python-iso639==2024.4.27
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+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
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+regex==2022.4.24
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+rouge-score==0.1.2
+rpds-py==0.20.1
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+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
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+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
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+snowballstemmer==2.2.0
+sobol-seq==0.2.0
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+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
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+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+texttable==1.7.0
+thefuzz==0.22.1
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+tifffile==2023.7.10
+tiktoken==0.7.0
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+tokenizers==0.20.3
+toml==0.10.2
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+toolz==0.12.1
+torch-geometric==2.6.1
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+torchtext==0.4.0
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+typing-inspect==0.9.0
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+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_54696_y_test/pip-freeze.txt b/configs/s41467_024_54696_y_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d1a50684a62da5297853b2b76d27cce33b22b8e
--- /dev/null
+++ b/configs/s41467_024_54696_y_test/pip-freeze.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_54846_2_test/editable.txt b/configs/s41467_024_54846_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_54846_2_test/env.yml b/configs/s41467_024_54846_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0e0f99ddadeb1585f7393e380227c95414dc266c
--- /dev/null
+++ b/configs/s41467_024_54846_2_test/env.yml
@@ -0,0 +1,40 @@
+name: s41467_024_54846_2_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.7.12
+  - python_abi=3.7
+  - readline=8.2
+  - setuptools=65.3.0
+  - sqlite=3.50.4
+  - tk=8.6.13
+  - wheel=0.41.3
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - pandas==1.3.5
+    - pytz==2025.2
+    - six==1.17.0
+    - xarray==0.20.2
+    - zipp==3.15.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_54846_2_test
diff --git a/configs/s41467_024_54846_2_test/explicit.txt b/configs/s41467_024_54846_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1bf2d11681f07524b194549a0aa0eee5b7f6efb
--- /dev/null
+++ b/configs/s41467_024_54846_2_test/explicit.txt
@@ -0,0 +1,32 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.7-4_cp37m.conda#d5fa71a1bac31ad985348ffff6b399c4
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_5.conda#4e02a49aaa9d5190cb630fa43528fbe6
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_5.conda#8bba50c7f4679f08c861b597ad2bda6b
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.50.4-hbc0de68_0.conda#8376bd3854542be0c8c7cd07525d31c6
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hf930737_100_cpython.tar.bz2#416558a6f46b7a1fa8db7d0e98aff56a
+https://conda.anaconda.org/conda-forge/linux-64/setuptools-65.3.0-py37h89c1867_0.tar.bz2#c02e157903596c9f0c94d9b486f52581
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.3-pyhd8ed1ab_0.conda#3fc026b9c87d091c4b34a6c997324ae8
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_54846_2_test/meta.json b/configs/s41467_024_54846_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..aeb643371edeabe0471f4397ba593c08e7162e7c
--- /dev/null
+++ b/configs/s41467_024_54846_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_54846_2_test",
+  "python_version": "3.7.12",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_54846_2_test",
+  "exported_at": "2026-05-17T04:06:03Z"
+}
diff --git a/configs/s41467_024_54846_2_test/pip-clean.txt b/configs/s41467_024_54846_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e404d5f8e0586ad405d17133ea99c1f64a83bed6
--- /dev/null
+++ b/configs/s41467_024_54846_2_test/pip-clean.txt
@@ -0,0 +1,157 @@
+absl-py==2.1.0
+anndata==0.8.0
+annotated-types==0.5.0
+anyio==3.7.1
+ase==3.22.1
+asteval==0.9.31
+astunparse==1.6.3
+attridict==0.0.9
+biopython==1.81
+brukeropusreader==1.3.4
+cached-property==1.5.2
+cachetools==5.5.2
+chaospy==4.3.20
+cloudpickle==2.2.1
+coverage==7.2.7
+cvxopt==1.3.2
+cycler==0.11.0
+dgl==1.1.3
+distro==1.9.0
+et-xmlfile==1.1.0
+exceptiongroup==1.3.0
+flatbuffers==25.2.10
+fonttools==4.38.0
+fsspec==2023.1.0
+future==1.0.0
+gast==0.4.0
+google-auth==2.40.3
+google-auth-oauthlib==0.4.6
+google-pasta==0.2.0
+googledrivedownloader==0.4
+grpcio==1.62.3
+h11==0.14.0
+h5py==3.8.0
+httpcore==0.17.3
+httpx==0.24.1
+huggingface-hub==0.16.4
+imageio==2.31.2
+importlib-metadata==4.13.0
+inequalipy==1.0.5
+iniconfig==2.0.0
+isodate==0.6.1
+jax==0.3.25
+joblib==0.17.0
+keras==2.11.0
+kiwisolver==1.4.4
+Levenshtein==0.23.0
+libclang==18.1.1
+llvmlite==0.39.1
+lmfit==1.2.2
+lxml==5.4.0
+Markdown==3.4.4
+MarkupSafe==2.1.5
+matplotlib==3.5.3
+monai==0.8.1
+monty==2023.9.25
+mpmath==1.3.0
+natsort==8.4.0
+numba==0.56.4
+numpoly==1.3.4
+numpy==1.21.6
+nvidia-cublas-cu11==11.10.3.66
+nvidia-cuda-nvrtc-cu11==11.7.99
+nvidia-cuda-runtime-cu11==11.7.99
+nvidia-cudnn-cu11==8.5.0.96
+oauthlib==3.2.2
+openai==1.39.0
+opencv-python==4.12.0.88
+openpyxl==3.1.3
+opt-einsum==3.3.0
+packaging==23.1
+palettable==3.3.3
+pandas==1.3.5
+patsy==1.0.1
+PICOS==2.6.1
+Pillow==9.5.0
+platformdirs==4.0.0
+pluggy==1.2.0
+ply==3.11
+pooch==1.8.2
+prettytable==3.7.0
+protobuf==3.19.6
+psutil==5.9.7
+pyasn1==0.5.1
+pyasn1-modules==0.3.0
+pydantic==2.5.3
+pydantic_core==2.14.6
+pyFFTW==0.13.0
+pymatgen==2022.0.17
+pynndescent==0.5.13
+Pyomo==6.6.2
+pyparsing==3.1.0
+pytest==7.4.4
+pytest-cov==4.1.0
+python-dateutil==2.8.2
+python-dotenv==0.21.1
+python-louvain==0.16
+pytz==2025.2
+pyvista==0.38.6
+PyWavelets==1.3.0
+PyYAML==6.0.1
+rapidfuzz==3.4.0
+rdflib==6.3.2
+rdkit-pypi==2022.9.5
+reedsolo==1.7.0
+regex==2024.4.16
+requests-oauthlib==2.0.0
+rsa==4.9.1
+ruamel.yaml==0.18.13
+ruamel.yaml.clib==0.2.8
+scanpy==1.9.3
+-e git+https://github.com/m-gallegos/SchNet4AIM.git@9e6be59a313099d4af6c013a55734ff72df76d7a#egg=SchNet4AIM
+scikit-image==0.19.3
+scikit-learn==1.0.2
+scipy==1.7.3
+scooby==0.7.3
+seaborn==0.12.2
+session_info==1.0.1
+shap==0.42.1
+shapely==2.0.7
+six==1.17.0
+slicer==0.0.7
+sniffio==1.3.1
+spglib==2.2.0
+statsmodels==0.13.5
+stdlib-list==0.10.0
+sympy==1.10.1
+tabulate==0.9.0
+tensorboard==2.11.2
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+tensorflow==2.11.0
+tensorflow-addons==0.19.0
+tensorflow-estimator==2.11.0
+tensorflow-io-gcs-filesystem==0.34.0
+termcolor==2.3.0
+threadpoolctl==3.1.0
+tifffile==2021.11.2
+tokenizers==0.13.3
+tomli==2.0.1
+torch==1.13.1
+torch-geometric==1.7.2
+torch-scatter==2.1.1+pt113cpu
+torch-sparse==0.6.17+pt113cpu
+torchvision==0.14.1
+tqdm==4.65.0
+transformers==4.24.0
+typeguard==4.1.2
+typing_extensions==4.7.1
+umap-learn==0.5.7
+uncertainties==3.1.7
+unittest-xml-reporting==3.2.0
+vtk==9.3.1
+Werkzeug==2.2.3
+wrapt==1.16.0
+xarray==0.20.2
+xlrd==2.0.2
+zipp==3.15.0
diff --git a/configs/s41467_024_54846_2_test/pip-freeze.txt b/configs/s41467_024_54846_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e404d5f8e0586ad405d17133ea99c1f64a83bed6
--- /dev/null
+++ b/configs/s41467_024_54846_2_test/pip-freeze.txt
@@ -0,0 +1,157 @@
+absl-py==2.1.0
+anndata==0.8.0
+annotated-types==0.5.0
+anyio==3.7.1
+ase==3.22.1
+asteval==0.9.31
+astunparse==1.6.3
+attridict==0.0.9
+biopython==1.81
+brukeropusreader==1.3.4
+cached-property==1.5.2
+cachetools==5.5.2
+chaospy==4.3.20
+cloudpickle==2.2.1
+coverage==7.2.7
+cvxopt==1.3.2
+cycler==0.11.0
+dgl==1.1.3
+distro==1.9.0
+et-xmlfile==1.1.0
+exceptiongroup==1.3.0
+flatbuffers==25.2.10
+fonttools==4.38.0
+fsspec==2023.1.0
+future==1.0.0
+gast==0.4.0
+google-auth==2.40.3
+google-auth-oauthlib==0.4.6
+google-pasta==0.2.0
+googledrivedownloader==0.4
+grpcio==1.62.3
+h11==0.14.0
+h5py==3.8.0
+httpcore==0.17.3
+httpx==0.24.1
+huggingface-hub==0.16.4
+imageio==2.31.2
+importlib-metadata==4.13.0
+inequalipy==1.0.5
+iniconfig==2.0.0
+isodate==0.6.1
+jax==0.3.25
+joblib==0.17.0
+keras==2.11.0
+kiwisolver==1.4.4
+Levenshtein==0.23.0
+libclang==18.1.1
+llvmlite==0.39.1
+lmfit==1.2.2
+lxml==5.4.0
+Markdown==3.4.4
+MarkupSafe==2.1.5
+matplotlib==3.5.3
+monai==0.8.1
+monty==2023.9.25
+mpmath==1.3.0
+natsort==8.4.0
+numba==0.56.4
+numpoly==1.3.4
+numpy==1.21.6
+nvidia-cublas-cu11==11.10.3.66
+nvidia-cuda-nvrtc-cu11==11.7.99
+nvidia-cuda-runtime-cu11==11.7.99
+nvidia-cudnn-cu11==8.5.0.96
+oauthlib==3.2.2
+openai==1.39.0
+opencv-python==4.12.0.88
+openpyxl==3.1.3
+opt-einsum==3.3.0
+packaging==23.1
+palettable==3.3.3
+pandas==1.3.5
+patsy==1.0.1
+PICOS==2.6.1
+Pillow==9.5.0
+platformdirs==4.0.0
+pluggy==1.2.0
+ply==3.11
+pooch==1.8.2
+prettytable==3.7.0
+protobuf==3.19.6
+psutil==5.9.7
+pyasn1==0.5.1
+pyasn1-modules==0.3.0
+pydantic==2.5.3
+pydantic_core==2.14.6
+pyFFTW==0.13.0
+pymatgen==2022.0.17
+pynndescent==0.5.13
+Pyomo==6.6.2
+pyparsing==3.1.0
+pytest==7.4.4
+pytest-cov==4.1.0
+python-dateutil==2.8.2
+python-dotenv==0.21.1
+python-louvain==0.16
+pytz==2025.2
+pyvista==0.38.6
+PyWavelets==1.3.0
+PyYAML==6.0.1
+rapidfuzz==3.4.0
+rdflib==6.3.2
+rdkit-pypi==2022.9.5
+reedsolo==1.7.0
+regex==2024.4.16
+requests-oauthlib==2.0.0
+rsa==4.9.1
+ruamel.yaml==0.18.13
+ruamel.yaml.clib==0.2.8
+scanpy==1.9.3
+-e git+https://github.com/m-gallegos/SchNet4AIM.git@9e6be59a313099d4af6c013a55734ff72df76d7a#egg=SchNet4AIM
+scikit-image==0.19.3
+scikit-learn==1.0.2
+scipy==1.7.3
+scooby==0.7.3
+seaborn==0.12.2
+session_info==1.0.1
+shap==0.42.1
+shapely==2.0.7
+six==1.17.0
+slicer==0.0.7
+sniffio==1.3.1
+spglib==2.2.0
+statsmodels==0.13.5
+stdlib-list==0.10.0
+sympy==1.10.1
+tabulate==0.9.0
+tensorboard==2.11.2
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+tensorflow==2.11.0
+tensorflow-addons==0.19.0
+tensorflow-estimator==2.11.0
+tensorflow-io-gcs-filesystem==0.34.0
+termcolor==2.3.0
+threadpoolctl==3.1.0
+tifffile==2021.11.2
+tokenizers==0.13.3
+tomli==2.0.1
+torch==1.13.1
+torch-geometric==1.7.2
+torch-scatter==2.1.1+pt113cpu
+torch-sparse==0.6.17+pt113cpu
+torchvision==0.14.1
+tqdm==4.65.0
+transformers==4.24.0
+typeguard==4.1.2
+typing_extensions==4.7.1
+umap-learn==0.5.7
+uncertainties==3.1.7
+unittest-xml-reporting==3.2.0
+vtk==9.3.1
+Werkzeug==2.2.3
+wrapt==1.16.0
+xarray==0.20.2
+xlrd==2.0.2
+zipp==3.15.0
diff --git a/configs/s41467_024_55291_x_test/editable.txt b/configs/s41467_024_55291_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_55291_x_test/env.yml b/configs/s41467_024_55291_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c2ce7fb45a3074e170b2084f71e4ed773620db67
--- /dev/null
+++ b/configs/s41467_024_55291_x_test/env.yml
@@ -0,0 +1,69 @@
+name: s41467_024_55291_x_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - biothings-client==0.4.1
+    - bounded-pool-executor==0.0.3
+    - catalogue==1.0.2
+    - certifi==2026.2.25
+    - charset-normalizer==3.4.3
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - en-core-sci-md==0.2.5
+    - en-ner-jnlpba-md==0.3.0
+    - fonttools==4.57.0
+    - httpx==0.28.1
+    - idna==3.10
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - mygene==3.2.2
+    - mysql-connector-python==9.0.0
+    - nmslib==2.1.1
+    - numpy==1.23.5
+    - packaging==25.0
+    - pandas==1.4.2
+    - pillow==10.4.0
+    - pubmed-parser==0.3.1
+    - pybind11==2.6.1
+    - pyparsing==3.1.4
+    - pysbd==0.3.4
+    - python-dateutil==2.9.0.post0
+    - requests==2.32.4
+    - six==1.16.0
+    - spacy==2.3.4
+    - srsly==1.0.7
+    - thinc==7.4.6
+    - tqdm==4.67.1
+    - urllib3==2.2.3
+    - wasabi==0.10.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_55291_x_test
diff --git a/configs/s41467_024_55291_x_test/explicit.txt b/configs/s41467_024_55291_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_55291_x_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_55291_x_test/meta.json b/configs/s41467_024_55291_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d586ff77132dfcbddbaf95a2c448cf782e1a71c2
--- /dev/null
+++ b/configs/s41467_024_55291_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_55291_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_55291_x_test",
+  "exported_at": "2026-05-17T04:06:01Z"
+}
diff --git a/configs/s41467_024_55291_x_test/pip-clean.txt b/configs/s41467_024_55291_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3bb62a12c2c51224d0050caa7102fc12cc5d6572
--- /dev/null
+++ b/configs/s41467_024_55291_x_test/pip-clean.txt
@@ -0,0 +1,468 @@
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+en_ner_jnlpba_md @ https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.3.0/en_ner_jnlpba_md-0.3.0.tar.gz#sha256=40068eeaaced06834758fadae40a5eb8d9fa821692b1332d7c6ed24853bb1d00
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diff --git a/configs/s41467_024_55291_x_test/pip-freeze.txt b/configs/s41467_024_55291_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3bb62a12c2c51224d0050caa7102fc12cc5d6572
--- /dev/null
+++ b/configs/s41467_024_55291_x_test/pip-freeze.txt
@@ -0,0 +1,468 @@
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+en_ner_jnlpba_md @ https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.3.0/en_ner_jnlpba_md-0.3.0.tar.gz#sha256=40068eeaaced06834758fadae40a5eb8d9fa821692b1332d7c6ed24853bb1d00
+equinox==0.10.4
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+fastapi-sso==0.16.0
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+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mygene==3.2.2
+mypy-extensions==1.0.0
+mysql-connector-python==9.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+nmslib==2.1.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.23.5
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+pubmed_parser==0.3.1
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pybind11==2.6.1
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+pysbd==0.3.4
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy==2.3.4
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+srsly==1.0.7
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+thinc==7.4.6
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+wasabi==0.10.1
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_55419_z_test/editable.txt b/configs/s41467_024_55419_z_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_55419_z_test/env.yml b/configs/s41467_024_55419_z_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..67598bbed62bf248d65c7bbd50e9a5d1e456d33b
--- /dev/null
+++ b/configs/s41467_024_55419_z_test/env.yml
@@ -0,0 +1,58 @@
+name: s41467_024_55419_z_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_55419_z_test
diff --git a/configs/s41467_024_55419_z_test/explicit.txt b/configs/s41467_024_55419_z_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_55419_z_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_024_55419_z_test/meta.json b/configs/s41467_024_55419_z_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..b04516359fb0ce87af7816d7648fbddb3a24cba5
--- /dev/null
+++ b/configs/s41467_024_55419_z_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_55419_z_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_55419_z_test",
+  "exported_at": "2026-05-17T04:06:04Z"
+}
diff --git a/configs/s41467_024_55419_z_test/pip-clean.txt b/configs/s41467_024_55419_z_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cb97759d3d8610433b1907f3311948b9f94ed5f
--- /dev/null
+++ b/configs/s41467_024_55419_z_test/pip-clean.txt
@@ -0,0 +1,460 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
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+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
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+xxhash==2.0.2
+Yapsy==1.12.2
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+youtube-search==2.1.2
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+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_55419_z_test/pip-freeze.txt b/configs/s41467_024_55419_z_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cb97759d3d8610433b1907f3311948b9f94ed5f
--- /dev/null
+++ b/configs/s41467_024_55419_z_test/pip-freeze.txt
@@ -0,0 +1,460 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
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+async-timeout==4.0.3
+attrs==25.3.0
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+azure-core==1.33.0
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+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
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+blessed==1.20.0
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+boto3==1.36.0
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+chaospy==3.3.9
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+confection==0.1.4
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+cryptography==42.0.5
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+Cython==0.29.30
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1+cpu
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_55462_w_test/editable.txt b/configs/s41467_024_55462_w_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_55462_w_test/env.yml b/configs/s41467_024_55462_w_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9a7de8e3f02f7f882da467017b8905c15f587a66
--- /dev/null
+++ b/configs/s41467_024_55462_w_test/env.yml
@@ -0,0 +1,60 @@
+name: s41467_024_55462_w_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - appdirs=1.4.4
+  - brotli-python=1.1.0
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - certifi=2024.2.2
+  - charset-normalizer=3.3.2
+  - idna=3.10
+  - joblib=1.4.2
+  - ld_impl_linux-64=2.44
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgomp=15.1.0
+  - liblapack=3.9.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.25
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - networkx=2.8.8
+  - numpy=1.24.4
+  - openssl=3.5.2
+  - packaging=25.0
+  - pip=22.1.2
+  - pooch=0.6.0
+  - pysocks=1.7.1
+  - python=3.8.20
+  - python_abi=3.8
+  - readline=8.2
+  - requests=2.32.3
+  - scipy=1.10.1
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - urllib3=2.2.1
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - rdkit-pypi==2022.9.5
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_55462_w_test
diff --git a/configs/s41467_024_55462_w_test/explicit.txt b/configs/s41467_024_55462_w_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03794734351587be9166bb6a88be42ef364d82a9
--- /dev/null
+++ b/configs/s41467_024_55462_w_test/explicit.txt
@@ -0,0 +1,55 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_4.conda#8a4ab7ff06e4db0be22485332666da0f
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_4.conda#53e876bc2d2648319e94c33c57b9ec74
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_4.conda#2d34729cbc1da0ec988e57b13b712067
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.1.0-h69a702a_4.conda#b1a97c0f2c4f1bb2b8872a21fc7e17a7
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.25-pthreads_h413a1c8_0.conda#d172b34a443b95f86089e8229ddc9a17
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2#5f095bc6454094e96f146491fd03633b
+https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py38h17151c0_1.conda#7a5a699c8992fc51ef25e980f4502c2a
+https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333
+https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda#7f4a9e3fcff3f6356ae99244a014da6a
+https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_0.conda#7ba2ede0e7c795ff95088daf0dc59753
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-20_linux64_openblas.conda#2b7bb4f7562c8cf334fc2e20c2d28abc
+https://conda.anaconda.org/conda-forge/noarch/networkx-2.8.8-pyhd8ed1ab_0.tar.bz2#bb45ff9deddb045331fd039949f39650
+https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda#58335b26c38bf4a20f399384c33cbcf9
+https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha2e5f31_6.tar.bz2#2a7de29fb590ca14b5243c4c812c8025
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/joblib-1.4.2-pyhd8ed1ab_0.conda#25df261d4523d9f9783bcdb7208d872f
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-20_linux64_openblas.conda#36d486d72ab64ffea932329a1d3729a3
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-20_linux64_openblas.conda#6fabc51f5e647d09cc010c40061557e0
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
+https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.1-pyhd8ed1ab_0.conda#08807a87fa7af10754d46f63b368e016
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.24.4-py38h59b608b_0.conda#8c3e050afeeb2b32575bdb8955cc67b2
+https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda#5ede4753180c7a550a443c430dc8ab52
+https://conda.anaconda.org/conda-forge/linux-64/pooch-0.6.0-py38_0.tar.bz2#ac189deff84c49625c7292a61a525723
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.10.1-py38h59b608b_3.conda#2f2a57462fcfbc67dfdbb0de6f7484c2
diff --git a/configs/s41467_024_55462_w_test/meta.json b/configs/s41467_024_55462_w_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..61dcab0c247eaeef9cb42d1c0271ea6aa30bda78
--- /dev/null
+++ b/configs/s41467_024_55462_w_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_55462_w_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_55462_w_test",
+  "exported_at": "2026-05-17T04:06:02Z"
+}
diff --git a/configs/s41467_024_55462_w_test/pip-clean.txt b/configs/s41467_024_55462_w_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bea74b542a0af86fc16e3838755effb11b1e274
--- /dev/null
+++ b/configs/s41467_024_55462_w_test/pip-clean.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
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+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
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+botocore==1.36.26
+botorch==0.8.5
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+Brotli==1.1.0
+bs4==0.0.2
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+chaospy==3.3.9
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+cloudpathlib==0.16.0
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+confection==0.1.4
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+conllu==0.11
+coverage==7.6.1
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+cymem==2.0.8
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+datasets==2.19.0
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+Deprecated==1.2.14
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+editdistance==0.6.0
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+fairseq==0.10.2
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+nvidia-ml-py==12.535.133
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+parsimonious==0.8.1
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+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
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+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
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+regex==2022.4.24
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+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
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+sentry-sdk==2.39.0
+session_info==1.0.1
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+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
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+stdlib-list==0.10.0
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+streamlit-antd-components==0.3.1
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+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+thefuzz==0.22.1
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+tifffile==2023.7.10
+tiktoken==0.7.0
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+toml==0.10.2
+tomlkit==0.12.0
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+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+tqdm==4.67.1
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+transformers==4.46.3
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+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_024_55462_w_test/pip-freeze.txt b/configs/s41467_024_55462_w_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9254d9522dafa15d27a09eeb3bef2df3e858af5
--- /dev/null
+++ b/configs/s41467_024_55462_w_test/pip-freeze.txt
@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+appdirs @ file:///home/conda/feedstock_root/build_artifacts/appdirs_1603108395799/work
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
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+botorch==0.8.5
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+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
+cffi==1.15.0
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+chaospy==3.3.9
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+cloudpathlib==0.16.0
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+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
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+equinox==0.10.4
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+eval_type_backport==0.2.2
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+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
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+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+icetk==0.0.4
+idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1726459485162/work
+igraph==0.11.8
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+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1687808301083/work
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+rdkit-pypi==2022.9.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1683900206454/work/base/dist/scipy-1.10.1-cp38-cp38-linux_x86_64.whl#sha256=13ab5c17dedeb97a65ba90de1c51475f2d3ae0fe50bc43e9b018cc2943541de4
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1708239446578/work
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_55825_x_test/editable.txt b/configs/s41467_025_55825_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_55825_x_test/env.yml b/configs/s41467_025_55825_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..073eaf424c40e041b1573898045ad27a82df9fc2
--- /dev/null
+++ b/configs/s41467_025_55825_x_test/env.yml
@@ -0,0 +1,69 @@
+name: s41467_025_55825_x_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - absl-py==0.15.0
+    - astunparse==1.6.3
+    - flatbuffers==1.12
+    - gast==0.4.0
+    - google-auth==2.43.0
+    - google-auth-oauthlib==0.4.6
+    - grpcio==1.34.1
+    - h5py==3.1.0
+    - idna==3.11
+    - joblib==1.4.2
+    - keras-nightly==2.5.0.dev2021032900
+    - lazy-loader==0.4
+    - networkx==3.1
+    - numpy==1.21.5
+    - opencv-python==4.13.0.92
+    - opt-einsum==3.4.0
+    - packaging==25.0
+    - pandas==1.4.4
+    - pillow==10.4.0
+    - protobuf==3.20.3
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - python-dateutil==2.9.0.post0
+    - pytz==2026.1.post1
+    - scikit-image==0.20.0
+    - scipy==1.9.1
+    - six==1.15.0
+    - tensorboard==2.11.2
+    - tensorboard-data-server==0.6.1
+    - tensorflow==2.5.0
+    - tensorflow-estimator==2.5.0
+    - termcolor==2.4.0
+    - typing-extensions==3.7.4.3
+    - urllib3==2.2.3
+    - wrapt==1.12.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_55825_x_test
diff --git a/configs/s41467_025_55825_x_test/explicit.txt b/configs/s41467_025_55825_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_55825_x_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_55825_x_test/meta.json b/configs/s41467_025_55825_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..094229be91da9f6f7310b9596083d4627a4c5819
--- /dev/null
+++ b/configs/s41467_025_55825_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_55825_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_55825_x_test",
+  "exported_at": "2026-05-17T04:06:08Z"
+}
diff --git a/configs/s41467_025_55825_x_test/pip-clean.txt b/configs/s41467_025_55825_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be423c51b6d126a813c7c4c7bf78f3ea22ccd38e
--- /dev/null
+++ b/configs/s41467_025_55825_x_test/pip-clean.txt
@@ -0,0 +1,466 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
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+unstructured==0.11.0
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+unstructured-inference==0.7.15
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+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
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+Werkzeug==2.0.2
+word2number==1.1
+wrapt==1.12.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_55825_x_test/pip-freeze.txt b/configs/s41467_025_55825_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be423c51b6d126a813c7c4c7bf78f3ea22ccd38e
--- /dev/null
+++ b/configs/s41467_025_55825_x_test/pip-freeze.txt
@@ -0,0 +1,466 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
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+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+blessed==1.20.0
+blis==0.7.11
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+botorch==0.8.5
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+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
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+chaospy==3.3.9
+charset-normalizer==3.4.7
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+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
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+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+get-annotations==0.1.2
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+GitPython==3.1.43
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+google-auth-oauthlib==0.4.6
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+langchain==0.1.16
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+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyasn1==0.6.1
+pyasn1_modules==0.4.2
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-image==0.20.0
+scipy==1.9.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard==2.11.2
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+tensorflow==2.5.0
+tensorflow-estimator==2.5.0
+termcolor==2.4.0
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+wrapt==1.12.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56036_0_test/editable.txt b/configs/s41467_025_56036_0_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_56036_0_test/env.yml b/configs/s41467_025_56036_0_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7b501515a546fe60801dc03cf52576e0047be9b6
--- /dev/null
+++ b/configs/s41467_025_56036_0_test/env.yml
@@ -0,0 +1,51 @@
+name: s41467_025_56036_0_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - glob2==0.7
+    - kiwisolver==1.4.7
+    - matplotlib==3.5.2
+    - numpy==1.21.5
+    - opencv-python==4.7.0.68
+    - packaging==25.0
+    - pandas==1.4.4
+    - pillow==10.4.0
+    - psutil==5.9.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scipy==1.9.1
+    - six==1.17.0
+    - tqdm==4.67.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56036_0_test
diff --git a/configs/s41467_025_56036_0_test/explicit.txt b/configs/s41467_025_56036_0_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_56036_0_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_56036_0_test/meta.json b/configs/s41467_025_56036_0_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..32c27969b31fd607a0d0ec5b94f1e159fe72bea9
--- /dev/null
+++ b/configs/s41467_025_56036_0_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_56036_0_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56036_0_test",
+  "exported_at": "2026-05-17T04:06:08Z"
+}
diff --git a/configs/s41467_025_56036_0_test/pip-clean.txt b/configs/s41467_025_56036_0_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..156dfb76f86bf642291baaac32c240d1aedce5f6
--- /dev/null
+++ b/configs/s41467_025_56036_0_test/pip-clean.txt
@@ -0,0 +1,454 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+glob2==0.7
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.5.2
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tzdata==2024.1
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+word2number==1.1
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+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56036_0_test/pip-freeze.txt b/configs/s41467_025_56036_0_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..156dfb76f86bf642291baaac32c240d1aedce5f6
--- /dev/null
+++ b/configs/s41467_025_56036_0_test/pip-freeze.txt
@@ -0,0 +1,454 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+alabaster==0.7.12
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+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
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+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
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+azure-storage-blob==12.26.0
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+backoff==2.2.1
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+better-abc==0.0.3
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+bitsandbytes==0.43.1
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+chaospy==3.3.9
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+coverage==7.6.1
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+cryptography==42.0.5
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+tabulate==0.8.9
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+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56078_4_test/env.yml b/configs/s41467_025_56078_4_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..21d8f32ef1b2a01c675af9df9a34f13279b28a40
--- /dev/null
+++ b/configs/s41467_025_56078_4_test/env.yml
@@ -0,0 +1,75 @@
+name: s41467_025_56078_4_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - absl-py==2.3.1
+    - addict==2.4.0
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - google-auth==2.43.0
+    - google-auth-oauthlib==1.0.0
+    - grpcio==1.70.0
+    - idna==3.11
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - opencv-python==4.12.0.88
+    - packaging==25.0
+    - protobuf==5.29.5
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - scikit-image==0.21.0
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - tb-nightly==2.14.0a20230808
+    - tensorboard-data-server==0.7.2
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - tqdm==4.67.1
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+    - yapf==0.43.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56078_4_test
diff --git a/configs/s41467_025_56140_1_test/editable.txt b/configs/s41467_025_56140_1_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_56140_1_test/env.yml b/configs/s41467_025_56140_1_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d322a0128f6457e90b84331fef9445c3eb697b5e
--- /dev/null
+++ b/configs/s41467_025_56140_1_test/env.yml
@@ -0,0 +1,40 @@
+name: s41467_025_56140_1_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - mpmath==1.3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - pyserial==3.5
+    - six==1.17.0
+    - sympy==1.13.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56140_1_test
diff --git a/configs/s41467_025_56140_1_test/explicit.txt b/configs/s41467_025_56140_1_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_56140_1_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_56140_1_test/meta.json b/configs/s41467_025_56140_1_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..42658093798bcf9b77d2a0a3bafda1dbcf181567
--- /dev/null
+++ b/configs/s41467_025_56140_1_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_56140_1_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56140_1_test",
+  "exported_at": "2026-05-17T04:06:07Z"
+}
diff --git a/configs/s41467_025_56140_1_test/pip-clean.txt b/configs/s41467_025_56140_1_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7048b1624ae97e82fcb2885a14280f960177bd51
--- /dev/null
+++ b/configs/s41467_025_56140_1_test/pip-clean.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
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+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
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+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
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+onnxruntime==1.15.1
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+openpyxl==3.0.9
+opentelemetry-api==1.24.0
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+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
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+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+pyserial==3.5
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56140_1_test/pip-freeze.txt b/configs/s41467_025_56140_1_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7048b1624ae97e82fcb2885a14280f960177bd51
--- /dev/null
+++ b/configs/s41467_025_56140_1_test/pip-freeze.txt
@@ -0,0 +1,446 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
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+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
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+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
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+hf_transfer==0.1.9
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+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
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+inequalipy==1.0.5
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+isodate==0.7.2
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+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
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+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+pyserial==3.5
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56162_9_test/editable.txt b/configs/s41467_025_56162_9_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_56162_9_test/env.yml b/configs/s41467_025_56162_9_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d6c38ab897ed5856871196aef3bcc1b355884529
--- /dev/null
+++ b/configs/s41467_025_56162_9_test/env.yml
@@ -0,0 +1,57 @@
+name: s41467_025_56162_9_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - certifi==2026.4.22
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - idna==3.13
+    - importlib-resources==6.4.5
+    - joblib==1.4.2
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - nibabel==5.2.1
+    - nilearn==0.10.4
+    - numpy==1.24.4
+    - packaging==25.0
+    - pandas==2.0.3
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - requests==2.32.4
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - threadpoolctl==3.5.0
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56162_9_test
diff --git a/configs/s41467_025_56162_9_test/explicit.txt b/configs/s41467_025_56162_9_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_56162_9_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_56162_9_test/meta.json b/configs/s41467_025_56162_9_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a0f0d90f04a4bd6c9bac9cd938cb6432fc0db218
--- /dev/null
+++ b/configs/s41467_025_56162_9_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_56162_9_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56162_9_test",
+  "exported_at": "2026-05-17T04:06:12Z"
+}
diff --git a/configs/s41467_025_56162_9_test/pip-clean.txt b/configs/s41467_025_56162_9_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4988eb0c2e89c67dd9b97f8a16a8c2a25e74cf11
--- /dev/null
+++ b/configs/s41467_025_56162_9_test/pip-clean.txt
@@ -0,0 +1,457 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.13
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
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+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
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+monotonic==1.6
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+onnxruntime==1.15.1
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+ordered-set==4.1.0
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+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
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+pathlib==1.0.1
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+pdf2image==1.17.0
+pfzy==0.3.4
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+pikepdf==8.4.1
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+ray==2.10.0
+rdkit==2024.3.5
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+regex==2022.4.24
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+sentence-transformers==2.2.2
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56162_9_test/pip-freeze.txt b/configs/s41467_025_56162_9_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4988eb0c2e89c67dd9b97f8a16a8c2a25e74cf11
--- /dev/null
+++ b/configs/s41467_025_56162_9_test/pip-freeze.txt
@@ -0,0 +1,457 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.13
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+nibabel==5.2.1
+nilearn==0.10.4
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56173_6_test/editable.txt b/configs/s41467_025_56173_6_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_56173_6_test/env.yml b/configs/s41467_025_56173_6_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..fc6d9528862391e747a65158a2ba1607ecb3bade
--- /dev/null
+++ b/configs/s41467_025_56173_6_test/env.yml
@@ -0,0 +1,43 @@
+name: s41467_025_56173_6_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - joblib==1.4.2
+    - numpy==1.24.4
+    - packaging==25.0
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - threadpoolctl==3.5.0
+    - torch==1.13.1+cpu
+    - typing-extensions==4.12.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56173_6_test
diff --git a/configs/s41467_025_56173_6_test/explicit.txt b/configs/s41467_025_56173_6_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_56173_6_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
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diff --git a/configs/s41467_025_56173_6_test/meta.json b/configs/s41467_025_56173_6_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..1f4d36edf01c4650688c99a790036eb58ae79b37
--- /dev/null
+++ b/configs/s41467_025_56173_6_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_56173_6_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56173_6_test",
+  "exported_at": "2026-05-17T04:06:11Z"
+}
diff --git a/configs/s41467_025_56173_6_test/pip-clean.txt b/configs/s41467_025_56173_6_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6cf088d59f3e34aea4bda37b3fa06b2d307499f
--- /dev/null
+++ b/configs/s41467_025_56173_6_test/pip-clean.txt
@@ -0,0 +1,446 @@
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diff --git a/configs/s41467_025_56173_6_test/pip-freeze.txt b/configs/s41467_025_56173_6_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6cf088d59f3e34aea4bda37b3fa06b2d307499f
--- /dev/null
+++ b/configs/s41467_025_56173_6_test/pip-freeze.txt
@@ -0,0 +1,446 @@
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+docstring_parser==0.17.0
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
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+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
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+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
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+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
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+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
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+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
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+importlib-metadata==7.0.0
+importlib_resources==6.4.5
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+iniconfig==1.1.1
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+iopath==0.1.10
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+itsdangerous==2.0.1
+jax==0.4.13
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+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
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+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
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+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
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+snowballstemmer==2.2.0
+sobol-seq==0.2.0
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+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
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+tiktoken==0.7.0
+timm==0.9.16
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+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==1.13.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
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+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
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+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56622_2_test/editable.txt b/configs/s41467_025_56622_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_56622_2_test/env.yml b/configs/s41467_025_56622_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0fdccd7052531f0e61b246450c53475dfc72018a
--- /dev/null
+++ b/configs/s41467_025_56622_2_test/env.yml
@@ -0,0 +1,59 @@
+name: s41467_025_56622_2_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - filelock==3.13.1
+    - fonttools==4.57.0
+    - fsspec==2024.6.1
+    - importlib-resources==6.4.5
+    - jinja2==3.1.6
+    - kiwisolver==1.4.7
+    - markupsafe==2.1.5
+    - matplotlib==3.7.5
+    - mpmath==1.3.0
+    - networkx==3.0
+    - numpy==1.24.4
+    - opencv-python==4.12.0.88
+    - packaging==25.0
+    - pandas==2.0.3
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - typing-extensions==4.12.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56622_2_test
diff --git a/configs/s41467_025_56622_2_test/explicit.txt b/configs/s41467_025_56622_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_56622_2_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_56622_2_test/meta.json b/configs/s41467_025_56622_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..996d09eedb9c199d2ccabe77046829458992e732
--- /dev/null
+++ b/configs/s41467_025_56622_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_56622_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56622_2_test",
+  "exported_at": "2026-05-17T04:06:19Z"
+}
diff --git a/configs/s41467_025_56622_2_test/pip-clean.txt b/configs/s41467_025_56622_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09c3c4e7207d20bf160b1990b4c834453efacfde
--- /dev/null
+++ b/configs/s41467_025_56622_2_test/pip-clean.txt
@@ -0,0 +1,458 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+torch==2.4.1+cpu
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+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+tornado==6.4
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+transformers==4.46.3
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+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
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+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
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+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_56622_2_test/pip-freeze.txt b/configs/s41467_025_56622_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09c3c4e7207d20bf160b1990b4c834453efacfde
--- /dev/null
+++ b/configs/s41467_025_56622_2_test/pip-freeze.txt
@@ -0,0 +1,458 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
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+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+blessed==1.20.0
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+boto3==1.36.0
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+botorch==0.8.5
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+chaospy==3.3.9
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+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
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+coloredlogs==15.0.1
+confection==0.1.4
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+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
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+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
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+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
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+dnspython==2.6.1
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+editdistance==0.6.0
+effdet==0.4.1
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+fancy-einsum==0.0.3
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+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.0
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+opencv-python==4.12.0.88
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+torchvision==0.19.1+cpu
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_57505_2_test/editable.txt b/configs/s41467_025_57505_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_57505_2_test/env.yml b/configs/s41467_025_57505_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..29d2a40cea153db406968d73dbdf69be0c55adad
--- /dev/null
+++ b/configs/s41467_025_57505_2_test/env.yml
@@ -0,0 +1,47 @@
+name: s41467_025_57505_2_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - networkx==3.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_57505_2_test
diff --git a/configs/s41467_025_57505_2_test/explicit.txt b/configs/s41467_025_57505_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_57505_2_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_57505_2_test/meta.json b/configs/s41467_025_57505_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..42c7c089147b185e9a83c38deaf7f1470a6b8732
--- /dev/null
+++ b/configs/s41467_025_57505_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_57505_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_57505_2_test",
+  "exported_at": "2026-05-17T04:06:23Z"
+}
diff --git a/configs/s41467_025_57505_2_test/pip-clean.txt b/configs/s41467_025_57505_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1867db71e5b260c5515efcec08e4d5d07e30f97f
--- /dev/null
+++ b/configs/s41467_025_57505_2_test/pip-clean.txt
@@ -0,0 +1,451 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
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+parsimonious==0.8.1
+pathlib==1.0.1
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+pyfaidx==0.9.0.1
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+pypdfium2==4.29.0
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+pytesseract==0.3.10
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+python-decouple==3.8
+python-docx==1.1.0
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+python-iso639==2024.4.27
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+python-multipart==0.0.18
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+sentry-sdk==2.39.0
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+stdlib-list==0.10.0
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+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+transformers==4.46.3
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+typing-inspect==0.9.0
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+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_57505_2_test/pip-freeze.txt b/configs/s41467_025_57505_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1867db71e5b260c5515efcec08e4d5d07e30f97f
--- /dev/null
+++ b/configs/s41467_025_57505_2_test/pip-freeze.txt
@@ -0,0 +1,451 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
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+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+fschat==0.2.35
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+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
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+jmespath==0.10.0
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
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+kiwisolver==1.4.7
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+langchain==0.1.16
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+lazy_loader==0.4
+leidenalg==0.10.2
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+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
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+opentelemetry-semantic-conventions==0.45b0
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+overrides==7.7.0
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+parsimonious==0.8.1
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+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58011_1_test/editable.txt b/configs/s41467_025_58011_1_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_58011_1_test/env.yml b/configs/s41467_025_58011_1_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..167f501430fea0cbe08e544400bede2f7042edc8
--- /dev/null
+++ b/configs/s41467_025_58011_1_test/env.yml
@@ -0,0 +1,85 @@
+name: s41467_025_58011_1_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - audioread==3.0.1
+    - certifi==2026.2.25
+    - charset-normalizer==3.4.7
+    - decorator==5.2.1
+    - expelliarmus==1.1.12
+    - filelock==3.16.1
+    - fonttools==4.57.0
+    - fsspec==2025.3.0
+    - h5py==3.11.0
+    - idna==3.11
+    - importrosbag==1.0.4
+    - jinja2==3.1.6
+    - kiwisolver==1.4.7
+    - librosa==0.11.0
+    - lightning-utilities==0.11.9
+    - markupsafe==2.1.5
+    - matplotlib==3.7.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - pbr==7.0.3
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - pytorch-lightning==2.4.0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - soundfile==0.13.1
+    - soxr==0.3.7
+    - sympy==1.13.3
+    - threadpoolctl==3.5.0
+    - tonic==1.6.0
+    - torch==2.4.1+cpu
+    - torchmetrics==1.5.2
+    - tqdm==4.67.3
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58011_1_test
diff --git a/configs/s41467_025_58011_1_test/explicit.txt b/configs/s41467_025_58011_1_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_58011_1_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_58011_1_test/meta.json b/configs/s41467_025_58011_1_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..919926b87a0e39801b4337c763323dfc19875c05
--- /dev/null
+++ b/configs/s41467_025_58011_1_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58011_1_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58011_1_test",
+  "exported_at": "2026-05-17T04:06:31Z"
+}
diff --git a/configs/s41467_025_58011_1_test/pip-clean.txt b/configs/s41467_025_58011_1_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a995576506f72b6daca8071e12064fc2f985e50
--- /dev/null
+++ b/configs/s41467_025_58011_1_test/pip-clean.txt
@@ -0,0 +1,481 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+audioread==3.0.1
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.2.25
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+decorator==5.2.1
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+expelliarmus==1.1.12
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+h5py==3.11.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.11
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+importRosbag==1.0.4
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+librosa==0.11.0
+lightning-utilities==0.11.9
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib==3.7.5
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
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+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
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+nvidia-nccl-cu12==2.20.5
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+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
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+sphinxcontrib-devhelp==1.0.2
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+toml==0.10.2
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+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
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+torchtext==0.4.0
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+tzdata==2024.1
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+unittest-xml-reporting==3.2.0
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+unstructured-client==0.22.0
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+wandb==0.22.0
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+word2number==1.1
+xlrd==2.0.1
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+xxhash==2.0.2
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+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58011_1_test/pip-freeze.txt b/configs/s41467_025_58011_1_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a995576506f72b6daca8071e12064fc2f985e50
--- /dev/null
+++ b/configs/s41467_025_58011_1_test/pip-freeze.txt
@@ -0,0 +1,481 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+audioread==3.0.1
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+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
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+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
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+chaospy==3.3.9
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+click==8.1.7
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+confection==0.1.4
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+coverage==7.6.1
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+cryptography==42.0.5
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+dataclasses-json==0.6.4
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+deepdiff==7.0.1
+Deprecated==1.2.14
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+tonic==1.6.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchmetrics==1.5.2
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58055_3_test/editable.txt b/configs/s41467_025_58055_3_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_58055_3_test/env.yml b/configs/s41467_025_58055_3_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..34b67a3efaafa31578e994cb5da4000fc66b3a48
--- /dev/null
+++ b/configs/s41467_025_58055_3_test/env.yml
@@ -0,0 +1,62 @@
+name: s41467_025_58055_3_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.10.5
+  - ld_impl_linux-64=2.44
+  - libffi=3.5.2
+  - libgcc=15.2.0
+  - libgcc-ng=15.2.0
+  - libgomp=15.2.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.51.0
+  - libstdcxx=15.2.0
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.6.0
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - zstd=1.5.7
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cublas-cu12==12.1.3.1
+    - nvidia-cuda-cupti-cu12==12.1.105
+    - nvidia-cuda-nvrtc-cu12==12.1.105
+    - nvidia-cuda-runtime-cu12==12.1.105
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-cufft-cu12==11.0.2.54
+    - nvidia-curand-cu12==10.3.2.106
+    - nvidia-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - pillow==10.4.0
+    - pyyaml==6.0.3
+    - scipy==1.10.1
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - tqdm==4.67.1
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58055_3_test
diff --git a/configs/s41467_025_58055_3_test/explicit.txt b/configs/s41467_025_58055_3_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0def4cef8bb7c59c3e7becdcd5d90d7370f54a2
--- /dev/null
+++ b/configs/s41467_025_58055_3_test/explicit.txt
@@ -0,0 +1,33 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.0-h0c1763c_0.conda#a3205ecbffb255ca27e0540c8494a2ee
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1aa0949_5.conda#511ed8935448c1875776b60ad3daf3a1
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_58055_3_test/meta.json b/configs/s41467_025_58055_3_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0d0da7b4f9d620c778e6105dcc8fc90d64b9f2c3
--- /dev/null
+++ b/configs/s41467_025_58055_3_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58055_3_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58055_3_test",
+  "exported_at": "2026-05-17T04:06:31Z"
+}
diff --git a/configs/s41467_025_58055_3_test/pip-clean.txt b/configs/s41467_025_58055_3_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..187bf7770e287ddb40059ff31fd3d2ad26a09526
--- /dev/null
+++ b/configs/s41467_025_58055_3_test/pip-clean.txt
@@ -0,0 +1,462 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
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+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.1.105
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
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+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
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+pkgutil_resolve_name==1.3.10
+plac==0.9.6
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+pluggy==1.5.0
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+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
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+pytesseract==0.3.10
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+python-dateutil==2.9.0.post0
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+python-iso639==2024.4.27
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+python-multipart==0.0.18
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+PyWavelets==1.4.1
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+ray==2.10.0
+rdkit==2024.3.5
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+regex==2022.4.24
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+sphinxcontrib-devhelp==1.0.2
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+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
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+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+typing-utils==0.1.0
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+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58055_3_test/pip-freeze.txt b/configs/s41467_025_58055_3_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..187bf7770e287ddb40059ff31fd3d2ad26a09526
--- /dev/null
+++ b/configs/s41467_025_58055_3_test/pip-freeze.txt
@@ -0,0 +1,462 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
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+bitsandbytes==0.43.1
+blessed==1.20.0
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+cftime==1.6.4.post1
+chaospy==3.3.9
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+cohere==5.3.3
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+confection==0.1.4
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+conllu==0.11
+coverage==7.6.1
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+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
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+Deprecated==1.2.14
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+editdistance==0.6.0
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+openai==1.101.0
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+tzdata==2024.1
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58227_1_test/pip-freeze.txt b/configs/s41467_025_58227_1_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13d3c126ae0a04df1d1fd779605bc52de01c55fa
--- /dev/null
+++ b/configs/s41467_025_58227_1_test/pip-freeze.txt
@@ -0,0 +1,456 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+appdirs==1.4.4
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+depinfo==2.2.0
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+diskcache==5.6.3
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+gurobipy==11.0.3
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.13
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+optlang==1.8.2
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-libsbml==5.21.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruamel.yaml==0.18.16
+ruamel.yaml.clib==0.2.8
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+swiglpk==5.0.13
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58356_7_test/editable.txt b/configs/s41467_025_58356_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_58356_7_test/env.yml b/configs/s41467_025_58356_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7186c61faa482c6b65b42b8df1bc103f044fa320
--- /dev/null
+++ b/configs/s41467_025_58356_7_test/env.yml
@@ -0,0 +1,38 @@
+name: s41467_025_58356_7_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.10.5
+  - ld_impl_linux-64=2.44
+  - libffi=3.5.2
+  - libgcc=15.2.0
+  - libgcc-ng=15.2.0
+  - libgomp=15.2.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.51.0
+  - libstdcxx=15.2.0
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.6.0
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - zstd=1.5.7
+  - pip:
+    - numpy==1.24.4
+    - scipy==1.10.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58356_7_test
diff --git a/configs/s41467_025_58356_7_test/explicit.txt b/configs/s41467_025_58356_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0def4cef8bb7c59c3e7becdcd5d90d7370f54a2
--- /dev/null
+++ b/configs/s41467_025_58356_7_test/explicit.txt
@@ -0,0 +1,33 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.0-h0c1763c_0.conda#a3205ecbffb255ca27e0540c8494a2ee
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
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diff --git a/configs/s41467_025_58356_7_test/meta.json b/configs/s41467_025_58356_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..fee9191eb066525ba8ab20d3f848c0b72311ff36
--- /dev/null
+++ b/configs/s41467_025_58356_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58356_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58356_7_test",
+  "exported_at": "2026-05-17T04:06:31Z"
+}
diff --git a/configs/s41467_025_58356_7_test/pip-clean.txt b/configs/s41467_025_58356_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_025_58356_7_test/pip-clean.txt
@@ -0,0 +1,444 @@
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diff --git a/configs/s41467_025_58356_7_test/pip-freeze.txt b/configs/s41467_025_58356_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_025_58356_7_test/pip-freeze.txt
@@ -0,0 +1,444 @@
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+get-annotations==0.1.2
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+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
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+gpytorch==1.10
+gradio_client==0.16.0
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+gunicorn==23.0.0
+h11==0.14.0
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+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
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+itsdangerous==2.0.1
+jax==0.4.13
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+jaxtyping==0.2.19
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+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
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+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
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+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
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+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
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+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58439_5_test/editable.txt b/configs/s41467_025_58439_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_58439_5_test/env.yml b/configs/s41467_025_58439_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a9112f26ddd153881889d059e4b65c4baa340cbf
--- /dev/null
+++ b/configs/s41467_025_58439_5_test/env.yml
@@ -0,0 +1,50 @@
+name: s41467_025_58439_5_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - joblib==1.4.2
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - threadpoolctl==3.5.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58439_5_test
diff --git a/configs/s41467_025_58439_5_test/explicit.txt b/configs/s41467_025_58439_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_58439_5_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_58439_5_test/meta.json b/configs/s41467_025_58439_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..1db3426e24a3893e360a8a80b861f5287a13c240
--- /dev/null
+++ b/configs/s41467_025_58439_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58439_5_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58439_5_test",
+  "exported_at": "2026-05-17T04:06:34Z"
+}
diff --git a/configs/s41467_025_58439_5_test/pip-clean.txt b/configs/s41467_025_58439_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d0743492a8122236f77d0d6d25e166f78692433
--- /dev/null
+++ b/configs/s41467_025_58439_5_test/pip-clean.txt
@@ -0,0 +1,452 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
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+watchfiles==0.21.0
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+word2number==1.1
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+xxhash==2.0.2
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+youtube-search==2.1.2
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+zope.event==4.5.0
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diff --git a/configs/s41467_025_58439_5_test/pip-freeze.txt b/configs/s41467_025_58439_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d0743492a8122236f77d0d6d25e166f78692433
--- /dev/null
+++ b/configs/s41467_025_58439_5_test/pip-freeze.txt
@@ -0,0 +1,452 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
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+autoray==0.6.12
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+better-abc==0.0.3
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+chaospy==3.3.9
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+coverage==7.6.1
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+dataclasses==0.6
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+Deprecated==1.2.14
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58620_w_test/editable.txt b/configs/s41467_025_58620_w_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_58620_w_test/env.yml b/configs/s41467_025_58620_w_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9d78023d98b2f6f720f7125860ff591f47cd88e3
--- /dev/null
+++ b/configs/s41467_025_58620_w_test/env.yml
@@ -0,0 +1,41 @@
+name: s41467_025_58620_w_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - joblib==1.4.2
+    - numpy==1.24.4
+    - packaging==25.0
+    - pandas==2.0.3
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58620_w_test
diff --git a/configs/s41467_025_58620_w_test/explicit.txt b/configs/s41467_025_58620_w_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_58620_w_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_58620_w_test/meta.json b/configs/s41467_025_58620_w_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7f520899279b9afe582fde1d77b26281bec7d087
--- /dev/null
+++ b/configs/s41467_025_58620_w_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58620_w_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58620_w_test",
+  "exported_at": "2026-05-17T04:06:37Z"
+}
diff --git a/configs/s41467_025_58620_w_test/pip-clean.txt b/configs/s41467_025_58620_w_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_025_58620_w_test/pip-clean.txt
@@ -0,0 +1,444 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tzdata==2024.1
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+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
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+wandb==0.22.0
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+weasel==0.3.4
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+Werkzeug==2.0.2
+word2number==1.1
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+xxhash==2.0.2
+Yapsy==1.12.2
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+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58620_w_test/pip-freeze.txt b/configs/s41467_025_58620_w_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_025_58620_w_test/pip-freeze.txt
@@ -0,0 +1,444 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+alabaster==0.7.12
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+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
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+autoray==0.6.12
+awscli==1.32.93
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+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
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+chaospy==3.3.9
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+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58866_4_test/editable.txt b/configs/s41467_025_58866_4_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_58866_4_test/env.yml b/configs/s41467_025_58866_4_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b6497cadbe185cecd2c8b9b40495c56efb2904a3
--- /dev/null
+++ b/configs/s41467_025_58866_4_test/env.yml
@@ -0,0 +1,46 @@
+name: s41467_025_58866_4_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58866_4_test
diff --git a/configs/s41467_025_58866_4_test/explicit.txt b/configs/s41467_025_58866_4_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_58866_4_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_58866_4_test/meta.json b/configs/s41467_025_58866_4_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..cd256c10d9608e28f6267d78ab63ba6a51de5d71
--- /dev/null
+++ b/configs/s41467_025_58866_4_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58866_4_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58866_4_test",
+  "exported_at": "2026-05-17T04:06:41Z"
+}
diff --git a/configs/s41467_025_58866_4_test/pip-clean.txt b/configs/s41467_025_58866_4_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_58866_4_test/pip-clean.txt
@@ -0,0 +1,448 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
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+msgpack-numpy==0.4.3.2
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+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
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+overrides==7.7.0
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+pathlib==1.0.1
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+pikepdf==8.4.1
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+seaborn==0.13.2
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+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
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+snowballstemmer==2.2.0
+sobol-seq==0.2.0
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+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_58866_4_test/pip-freeze.txt b/configs/s41467_025_58866_4_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_58866_4_test/pip-freeze.txt
@@ -0,0 +1,448 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_59192_5_test/editable.txt b/configs/s41467_025_59192_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_59192_5_test/env.yml b/configs/s41467_025_59192_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..773195d259434b99e9ec15d0e0acb84312c73667
--- /dev/null
+++ b/configs/s41467_025_59192_5_test/env.yml
@@ -0,0 +1,39 @@
+name: s41467_025_59192_5_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - numpy==1.24.4
+    - opencv-python==4.13.0.92
+    - packaging==25.0
+    - six==1.17.0
+    - widget-state==0.0.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_59192_5_test
diff --git a/configs/s41467_025_59192_5_test/explicit.txt b/configs/s41467_025_59192_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_59192_5_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
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diff --git a/configs/s41467_025_59192_5_test/meta.json b/configs/s41467_025_59192_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..dd9c08afdc218517e85a3f5ecc2f802d2be68533
--- /dev/null
+++ b/configs/s41467_025_59192_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_59192_5_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_59192_5_test",
+  "exported_at": "2026-05-17T04:06:41Z"
+}
diff --git a/configs/s41467_025_59192_5_test/pip-clean.txt b/configs/s41467_025_59192_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a16befa5c66c98af7802616249c03b153005249d
--- /dev/null
+++ b/configs/s41467_025_59192_5_test/pip-clean.txt
@@ -0,0 +1,444 @@
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diff --git a/configs/s41467_025_59192_5_test/pip-freeze.txt b/configs/s41467_025_59192_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6487a390bb7b1a432fefb2d379f3513aceda799c
--- /dev/null
+++ b/configs/s41467_025_59192_5_test/pip-freeze.txt
@@ -0,0 +1,445 @@
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+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
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+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+opencv-python==4.13.0.92
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
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+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
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+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+widget_state @ file:///tmp/widget_state_shim
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_59232_0_test/editable.txt b/configs/s41467_025_59232_0_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_59232_0_test/env.yml b/configs/s41467_025_59232_0_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c661d2ab3dfa1d8a0ee51626d12d3916de76415e
--- /dev/null
+++ b/configs/s41467_025_59232_0_test/env.yml
@@ -0,0 +1,44 @@
+name: s41467_025_59232_0_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - ase==3.23.0
+    - fonttools==4.57.0
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.24.4
+    - packaging==25.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_59232_0_test
diff --git a/configs/s41467_025_59232_0_test/explicit.txt b/configs/s41467_025_59232_0_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_59232_0_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_59232_0_test/meta.json b/configs/s41467_025_59232_0_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..271d05cebca823a12ca773925a8445953c71a13e
--- /dev/null
+++ b/configs/s41467_025_59232_0_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_59232_0_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_59232_0_test",
+  "exported_at": "2026-05-17T04:06:45Z"
+}
diff --git a/configs/s41467_025_59232_0_test/pip-clean.txt b/configs/s41467_025_59232_0_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d00672c777f348b72ac8a94d636e718870afedc
--- /dev/null
+++ b/configs/s41467_025_59232_0_test/pip-clean.txt
@@ -0,0 +1,449 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+ase==3.23.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+typing-inspect==0.9.0
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+typing_extensions==4.13.2
+tzdata==2024.1
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+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_59232_0_test/pip-freeze.txt b/configs/s41467_025_59232_0_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d00672c777f348b72ac8a94d636e718870afedc
--- /dev/null
+++ b/configs/s41467_025_59232_0_test/pip-freeze.txt
@@ -0,0 +1,449 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+ase==3.23.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
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+chaospy==3.3.9
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+cloudpathlib==0.16.0
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+coloredlogs==15.0.1
+confection==0.1.4
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+conllu==0.11
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+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
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+dill==0.3.8
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+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
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+equinox==0.10.4
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+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
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+fancy-einsum==0.0.3
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+fastuuid==0.13.5
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+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_59839_3_test/editable.txt b/configs/s41467_025_59839_3_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_59839_3_test/env.yml b/configs/s41467_025_59839_3_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..570c8d31016335aeb55139e675b2d26b7f3a94d1
--- /dev/null
+++ b/configs/s41467_025_59839_3_test/env.yml
@@ -0,0 +1,41 @@
+name: s41467_025_59839_3_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - networkx==3.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - scikit-image==0.21.0
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_59839_3_test
diff --git a/configs/s41467_025_59839_3_test/explicit.txt b/configs/s41467_025_59839_3_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_59839_3_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_59839_3_test/meta.json b/configs/s41467_025_59839_3_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..46443ff41d36da421b51d8b3c6cec201ef3e5515
--- /dev/null
+++ b/configs/s41467_025_59839_3_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_59839_3_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_59839_3_test",
+  "exported_at": "2026-05-17T04:06:48Z"
+}
diff --git a/configs/s41467_025_59839_3_test/pip-clean.txt b/configs/s41467_025_59839_3_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7ed6d2a154c2775adfcfe74aa1fe489a15469c3
--- /dev/null
+++ b/configs/s41467_025_59839_3_test/pip-clean.txt
@@ -0,0 +1,447 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
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+tzdata==2024.1
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+vllm==0.2.7
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+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
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+word2number==1.1
+xlrd==2.0.1
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+xxhash==2.0.2
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+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_59839_3_test/pip-freeze.txt b/configs/s41467_025_59839_3_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7ed6d2a154c2775adfcfe74aa1fe489a15469c3
--- /dev/null
+++ b/configs/s41467_025_59839_3_test/pip-freeze.txt
@@ -0,0 +1,447 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
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+alabaster==0.7.12
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+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
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+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
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+chaospy==3.3.9
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+confection==0.1.4
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+conllu==0.11
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+cryptography==42.0.5
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+cymem==2.0.8
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+Deprecated==1.2.14
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+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_60789_z_test/editable.txt b/configs/s41467_025_60789_z_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_60789_z_test/env.yml b/configs/s41467_025_60789_z_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f81a9dc8f54b1bf3ec804ac93d078391ba0ec1b0
--- /dev/null
+++ b/configs/s41467_025_60789_z_test/env.yml
@@ -0,0 +1,40 @@
+name: s41467_025_60789_z_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.11.12
+  - ld_impl_linux-64=2.45
+  - libffi=3.5.2
+  - libgcc=15.2.0
+  - libgcc-ng=15.2.0
+  - libgomp=15.2.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.51.0
+  - libstdcxx=15.2.0
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.6.0
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - zstd=1.5.7
+  - pip:
+    - numpy==1.24.4
+    - pandas==2.0.3
+    - python-dateutil==2.9.0.post0
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_60789_z_test
diff --git a/configs/s41467_025_60789_z_test/explicit.txt b/configs/s41467_025_60789_z_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7867afd6690437631ec3bec7dfc9b816817b7bc7
--- /dev/null
+++ b/configs/s41467_025_60789_z_test/explicit.txt
@@ -0,0 +1,33 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda#f0991f0f84902f6b6009b4d2350a83aa
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.0-h0c1763c_0.conda#a3205ecbffb255ca27e0540c8494a2ee
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda#86bc20552bf46075e3d92b67f089172d
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45-h1aa0949_0.conda#1450224b3e7d17dfeb985364b77a4d47
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_60789_z_test/meta.json b/configs/s41467_025_60789_z_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6532adcb4a55198ee9ed269d7e4d240fb94d3985
--- /dev/null
+++ b/configs/s41467_025_60789_z_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_60789_z_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_60789_z_test",
+  "exported_at": "2026-05-17T04:06:56Z"
+}
diff --git a/configs/s41467_025_60789_z_test/pip-clean.txt b/configs/s41467_025_60789_z_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_025_60789_z_test/pip-clean.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
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+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
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+python-iso639==2024.4.27
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+ray==2.10.0
+rdkit==2024.3.5
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+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_60789_z_test/pip-freeze.txt b/configs/s41467_025_60789_z_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_025_60789_z_test/pip-freeze.txt
@@ -0,0 +1,443 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_60989_7_test/editable.txt b/configs/s41467_025_60989_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_60989_7_test/env.yml b/configs/s41467_025_60989_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..706529b5066eeb2a90c633588480e1ee22e3cc4a
--- /dev/null
+++ b/configs/s41467_025_60989_7_test/env.yml
@@ -0,0 +1,46 @@
+name: s41467_025_60989_7_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_60989_7_test
diff --git a/configs/s41467_025_60989_7_test/explicit.txt b/configs/s41467_025_60989_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_60989_7_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_60989_7_test/meta.json b/configs/s41467_025_60989_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..425b75f6af99ec674222e0c59c2d1c1a920b0289
--- /dev/null
+++ b/configs/s41467_025_60989_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_60989_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_60989_7_test",
+  "exported_at": "2026-05-17T04:07:04Z"
+}
diff --git a/configs/s41467_025_60989_7_test/pip-clean.txt b/configs/s41467_025_60989_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_60989_7_test/pip-clean.txt
@@ -0,0 +1,448 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
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+aioprometheus==23.12.0
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+annotated-types==0.6.0
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+APScheduler==3.11.2
+arxiv==2.1.0
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+attrs==25.3.0
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+autoray==0.6.12
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+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
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+beartype==0.14.1
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+chaospy==3.3.9
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+confection==0.1.4
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+cryptography==42.0.5
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+Deprecated==1.2.14
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+dnspython==2.6.1
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+pikepdf==8.4.1
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+seaborn==0.13.2
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+session_info==1.0.1
+sgmllib3k==1.0.0
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
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diff --git a/configs/s41467_025_60989_7_test/pip-freeze.txt b/configs/s41467_025_60989_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_60989_7_test/pip-freeze.txt
@@ -0,0 +1,448 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
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+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
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+attrs==25.3.0
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+awscli==1.32.93
+azure-core==1.33.0
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+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_61087_4_test/editable.txt b/configs/s41467_025_61087_4_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_61087_4_test/env.yml b/configs/s41467_025_61087_4_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..769537eedf34e98938237a184541cd959cedbee6
--- /dev/null
+++ b/configs/s41467_025_61087_4_test/env.yml
@@ -0,0 +1,44 @@
+name: s41467_025_61087_4_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.16.1
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_61087_4_test
diff --git a/configs/s41467_025_61087_4_test/explicit.txt b/configs/s41467_025_61087_4_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_61087_4_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_61087_4_test/meta.json b/configs/s41467_025_61087_4_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d97c7d62b1fba46ee76780e1eb213dde26e7771a
--- /dev/null
+++ b/configs/s41467_025_61087_4_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_61087_4_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_61087_4_test",
+  "exported_at": "2026-05-17T04:07:05Z"
+}
diff --git a/configs/s41467_025_61087_4_test/pip-clean.txt b/configs/s41467_025_61087_4_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_61087_4_test/pip-clean.txt
@@ -0,0 +1,448 @@
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diff --git a/configs/s41467_025_61087_4_test/pip-freeze.txt b/configs/s41467_025_61087_4_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_61087_4_test/pip-freeze.txt
@@ -0,0 +1,448 @@
+absl-py==2.3.1
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+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mpmath==1.3.0
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/configs/s41467_025_62171_5_test/editable.txt b/configs/s41467_025_62171_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_62171_5_test/env.yml b/configs/s41467_025_62171_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9285f08c2f6339ca19e63b33cc6f83c72e524714
--- /dev/null
+++ b/configs/s41467_025_62171_5_test/env.yml
@@ -0,0 +1,82 @@
+name: s41467_025_62171_5_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - absl-py==2.3.1
+    - alembic==1.14.1
+    - certifi==2025.11.12
+    - charset-normalizer==3.4.4
+    - colorlog==6.10.1
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - flatbuffers==25.9.23
+    - fonttools==4.57.0
+    - gast==0.4.0
+    - google-auth==2.43.0
+    - google-auth-oauthlib==1.0.0
+    - grpcio==1.70.0
+    - h5py==3.11.0
+    - idna==3.11
+    - importlib-resources==6.4.5
+    - joblib==1.4.2
+    - keras==2.13.1
+    - kiwisolver==1.4.7
+    - libclang==18.1.1
+    - mako==1.3.10
+    - markupsafe==2.1.5
+    - matplotlib==3.7.5
+    - numpy==1.24.3
+    - optuna==4.5.0
+    - packaging==25.0
+    - pandas==2.0.3
+    - pillow==10.4.0
+    - protobuf==4.25.8
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - tensorboard==2.13.0
+    - tensorboard-data-server==0.7.2
+    - tensorflow==2.13.1
+    - tensorflow-estimator==2.13.0
+    - tensorflow-io-gcs-filesystem==0.34.0
+    - termcolor==2.4.0
+    - threadpoolctl==3.5.0
+    - typing-extensions==4.5.0
+    - urllib3==2.2.3
+    - wrapt==2.0.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_62171_5_test
diff --git a/configs/s41467_025_62171_5_test/explicit.txt b/configs/s41467_025_62171_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_62171_5_test/explicit.txt
@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_62171_5_test/meta.json b/configs/s41467_025_62171_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9e515b18535f0076335f1f0c3087cf0e7bc971cf
--- /dev/null
+++ b/configs/s41467_025_62171_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_62171_5_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_62171_5_test",
+  "exported_at": "2026-05-17T04:07:14Z"
+}
diff --git a/configs/s41467_025_62171_5_test/pip-clean.txt b/configs/s41467_025_62171_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2666c02c42c78951c6a358dda7cffbfb915f21c3
--- /dev/null
+++ b/configs/s41467_025_62171_5_test/pip-clean.txt
@@ -0,0 +1,477 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+alembic==1.14.1
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2025.11.12
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+colorlog==6.10.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+contourpy==1.1.1
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler==0.12.1
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
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+youtube-search==2.1.2
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+zope.event==4.5.0
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diff --git a/configs/s41467_025_62171_5_test/pip-freeze.txt b/configs/s41467_025_62171_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2666c02c42c78951c6a358dda7cffbfb915f21c3
--- /dev/null
+++ b/configs/s41467_025_62171_5_test/pip-freeze.txt
@@ -0,0 +1,477 @@
+absl-py==2.3.1
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+aiofiles==23.2.1
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+arxiv==2.1.0
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow==10.4.0
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+protobuf==4.25.8
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyasn1==0.6.1
+pyasn1_modules==0.4.2
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn==1.3.2
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard==2.13.0
+tensorboard-data-server==0.7.2
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+tensorflow==2.13.1
+tensorflow-estimator==2.13.0
+tensorflow-io-gcs-filesystem==0.34.0
+termcolor==2.4.0
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+wrapt==2.0.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0
diff --git a/docker_build/Dockerfile.conda-env b/docker_build/Dockerfile.conda-env
new file mode 100644
index 0000000000000000000000000000000000000000..08505e4e05a6fff64304814e306dbc882c33f110
--- /dev/null
+++ b/docker_build/Dockerfile.conda-env
@@ -0,0 +1,50 @@
+# Dockerfile for "conda-pack-style" sample images.
+# Image only contains the activated conda env + system toolchain.
+# Sample code + pipeline are mounted at runtime via -v.
+#
+# Build args:
+#   PACK_FILE     e.g. 001_rm_bench_test.tar.gz   (file in build context)
+#   ENV_DIR_NAME  e.g. py-001                      (folder under /opt/conda/envs)
+#
+# Build (on remote, from /home/dockerfiles/):
+#   docker buildx build \
+#     --build-arg PACK_FILE=001_rm_bench_test.tar.gz \
+#     --build-arg ENV_DIR_NAME=py-001 \
+#     -t mmsci-py-001 -f Dockerfile.conda-env .
+#
+# Run:
+#   docker run --rm -it --gpus all \
+#     -v /home/code:/workspace/code:ro \
+#     -v /home/code/data:/workspace/data:ro \
+#     mmsci-py-001 bash -lc 'python -V'
+
+FROM nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu22.04
+
+ARG PACK_FILE
+ARG ENV_DIR_NAME
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    LANG=C.UTF-8 LC_ALL=C.UTF-8 \
+    TZ=Etc/UTC
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        ca-certificates curl wget git build-essential gcc g++ make \
+        libgl1 libglib2.0-0 libsm6 libxext6 libxrender1 libgomp1 \
+        libstdc++6 procps less vim-tiny \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN mkdir -p /opt/conda/envs/${ENV_DIR_NAME}
+
+COPY ${PACK_FILE} /tmp/env.tar.gz
+RUN tar -xzf /tmp/env.tar.gz -C /opt/conda/envs/${ENV_DIR_NAME} \
+ && rm /tmp/env.tar.gz \
+ && /opt/conda/envs/${ENV_DIR_NAME}/bin/conda-unpack \
+ && echo "env unpacked: ${ENV_DIR_NAME}"
+
+WORKDIR /workspace
+
+ENV PATH=/opt/conda/envs/${ENV_DIR_NAME}/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ENV CONDA_PREFIX=/opt/conda/envs/${ENV_DIR_NAME}
+ENV LD_LIBRARY_PATH=/opt/conda/envs/${ENV_DIR_NAME}/lib
+
+CMD ["bash", "-lc", "python -V && which python && echo READY: $CONDA_PREFIX"]
diff --git a/docker_build/remote/README.md b/docker_build/remote/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..6b849330821a0e888d8fc94f6afabcb76a93aef7
--- /dev/null
+++ b/docker_build/remote/README.md
@@ -0,0 +1,113 @@
+# MMSciCode env reconstruction on the domestic server
+
+This bundle reconstructs the 204 MMSciCode conda envs on a domestic Chinese
+server using mirror sources (no need to download the 165 GB tarball repo).
+It then packs each env into a tarball and builds a Docker image per env.
+
+## Inputs (from HF: `MMSciCode/mmsci-envs-tmp`)
+
+```
+configs/
+  <env>/
+    env.yml           # conda env create -f
+    explicit.txt      # conda list --explicit --md5 (URL-pinned fallback)
+    pip-freeze.txt    # raw pip freeze from local env
+    pip-clean.txt     # pip-freeze with conda-built file:// stripped
+    editable.txt      # tab-separated: <egg-link name> \t <original source path>
+    meta.json         # python ver, has_cuda hint, editable_count
+editable_bundle.tar.gz  # only present if any env had editable installs
+```
+
+## Domestic-server prerequisites
+
+- conda (or miniconda) installed; conda >= 22.x
+- `mamba` from the base env: `conda install -n base -c conda-forge mamba conda-pack`
+- Docker (with `nvidia-docker` runtime if envs need GPU)
+- ~200 GB free disk for staging tarballs + ~300 GB for Docker images
+
+## Step 1 — configure mirrors
+
+```bash
+cp configs_repo/remote/condarc.template ~/.condarc
+mkdir -p ~/.config/pip
+cp configs_repo/remote/pip.conf.template ~/.config/pip/pip.conf
+```
+
+## Step 2 — fetch the artifacts
+
+```bash
+# example using huggingface_hub with HF_ENDPOINT=https://hf-mirror.com if needed
+huggingface-cli download MMSciCode/mmsci-envs-tmp \
+    --repo-type dataset \
+    --local-dir /home/mmsci/repo \
+    --include 'configs/**' 'editable_bundle.tar.gz'
+
+cd /home/mmsci/repo
+[ -f editable_bundle.tar.gz ] && tar -xzf editable_bundle.tar.gz   # -> editable_sources/
+```
+
+## Step 3 — build all envs (parallel) and pack each as a tarball
+
+```bash
+CONFIGS_DIR=/home/mmsci/repo/configs \
+OUT_DIR=/home/mmsci/conda_packs \
+EDITABLE_SRC=/home/mmsci/repo/editable_sources \
+MAMBA_BIN=/opt/conda/bin/mamba \
+CONDA_PACK=/opt/conda/bin/conda-pack \
+JOBS=4 \
+bash /home/mmsci/configs_repo/remote/build_envs_remote.sh
+```
+
+Outputs:
+- `$OUT_DIR/<env>.tar.gz` — per-env conda-pack tarball
+- `$OUT_DIR/build.state.tsv` — per-env status (done/skip/fail)
+- `$OUT_DIR/build.failed.txt` — failed envs (re-run script to retry; idempotent)
+- `$OUT_DIR/_logs/<env>.log` — per-env mamba + pack log
+
+Expect 5–15% of envs to fail on first pass (mirror gaps, conda-pack errors,
+editable misses). Inspect the failed logs and either:
+- Adjust env.yml (drop the offending pin, add a missing channel), or
+- Fall back to the original tarball from `MMSciCode/mmsci-envs-tmp` root:
+  `huggingface-cli download MMSciCode/mmsci-envs-tmp --include '<env>.tar.gz' --local-dir $OUT_DIR`
+
+## Step 4 — build Docker images
+
+Get the Dockerfile (from the source repo or the HF `docker_build/` upload):
+
+```bash
+PACKS_DIR=/home/mmsci/conda_packs \
+DOCKERFILE=/home/mmsci/configs_repo/Dockerfile.conda-env \
+IMAGE_PREFIX=mmsci-py \
+JOBS=2 \
+bash /home/mmsci/configs_repo/remote/build_docker_images.sh
+```
+
+Each env -> `mmsci-py-<sanitized-name>:latest`. The Dockerfile is the
+unmodified `Dockerfile.conda-env` — it only does `COPY tarball; tar -xzf;
+conda-unpack`, so build time per image is whatever your disk can write
+the tarball at (~30s–2min per image).
+
+## Troubleshooting
+
+**`PackageNotFoundError` during `mamba env create`**
+The Tsinghua/Aliyun mirrors don't have every conda-forge package. Try:
+```bash
+mamba env create -n <env> -f configs/<env>/env.yml \
+    --override-channels -c conda-forge -c defaults
+```
+If still missing, the explicit URL list often works:
+```bash
+conda create -n <env> --file configs/<env>/explicit.txt
+```
+(URLs point to anaconda.org which is reachable but slow; consider setting
+`CONDA_SUBDIR=linux-64`.)
+
+**`pip install` connection errors**
+Confirm `~/.config/pip/pip.conf` is in effect: `pip config list`. Some
+git+https URLs in `pip-freeze.txt` may need a proxy; consider running the
+build under `https_proxy=...` if you have a corporate proxy.
+
+**`conda-pack` editable-packages error**
+build_envs_remote.sh passes `--ignore-editable-packages` so this should not
+happen. If it does, the env has an editable install that wasn't recorded in
+`editable.txt` — re-export from the source machine.
diff --git a/docker_build/remote/build_docker_images.sh b/docker_build/remote/build_docker_images.sh
new file mode 100644
index 0000000000000000000000000000000000000000..6913397ebe1daa9f24051056ec15d1444004c0c9
--- /dev/null
+++ b/docker_build/remote/build_docker_images.sh
@@ -0,0 +1,88 @@
+#!/usr/bin/env bash
+# After build_envs_remote.sh produces tarballs, build one Docker image per env
+# using the existing Dockerfile.conda-env (unpack-style).
+#
+# Required env vars:
+#   PACKS_DIR     directory containing <env>.tar.gz (output of build_envs_remote.sh)
+#   DOCKERFILE    path to Dockerfile.conda-env
+#   IMAGE_PREFIX  e.g. mmsci-py   (image tag: <prefix>-<env-without-_test>)
+#   JOBS          parallel docker builds (default 2)
+#   LIST          optional list of envs; default = all tarballs in PACKS_DIR
+#
+# Each env -> image  mmsci-py-<sanitized-env>:latest
+
+set -uo pipefail
+
+: "${PACKS_DIR:?PACKS_DIR required}"
+: "${DOCKERFILE:?DOCKERFILE required}"
+IMAGE_PREFIX="${IMAGE_PREFIX:-mmsci-py}"
+JOBS="${JOBS:-2}"
+LIST_FILE="${LIST:-}"
+
+LOG_DIR="$PACKS_DIR/_docker_logs"
+STATE="$PACKS_DIR/docker_build.state.tsv"
+FAILED="$PACKS_DIR/docker_build.failed.txt"
+
+mkdir -p "$LOG_DIR"
+[[ -s "$STATE" ]] || printf "env\timage_tag\tstatus\tseconds\n" > "$STATE"
+
+if [[ -z "$LIST_FILE" ]]; then
+    LIST_FILE="$PACKS_DIR/_docker_envs.txt"
+    ls "$PACKS_DIR"/*.tar.gz 2>/dev/null | xargs -n1 basename | sed 's/.tar.gz$//' | sort > "$LIST_FILE"
+fi
+total=$(wc -l < "$LIST_FILE")
+echo "[$(date +%T)] building $total docker images, JOBS=$JOBS"
+
+export PACKS_DIR DOCKERFILE IMAGE_PREFIX LOG_DIR STATE FAILED
+
+# tag = lowercase, _ -> -, strip trailing -test
+tag_for() {
+    local env="$1"
+    local t="${env,,}"
+    t="${t//_/-}"
+    t="${t%-test}"
+    echo "${IMAGE_PREFIX}-${t}"
+}
+export -f tag_for
+
+build_one() {
+    local env="$1"
+    local tag=$(tag_for "$env")
+    local pack="$env.tar.gz"
+    local log="$LOG_DIR/$env.log"
+    : > "$log"
+
+    if [[ ! -s "$PACKS_DIR/$pack" ]]; then
+        echo "[missing-pack] $env"
+        printf "%s\t%s\tfail_missing\t0\n" "$env" "$tag" >> "$STATE"
+        echo "$env  missing_pack" >> "$FAILED"
+        return 1
+    fi
+
+    local t0=$(date +%s)
+    echo "[build] $env -> $tag" | tee -a "$log"
+
+    # Run from PACKS_DIR so COPY ${PACK_FILE} resolves
+    if ! docker build \
+            --build-arg PACK_FILE="$pack" \
+            --build-arg ENV_DIR_NAME="${tag#${IMAGE_PREFIX}-}" \
+            -t "$tag:latest" \
+            -f "$DOCKERFILE" \
+            "$PACKS_DIR" >>"$log" 2>&1; then
+        local dt=$(( $(date +%s) - t0 ))
+        echo "[FAIL] $env after ${dt}s"
+        printf "%s\t%s\tfail_build\t%s\n" "$env" "$tag" "$dt" >> "$STATE"
+        echo "$env  build" >> "$FAILED"
+        return 1
+    fi
+
+    local dt=$(( $(date +%s) - t0 ))
+    echo "[done] $tag in ${dt}s"
+    printf "%s\t%s\tdone\t%s\n" "$env" "$tag" "$dt" >> "$STATE"
+}
+export -f build_one
+
+cat "$LIST_FILE" | xargs -n1 -P "$JOBS" -I{} bash -c 'build_one "$@"' _ {}
+
+echo "[$(date +%T)] all done"
+awk -F'\t' 'NR>1{c[$3]++} END{for(k in c)printf "  %-12s %4d\n",k,c[k]}' "$STATE"
diff --git a/docker_build/remote/build_envs_remote.sh b/docker_build/remote/build_envs_remote.sh
new file mode 100644
index 0000000000000000000000000000000000000000..83d0b6a3e6f052f040a0f0dc7fa9c1928e0449e8
--- /dev/null
+++ b/docker_build/remote/build_envs_remote.sh
@@ -0,0 +1,125 @@
+#!/usr/bin/env bash
+# Domestic-server pipeline:
+#   1. Read configs/<env>/env.yml
+#   2. mamba env create -n <env> -f env.yml (uses ~/.condarc mirrors)
+#   3. If editable.txt non-empty: pip install -e <path> for each entry (source must be present)
+#   4. conda-pack the new env into out/<env>.tar.gz (matches local pipeline)
+#
+# Idempotent: skips envs whose tarball already exists. Failure-tolerant.
+# Parallel via xargs -P. Per-env status in state.tsv, failures in failed.txt.
+#
+# Required env vars:
+#   CONFIGS_DIR    e.g. /home/user/mmsci/configs
+#   OUT_DIR        e.g. /home/user/mmsci/conda_packs
+#   EDITABLE_SRC   e.g. /home/user/mmsci/editable_sources   (root containing editable source trees; optional)
+#   MAMBA_BIN      e.g. /opt/conda/bin/mamba                (default: 'mamba' on PATH)
+#   CONDA_PACK     e.g. /opt/conda/bin/conda-pack           (default: 'conda-pack' on PATH)
+#   JOBS           parallel envs (default 4)
+#   LIST           optional file of env names; default = all dirs under CONFIGS_DIR
+
+set -uo pipefail
+
+: "${CONFIGS_DIR:?CONFIGS_DIR required}"
+: "${OUT_DIR:?OUT_DIR required}"
+EDITABLE_SRC="${EDITABLE_SRC:-}"
+MAMBA_BIN="${MAMBA_BIN:-mamba}"
+CONDA_PACK="${CONDA_PACK:-conda-pack}"
+JOBS="${JOBS:-4}"
+LIST_FILE="${LIST:-}"
+
+LOG_DIR="$OUT_DIR/_logs"
+STATE="$OUT_DIR/build.state.tsv"
+FAILED="$OUT_DIR/build.failed.txt"
+
+mkdir -p "$OUT_DIR" "$LOG_DIR"
+[[ -s "$STATE" ]] || printf "env\tstatus\tphase\tseconds\tsize_bytes\n" > "$STATE"
+
+if [[ -z "$LIST_FILE" ]]; then
+    LIST_FILE="$OUT_DIR/_envs.txt"
+    find "$CONFIGS_DIR" -mindepth 1 -maxdepth 1 -type d -printf '%f\n' | sort > "$LIST_FILE"
+fi
+total=$(wc -l < "$LIST_FILE")
+echo "[$(date +%T)] building $total envs, JOBS=$JOBS"
+echo "  configs: $CONFIGS_DIR"
+echo "  out:     $OUT_DIR"
+echo "  mamba:   $MAMBA_BIN"
+echo "  pack:    $CONDA_PACK"
+echo "  editable_src: ${EDITABLE_SRC:-(none)}"
+
+export CONFIGS_DIR OUT_DIR EDITABLE_SRC MAMBA_BIN CONDA_PACK LOG_DIR STATE FAILED
+
+build_one() {
+    local env="$1"
+    local conf="$CONFIGS_DIR/$env"
+    local yml="$conf/env.yml"
+    local edit="$conf/editable.txt"
+    local meta="$conf/meta.json"
+    local dst="$OUT_DIR/$env.tar.gz"
+    local log="$LOG_DIR/$env.log"
+    : > "$log"
+
+    if [[ -s "$dst" ]]; then
+        echo "[skip] $env already packed"
+        printf "%s\tskip\t-\t0\t%s\n" "$env" "$(stat -c %s "$dst")" >> "$STATE"
+        return 0
+    fi
+    if [[ ! -s "$yml" ]]; then
+        echo "[missing-yml] $env"
+        printf "%s\tfail\tmissing_yml\t0\t0\n" "$env" >> "$STATE"
+        echo "$env  missing_yml" >> "$FAILED"
+        return 1
+    fi
+
+    local t0=$(date +%s)
+    echo "[create] $env" | tee -a "$log"
+    if ! "$MAMBA_BIN" env create -n "$env" -f "$yml" -y >>"$log" 2>&1; then
+        local dt=$(( $(date +%s) - t0 ))
+        echo "[FAIL create] $env after ${dt}s (see $log)"
+        printf "%s\tfail\tcreate\t%s\t0\n" "$env" "$dt" >> "$STATE"
+        echo "$env  create" >> "$FAILED"
+        return 1
+    fi
+
+    # editable installs (pip install -e <path>)
+    if [[ -s "$edit" && -n "$EDITABLE_SRC" ]]; then
+        while IFS=$'\t' read -r egg_name src_path; do
+            [[ -z "$src_path" ]] && continue
+            # remap original path -> EDITABLE_SRC/<env>/<basename>
+            local remap="$EDITABLE_SRC/$env/$(basename "$src_path")"
+            if [[ ! -d "$remap" ]]; then
+                echo "[editable-missing] $env: $remap" | tee -a "$log"
+                continue
+            fi
+            echo "[editable] $env: pip install -e $remap" | tee -a "$log"
+            if ! "$MAMBA_BIN" run -n "$env" pip install -e "$remap" >>"$log" 2>&1; then
+                echo "[FAIL editable] $env: $remap" | tee -a "$log"
+            fi
+        done < "$edit"
+    fi
+
+    # pack
+    echo "[pack] $env" | tee -a "$log"
+    if ! "$CONDA_PACK" -n "$env" -o "$dst" --compress-level=4 -j 8 \
+            --ignore-missing-files --ignore-editable-packages --force >>"$log" 2>&1; then
+        local dt=$(( $(date +%s) - t0 ))
+        echo "[FAIL pack] $env after ${dt}s"
+        printf "%s\tfail\tpack\t%s\t0\n" "$env" "$dt" >> "$STATE"
+        echo "$env  pack" >> "$FAILED"
+        rm -f "$dst"
+        return 1
+    fi
+
+    local dt=$(( $(date +%s) - t0 ))
+    local sz=$(stat -c %s "$dst")
+    echo "[done] $env -> $(numfmt --to=iec "$sz") in ${dt}s"
+    printf "%s\tdone\t-\t%s\t%s\n" "$env" "$dt" "$sz" >> "$STATE"
+}
+export -f build_one
+
+cat "$LIST_FILE" | xargs -n1 -P "$JOBS" -I{} bash -c 'build_one "$@"' _ {}
+
+echo "[$(date +%T)] all done"
+echo "summary:"
+awk -F'\t' 'NR>1{c[$2]++} END{for(k in c)printf "  %-8s %4d\n",k,c[k]}' "$STATE"
+echo "total tarballs:  $(ls "$OUT_DIR"/*.tar.gz 2>/dev/null | wc -l)"
+echo "total size:      $(du -shc "$OUT_DIR"/*.tar.gz 2>/dev/null | tail -1 | cut -f1)"
diff --git a/docker_build/remote/condarc.template b/docker_build/remote/condarc.template
new file mode 100644
index 0000000000000000000000000000000000000000..937356f5453214bda6419ed1f4e9ed8ba1fef680
--- /dev/null
+++ b/docker_build/remote/condarc.template
@@ -0,0 +1,27 @@
+# ~/.condarc for domestic-server builds.
+# Puts Tsinghua first (most coverage), then Aliyun fallback.
+# pip is configured separately in pip.conf.
+
+channels:
+  - defaults
+
+default_channels:
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2
+
+custom_channels:
+  conda-forge: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
+  bioconda:    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
+  pytorch:     https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
+  nvidia:      https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
+  fastai:      https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
+  rapidsai:    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
+
+show_channel_urls: true
+ssl_verify: true
+remote_connect_timeout_secs: 30
+remote_read_timeout_secs: 120
+remote_max_retries: 5
+solver: libmamba
+auto_update_conda: false
diff --git a/docker_build/remote/pip.conf.template b/docker_build/remote/pip.conf.template
new file mode 100644
index 0000000000000000000000000000000000000000..5a9cd895ac2e93e1abb7c0d114b1f8136b1f20eb
--- /dev/null
+++ b/docker_build/remote/pip.conf.template
@@ -0,0 +1,17 @@
+# ~/.config/pip/pip.conf (or ~/.pip/pip.conf) for domestic-server builds.
+# Tsinghua primary, Aliyun + Douban as extras for coverage.
+
+[global]
+index-url = https://pypi.tuna.tsinghua.edu.cn/simple
+extra-index-url =
+    https://mirrors.aliyun.com/pypi/simple
+    https://pypi.doubanio.com/simple
+timeout = 60
+retries = 5
+disable-pip-version-check = true
+
+[install]
+trusted-host =
+    pypi.tuna.tsinghua.edu.cn
+    mirrors.aliyun.com
+    pypi.doubanio.com