diff --git a/configs/001_rm_bench_test/editable.txt b/configs/001_rm_bench_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/001_rm_bench_test/env.yml b/configs/001_rm_bench_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ccad4058b7e4b84b924517e84aeda90906e7a0f8
--- /dev/null
+++ b/configs/001_rm_bench_test/env.yml
@@ -0,0 +1,111 @@
+name: 001_rm_bench_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=2026.4.22
+  - certifi=2024.2.2
+  - 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=3.6.2
+  - 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
+  - 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:
+    - attrs==25.3.0
+    - charset-normalizer==3.4.3
+    - dill==0.3.8
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - multiprocess==0.70.16
+    - pyarrow==17.0.0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - six==1.17.0
+    - tokenizers==0.20.3
+    - torch==2.4.1+cpu
+    - transformers==4.46.3
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+    - websockets==13.1
+prefix: /home/lily/yz979/anaconda3/envs/001_rm_bench_test
diff --git a/configs/001_rm_bench_test/explicit.txt b/configs/001_rm_bench_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97506ac271b2f8bc3106fd54620b3ad289c51bd4
--- /dev/null
+++ b/configs/001_rm_bench_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-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
+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
+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/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-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0
+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-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/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
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+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/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614
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+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_5.conda#8bba50c7f4679f08c861b597ad2bda6b
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+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
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+https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda#f4084e4e6577797150f9b04a4560ceb0
+https://conda.anaconda.org/conda-forge/linux-64/openblas-0.3.30-pthreads_h6ec200e_2.conda#648d8dad79db72a3afd7d30f828050d8
+https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda#11b3379b191f63139e29c0d19dee24cd
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+https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.13.2-pyhd8ed1ab_2.conda#b713b116feaf98acdba93ad4d7f90ca1
+https://repo.anaconda.com/pkgs/main/linux-64/statsmodels-0.13.5-py38h7deecbd_1.conda#beb4872f21ed4f34d70e188a97777f0f
+https://conda.anaconda.org/conda-forge/noarch/seaborn-0.13.2-hd8ed1ab_2.conda#a79d8797f62715255308d92d3a91ef2e
diff --git a/configs/001_rm_bench_test/meta.json b/configs/001_rm_bench_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..992f59216bfddaedef95676ca38351a6193d937b
--- /dev/null
+++ b/configs/001_rm_bench_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "001_rm_bench_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/001_rm_bench_test",
+  "exported_at": "2026-05-17T04:03:10Z"
+}
diff --git a/configs/001_rm_bench_test/pip-clean.txt b/configs/001_rm_bench_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3295ff9d290698cc20156874b618ca3e629cb06
--- /dev/null
+++ b/configs/001_rm_bench_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
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diff --git a/configs/001_rm_bench_test/pip-freeze.txt b/configs/001_rm_bench_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..accf9ad604781954a9621ccdd2885aaa0c1c1780
--- /dev/null
+++ b/configs/001_rm_bench_test/pip-freeze.txt
@@ -0,0 +1,457 @@
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+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
+pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
+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 @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
+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==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
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+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
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+tifffile==2023.7.10
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+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
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+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/006_map_alignment_test/editable.txt b/configs/006_map_alignment_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27151104d7c25cd05830d036cad6b8068499d99a
--- /dev/null
+++ b/configs/006_map_alignment_test/editable.txt
@@ -0,0 +1 @@
+alignmap.egg-link	/data/lily/yz979/xx/MMSciCode/tmp_agentic/mmsci_6n2wjd1z/006_MAP_Multi-Human-Value_Alignment_Palette/code
diff --git a/configs/006_map_alignment_test/env.yml b/configs/006_map_alignment_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..919e4dff5031e511677a95f5c15b1e6ce204d122
--- /dev/null
+++ b/configs/006_map_alignment_test/env.yml
@@ -0,0 +1,109 @@
+name: 006_map_alignment_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:
+    - filelock==3.16.1
+    - fsspec==2024.3.1
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - psutil==7.2.2
+    - pytest==8.3.5
+    - pyyaml==6.0.3
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - trl==0.11.4
+    - tyro==1.0.13
+prefix: /home/lily/yz979/anaconda3/envs/006_map_alignment_test
diff --git a/configs/006_map_alignment_test/explicit.txt b/configs/006_map_alignment_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b3c660a068b88b956abacead2624b4ba1bc988d
--- /dev/null
+++ b/configs/006_map_alignment_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
+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
+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/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-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/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
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+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/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614
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+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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+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
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+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_2.conda#dfc5aae7b043d9f56ba99514d5e60625
+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h8261f1e_0.conda#72b531694ebe4e8aa6f5745d1015c1b4
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda#000e85703f0fd9594c81710dd5066471
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diff --git a/configs/006_map_alignment_test/meta.json b/configs/006_map_alignment_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..df8d9d5c1ff52a68b9633e55fa78657b5cfaf56a
--- /dev/null
+++ b/configs/006_map_alignment_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "006_map_alignment_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 1,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/006_map_alignment_test",
+  "exported_at": "2026-05-17T04:03:10Z"
+}
diff --git a/configs/006_map_alignment_test/pip-clean.txt b/configs/006_map_alignment_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..620c8d8fef989de3eefd71219056f728d6f211e7
--- /dev/null
+++ b/configs/006_map_alignment_test/pip-clean.txt
@@ -0,0 +1,451 @@
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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==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
+trl==0.11.4
+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
+tyro==1.0.13
+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/006_map_alignment_test/pip-freeze.txt b/configs/006_map_alignment_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea70b50624e37202fafc8eaa32d8643bc4fa0f65
--- /dev/null
+++ b/configs/006_map_alignment_test/pip-freeze.txt
@@ -0,0 +1,463 @@
+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 @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
+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
+colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work
+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
+cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
+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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+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
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+fschat==0.2.35
+fsspec==2025.3.0
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+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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+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 @ file:///home/conda/feedstock_root/build_artifacts/idna_1726459485162/work
+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 @ file:///croot/kiwisolver_1672387140495/work
+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 @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1632416634429/work
+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
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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
+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
+pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
+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 @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
+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
+scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work
+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
+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
+trl==0.11.4
+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
+tyro==1.0.13
+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/007_spa_test/editable.txt b/configs/007_spa_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/007_spa_test/env.yml b/configs/007_spa_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..67280a68ca72520a07eea1d07ebd774aaf580e86
--- /dev/null
+++ b/configs/007_spa_test/env.yml
@@ -0,0 +1,98 @@
+name: 007_spa_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
+    - torch==2.4.1+cpu
+prefix: /home/lily/yz979/anaconda3/envs/007_spa_test
diff --git a/configs/007_spa_test/explicit.txt b/configs/007_spa_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b3c660a068b88b956abacead2624b4ba1bc988d
--- /dev/null
+++ b/configs/007_spa_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
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+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
+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
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+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/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614
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+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/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7
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+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
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+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_2.conda#dfc5aae7b043d9f56ba99514d5e60625
+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h8261f1e_0.conda#72b531694ebe4e8aa6f5745d1015c1b4
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda#000e85703f0fd9594c81710dd5066471
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+https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda#f4084e4e6577797150f9b04a4560ceb0
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+https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda#11b3379b191f63139e29c0d19dee24cd
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+https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py38h17151c0_1.conda#7a5a699c8992fc51ef25e980f4502c2a
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+https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.13.2-pyhd8ed1ab_2.conda#b713b116feaf98acdba93ad4d7f90ca1
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+https://conda.anaconda.org/conda-forge/noarch/seaborn-0.13.2-hd8ed1ab_2.conda#a79d8797f62715255308d92d3a91ef2e
diff --git a/configs/007_spa_test/meta.json b/configs/007_spa_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4b91bac23cb4ca5b69a4cc42454c7688cd0a614b
--- /dev/null
+++ b/configs/007_spa_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "007_spa_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/007_spa_test",
+  "exported_at": "2026-05-17T04:03:12Z"
+}
diff --git a/configs/007_spa_test/pip-clean.txt b/configs/007_spa_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30c2e60d97c6f5b7b0f9573e52a3ecdf932b0074
--- /dev/null
+++ b/configs/007_spa_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
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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
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+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
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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
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+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
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+dataclasses-json==0.6.4
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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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diff --git a/configs/007_spa_test/pip-freeze.txt b/configs/007_spa_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f8b81e4fb1b9af5d6072ea97d8e31a05609957f
--- /dev/null
+++ b/configs/007_spa_test/pip-freeze.txt
@@ -0,0 +1,456 @@
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+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==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
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+strsimpy==0.2.1
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
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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
+tqdm==4.67.1
+transformer-lens==2.16.1
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+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
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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
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+urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1708239446578/work
+uvicorn==0.29.0
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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/011_gp_hdbo_test/editable.txt b/configs/011_gp_hdbo_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/011_gp_hdbo_test/env.yml b/configs/011_gp_hdbo_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..fec582e2bb51087e89c2591c78a974ebbcc6d9c8
--- /dev/null
+++ b/configs/011_gp_hdbo_test/env.yml
@@ -0,0 +1,42 @@
+name: 011_gp_hdbo_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:
+    - mpmath==1.3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.1.2+cpu
+prefix: /home/lily/yz979/anaconda3/envs/011_gp_hdbo_test
diff --git a/configs/011_gp_hdbo_test/explicit.txt b/configs/011_gp_hdbo_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/011_gp_hdbo_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/011_gp_hdbo_test/meta.json b/configs/011_gp_hdbo_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f11d2d2ad3fbb5cc45e67ff88f8e761602d695ef
--- /dev/null
+++ b/configs/011_gp_hdbo_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "011_gp_hdbo_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/011_gp_hdbo_test",
+  "exported_at": "2026-05-17T04:03:07Z"
+}
diff --git a/configs/011_gp_hdbo_test/pip-clean.txt b/configs/011_gp_hdbo_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..693bc5c77f3e6c421bcf340e50513265797a0b39
--- /dev/null
+++ b/configs/011_gp_hdbo_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
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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
+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
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+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
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+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
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+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
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+jsonpatch==1.33
+jsonpath-python==1.0.6
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+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
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+language_data==1.2.0
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+linear-operator==0.4.0
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+Unidecode==1.3.2
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+xlrd==2.0.1
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+youtube-search==2.1.2
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diff --git a/configs/011_gp_hdbo_test/pip-freeze.txt b/configs/011_gp_hdbo_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..693bc5c77f3e6c421bcf340e50513265797a0b39
--- /dev/null
+++ b/configs/011_gp_hdbo_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
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+APScheduler==3.11.2
+arxiv==2.1.0
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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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diff --git a/configs/015_guidance_free_ar_generation_test/editable.txt b/configs/015_guidance_free_ar_generation_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/015_guidance_free_ar_generation_test/env.yml b/configs/015_guidance_free_ar_generation_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ee9de9ec665aea96bce453aed77f4be008d11af7
--- /dev/null
+++ b/configs/015_guidance_free_ar_generation_test/env.yml
@@ -0,0 +1,47 @@
+name: 015_guidance_free_ar_generation_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
+    - diffusers==0.36.0
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - idna==3.13
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - six==1.17.0
+    - torch==2.4.1+cpu
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/015_guidance_free_ar_generation_test
diff --git a/configs/015_guidance_free_ar_generation_test/explicit.txt b/configs/015_guidance_free_ar_generation_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/015_guidance_free_ar_generation_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/015_guidance_free_ar_generation_test/meta.json b/configs/015_guidance_free_ar_generation_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..b20fcfea0a52c08bc734b105f37c490f365dbf10
--- /dev/null
+++ b/configs/015_guidance_free_ar_generation_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "015_guidance_free_ar_generation_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/015_guidance_free_ar_generation_test",
+  "exported_at": "2026-05-17T04:03:20Z"
+}
diff --git a/configs/015_guidance_free_ar_generation_test/pip-clean.txt b/configs/015_guidance_free_ar_generation_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fb480dcb919f176b4b7f51770fc269afecf13ae
--- /dev/null
+++ b/configs/015_guidance_free_ar_generation_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==2026.4.22
+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
+diffusers==0.36.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
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+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
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+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
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+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==3.13
+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
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+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
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+parsimonious==0.8.1
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+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/015_guidance_free_ar_generation_test/pip-freeze.txt b/configs/015_guidance_free_ar_generation_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fb480dcb919f176b4b7f51770fc269afecf13ae
--- /dev/null
+++ b/configs/015_guidance_free_ar_generation_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
+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
+diffusers==0.36.0
+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==3.13
+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
+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-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==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/029_test/editable.txt b/configs/029_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/029_test/env.yml b/configs/029_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..55a2c31ef18d20a32ded66ccb9f4eef60a7f86d2
--- /dev/null
+++ b/configs/029_test/env.yml
@@ -0,0 +1,66 @@
+name: 029_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:
+    - appdirs==1.4.4
+    - certifi==2026.2.25
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - diskcache==5.6.3
+    - fonttools==4.57.0
+    - fsspec==2025.3.0
+    - httpx==0.28.1
+    - idna==3.10
+    - importlib-resources==6.4.5
+    - inflate64==1.0.0
+    - jinja2==3.1.6
+    - kiwisolver==1.4.7
+    - markupsafe==2.1.5
+    - matplotlib==3.7.5
+    - multivolumefile==0.2.3
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - psutil==7.2.2
+    - py7zr==0.22.0
+    - pybcj==1.0.2
+    - pycryptodomex==3.23.0
+    - pyparsing==3.1.4
+    - pyppmd==1.1.0
+    - pyyaml==6.0.3
+    - pyzstd==0.18.0
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/029_test
diff --git a/configs/029_test/explicit.txt b/configs/029_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/029_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/029_test/meta.json b/configs/029_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c040ec4aa4562d06c98d31a7a458e3716d4960e3
--- /dev/null
+++ b/configs/029_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "029_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/029_test",
+  "exported_at": "2026-05-17T04:03:34Z"
+}
diff --git a/configs/029_test/pip-clean.txt b/configs/029_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62d1d7f50b90f90820f9860774bce5748bec68df
--- /dev/null
+++ b/configs/029_test/pip-clean.txt
@@ -0,0 +1,464 @@
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diff --git a/configs/029_test/pip-freeze.txt b/configs/029_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62d1d7f50b90f90820f9860774bce5748bec68df
--- /dev/null
+++ b/configs/029_test/pip-freeze.txt
@@ -0,0 +1,464 @@
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+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
+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
+inflate64==1.0.0
+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
+multivolumefile==0.2.3
+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
+psutil==7.2.2
+PuLP==3.1.1
+pulsar-client==3.5.0
+py7zr==0.22.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pybcj==1.0.2
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pycryptodomex==3.23.0
+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
+pyppmd==1.1.0
+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
+pyzstd==0.18.0
+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/030_test/editable.txt b/configs/030_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/030_test/env.yml b/configs/030_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..122802575b290ab3e901ae9a638493f79fa6e376
--- /dev/null
+++ b/configs/030_test/env.yml
@@ -0,0 +1,55 @@
+name: 030_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==3.13.1
+    - 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
+    - psutil==7.2.2
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torch-scatter==2.1.2+pt24cpu
+    - torch-sparse==0.6.18+pt24cpu
+    - typing-extensions==4.12.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/030_test
diff --git a/configs/030_test/explicit.txt b/configs/030_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/030_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/030_test/meta.json b/configs/030_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..16191b22dfd37fcb455aa7fd7fceb8d70cf84bca
--- /dev/null
+++ b/configs/030_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "030_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/030_test",
+  "exported_at": "2026-05-17T04:03:40Z"
+}
diff --git a/configs/030_test/pip-clean.txt b/configs/030_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2a267801f075a73f10561177daf61c5edc102d3
--- /dev/null
+++ b/configs/030_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
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+torch_sparse==0.6.18+pt24cpu
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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
+urllib3==2.2.3
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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
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+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/030_test/pip-freeze.txt b/configs/030_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2a267801f075a73f10561177daf61c5edc102d3
--- /dev/null
+++ b/configs/030_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
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+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
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+awscli==1.32.93
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+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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+certifi==2026.4.22
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+chaospy==3.3.9
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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
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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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
+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
+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+cpu
+torch-geometric==2.6.1
+torch_scatter==2.1.2+pt24cpu
+torch_sparse==0.6.18+pt24cpu
+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/040_test/editable.txt b/configs/040_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/040_test/env.yml b/configs/040_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c2b5d84b582eb9432fa40563867ada0a051700c9
--- /dev/null
+++ b/configs/040_test/env.yml
@@ -0,0 +1,52 @@
+name: 040_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:
+    - easydict==1.13
+    - filelock==3.13.1
+    - fsspec==2024.6.1
+    - jinja2==3.1.4
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.0
+    - 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
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/040_test
diff --git a/configs/040_test/explicit.txt b/configs/040_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/040_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/040_test/meta.json b/configs/040_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3480924b5c1dabcbdc9c20d0913b77563ecd97a5
--- /dev/null
+++ b/configs/040_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "040_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/040_test",
+  "exported_at": "2026-05-17T04:03:45Z"
+}
diff --git a/configs/040_test/pip-clean.txt b/configs/040_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e93854d649bc010a9b1320ebb80f28e34e71065
--- /dev/null
+++ b/configs/040_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
+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
+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==3.13.1
+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
+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
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+markdown-it-py==3.0.0
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+markdownify==0.11.6
+MarkupSafe==2.1.5
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+networkx==3.0
+neuroHarmonize==2.4.5
+nh3==0.2.17
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+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
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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
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+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
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+overrides==7.7.0
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+parsimonious==0.8.1
+pathlib==1.0.1
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+pdf2image==1.17.0
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+pikepdf==8.4.1
+pip-search==0.0.12
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+plac==0.9.6
+plotly==6.3.0
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+pondpond==1.4.1
+pooch==1.8.2
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+pyarrow==17.0.0
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+pydeck==0.9.0b1
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+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
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+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
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+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
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+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
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+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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+rouge-score==0.1.2
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+scipy==1.10.1
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+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
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+sphinxcontrib-devhelp==1.0.2
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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
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+svgwrite==1.4.3
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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
+timm==0.9.16
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+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
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+transformer-lens==2.16.1
+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/040_test/pip-freeze.txt b/configs/040_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e93854d649bc010a9b1320ebb80f28e34e71065
--- /dev/null
+++ b/configs/040_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
+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
+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
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+fbpca==1.0
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+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
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+future==0.18.2
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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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+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
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
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+isodate==0.7.2
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+jiter==0.9.1
+jmespath==0.10.0
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+jsonnet==0.17.0
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+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
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+layoutparser==0.3.4
+lazy_loader==0.4
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+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
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+natsort==8.4.0
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+neuroHarmonize==2.4.5
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+nvidia-cublas-cu11==11.10.3.66
+nvidia-cuda-nvrtc-cu11==11.7.99
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+nvidia-cudnn-cu11==8.5.0.96
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
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+onnxruntime==1.15.1
+openai==1.101.0
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+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
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+packaging==26.2
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+parsimonious==0.8.1
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+pdf2image==1.17.0
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+pondpond==1.4.1
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+rdkit==2024.3.5
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+regex==2022.4.24
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+rich==13.7.1
+rouge-score==0.1.2
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+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
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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
+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/043_test/editable.txt b/configs/043_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/043_test/env.yml b/configs/043_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7327cc4fc2a5bf10b37b14c5210b7b7e5e53849d
--- /dev/null
+++ b/configs/043_test/env.yml
@@ -0,0 +1,75 @@
+name: 043_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==1.24.4
+    - nvidia-cublas-cu11==11.10.3.66
+    - nvidia-cublas-cu12==12.9.2.10
+    - nvidia-cuda-cupti-cu12==12.9.79
+    - nvidia-cuda-nvrtc-cu11==11.7.99
+    - nvidia-cuda-nvrtc-cu12==12.9.86
+    - nvidia-cuda-runtime-cu11==11.7.99
+    - nvidia-cuda-runtime-cu12==12.9.79
+    - nvidia-cudnn-cu11==8.5.0.96
+    - 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
+    - opencv-python==4.13.0.92
+    - packaging==20.9
+    - pillow==10.4.0
+    - pyyaml==6.0.3
+    - randaugment==1.0.2
+    - 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
+    - torchsample==0.1.0
+    - torchvision==0.16.2
+    - triton==2.1.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+    - wcwidth==0.2.14
+prefix: /home/lily/yz979/anaconda3/envs/043_test
diff --git a/configs/043_test/explicit.txt b/configs/043_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/043_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/043_test/meta.json b/configs/043_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..e345a3f6c9f229c65181ed5424bf90c5ee6b1bbc
--- /dev/null
+++ b/configs/043_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "043_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/043_test",
+  "exported_at": "2026-05-17T04:03:52Z"
+}
diff --git a/configs/043_test/pip-clean.txt b/configs/043_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b83c58573e460473dcb2485ce4168b2f4a5c87e4
--- /dev/null
+++ b/configs/043_test/pip-clean.txt
@@ -0,0 +1,475 @@
+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-cu11==11.10.3.66
+nvidia-cublas-cu12==12.9.2.10
+nvidia-cuda-cupti-cu12==12.9.79
+nvidia-cuda-nvrtc-cu11==11.7.99
+nvidia-cuda-nvrtc-cu12==12.9.86
+nvidia-cuda-runtime-cu11==11.7.99
+nvidia-cuda-runtime-cu12==12.9.79
+nvidia-cudnn-cu11==8.5.0.96
+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-ml-py==12.535.133
+nvidia-nccl-cu12==2.18.1
+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
+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
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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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/043_test/pip-freeze.txt b/configs/043_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b83c58573e460473dcb2485ce4168b2f4a5c87e4
--- /dev/null
+++ b/configs/043_test/pip-freeze.txt
@@ -0,0 +1,475 @@
+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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+attrs==25.3.0
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+azure-storage-blob==12.26.0
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+torchsample==0.1.0
+torchtext==0.4.0
+torchvision==0.16.2
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==2.1.0
+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/047_test/editable.txt b/configs/047_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/047_test/env.yml b/configs/047_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..cb68bed3eb1c9973219e1fe946d2eb8bd9296747
--- /dev/null
+++ b/configs/047_test/env.yml
@@ -0,0 +1,74 @@
+name: 047_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
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - filelock==3.16.1
+    - fonttools==4.57.0
+    - fsspec==2024.3.1
+    - 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
+    - peft==0.13.2
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - 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==2.4.1
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/047_test
diff --git a/configs/047_test/explicit.txt b/configs/047_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/047_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/047_test/meta.json b/configs/047_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a6a1ca64af3f5c6328b962c78f84ef494be771ca
--- /dev/null
+++ b/configs/047_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "047_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/047_test",
+  "exported_at": "2026-05-17T04:03:55Z"
+}
diff --git a/configs/047_test/pip-clean.txt b/configs/047_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c923ae9a470c4b02200ef6162ec5fa3972773c09
--- /dev/null
+++ b/configs/047_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
+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
+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
+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
+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
+peft==0.13.2
+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
+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/047_test/pip-freeze.txt b/configs/047_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c923ae9a470c4b02200ef6162ec5fa3972773c09
--- /dev/null
+++ b/configs/047_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
+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
+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
+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
+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
+peft==0.13.2
+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
+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/056_test/editable.txt b/configs/056_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/056_test/env.yml b/configs/056_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ceccf860dda52105e7de84a000f3a74956fd60f2
--- /dev/null
+++ b/configs/056_test/env.yml
@@ -0,0 +1,61 @@
+name: 056_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
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1
+    - torchdiffeq==0.2.5
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+prefix: /home/lily/yz979/anaconda3/envs/056_test
diff --git a/configs/056_test/explicit.txt b/configs/056_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/056_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/056_test/meta.json b/configs/056_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..95726e049301c2736d345e8a3022ef89870799e1
--- /dev/null
+++ b/configs/056_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "056_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/056_test",
+  "exported_at": "2026-05-17T04:04:04Z"
+}
diff --git a/configs/056_test/pip-clean.txt b/configs/056_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a84f8f4f9e85499ba779721b286afa3286636258
--- /dev/null
+++ b/configs/056_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
+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
+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
+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
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+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==2.4.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchdiffeq==0.2.5
+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/056_test/pip-freeze.txt b/configs/056_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a84f8f4f9e85499ba779721b286afa3286636258
--- /dev/null
+++ b/configs/056_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
+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==12.9.2.10
+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
+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
+torchdiffeq==0.2.5
+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/059_test/editable.txt b/configs/059_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/059_test/env.yml b/configs/059_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..cc5d30ffb217f708f79e87c08e564d9e45942262
--- /dev/null
+++ b/configs/059_test/env.yml
@@ -0,0 +1,62 @@
+name: 059_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==12.9.2.10
+    - 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
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - rouge-score==0.1.2
+    - 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/059_test
diff --git a/configs/059_test/explicit.txt b/configs/059_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/059_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
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diff --git a/configs/059_test/meta.json b/configs/059_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..721e26fe44b6cf4ec14636ad14b4593e24a3dd0a
--- /dev/null
+++ b/configs/059_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "059_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/059_test",
+  "exported_at": "2026-05-17T04:04:06Z"
+}
diff --git a/configs/059_test/pip-clean.txt b/configs/059_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6909a4a7ac800bf583618ecad230c1e43e3c00e
--- /dev/null
+++ b/configs/059_test/pip-clean.txt
@@ -0,0 +1,463 @@
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diff --git a/configs/059_test/pip-freeze.txt b/configs/059_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6909a4a7ac800bf583618ecad230c1e43e3c00e
--- /dev/null
+++ b/configs/059_test/pip-freeze.txt
@@ -0,0 +1,463 @@
+absl-py==2.3.1
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+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==12.9.2.10
+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-ml-py==12.535.133
+nvidia-nccl-cu12==2.18.1
+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
+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==2.1.2
+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==2.1.0
+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/065_test/editable.txt b/configs/065_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/065_test/env.yml b/configs/065_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1e8e2232c255f2341addbcd8ec4b3451b4ec9400
--- /dev/null
+++ b/configs/065_test/env.yml
@@ -0,0 +1,60 @@
+name: 065_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=3.5.4
+  - 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==2025.3.0
+    - google-auth==2.41.1
+    - google-auth-oauthlib==1.0.0
+    - idna==3.10
+    - jinja2==3.1.6
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.1
+    - numpy==1.24.4
+    - nvidia-cudnn-cu12==9.1.0.70
+    - nvidia-nccl-cu12==2.20.5
+    - packaging==25.0
+    - protobuf==5.29.6
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - tensorboard==2.14.0
+    - tensorboard-data-server==0.7.2
+    - torch==2.0.1+cpu
+    - triton==3.0.0
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/065_test
diff --git a/configs/065_test/explicit.txt b/configs/065_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..519dd4c543792147b565413766e3de659c7414ad
--- /dev/null
+++ b/configs/065_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-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
+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/065_test/meta.json b/configs/065_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c9ce53ab0f4f551e7f92d405b5e758a1d20df3e4
--- /dev/null
+++ b/configs/065_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "065_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/065_test",
+  "exported_at": "2026-05-17T04:04:14Z"
+}
diff --git a/configs/065_test/pip-clean.txt b/configs/065_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97083680edf4844777a64b4aba22022b0e34704a
--- /dev/null
+++ b/configs/065_test/pip-clean.txt
@@ -0,0 +1,462 @@
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diff --git a/configs/065_test/pip-freeze.txt b/configs/065_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97083680edf4844777a64b4aba22022b0e34704a
--- /dev/null
+++ b/configs/065_test/pip-freeze.txt
@@ -0,0 +1,462 @@
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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
+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-cudnn-cu12==9.1.0.70
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.20.5
+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
+protobuf==5.29.6
+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
+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==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==2.0.1+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
+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/076_test/editable.txt b/configs/076_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/076_test/env.yml b/configs/076_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..2b3cbbfa6509b0025ebacfcaa81f322301f422b6
--- /dev/null
+++ b/configs/076_test/env.yml
@@ -0,0 +1,65 @@
+name: 076_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:
+    - antlr4-python3-runtime==4.9.3
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - hydra-core==1.2.0
+    - idna==3.10
+    - importlib-resources==6.4.5
+    - 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
+    - omegaconf==2.3.0
+    - packaging==25.0
+    - pillow==10.4.0
+    - pytest==8.3.5
+    - pyyaml==6.0.3
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.1.2
+    - triton==2.1.0
+prefix: /home/lily/yz979/anaconda3/envs/076_test
diff --git a/configs/076_test/explicit.txt b/configs/076_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf
--- /dev/null
+++ b/configs/076_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/076_test/meta.json b/configs/076_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0d79e1bdace53890a4721e08e603c74f8ebd8ffc
--- /dev/null
+++ b/configs/076_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "076_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/076_test",
+  "exported_at": "2026-05-17T04:04:24Z"
+}
diff --git a/configs/076_test/pip-clean.txt b/configs/076_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b61e6111fe1ef83373ab283fbb72bba028b0748
--- /dev/null
+++ b/configs/076_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
+antlr4-python3-runtime==4.9.3
+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
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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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+tzdata==2024.1
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+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
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+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
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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
+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/076_test/pip-freeze.txt b/configs/076_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b61e6111fe1ef83373ab283fbb72bba028b0748
--- /dev/null
+++ b/configs/076_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
+antlr4-python3-runtime==4.9.3
+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-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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+chaospy==3.3.9
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+confection==0.1.4
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+coverage==7.6.1
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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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+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==2.1.2
+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==2.1.0
+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_44864_5_test/editable.txt b/configs/s41467_024_44864_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_44864_5_test/env.yml b/configs/s41467_024_44864_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0e2bff702a14dfb4490497ccd9be99f37df6184f
--- /dev/null
+++ b/configs/s41467_024_44864_5_test/env.yml
@@ -0,0 +1,89 @@
+name: s41467_024_44864_5_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - certifi=2024.2.2
+  - 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
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.25
+  - libpng=1.6.50
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.7.1
+  - libuuid=2.38.1
+  - 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
+  - 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
+  - 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
+  - seaborn=0.13.2
+  - seaborn-base=0.13.2
+  - setuptools=70.3.0
+  - statsmodels=0.13.5
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - tornado=6.2
+  - 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:
+    - contourpy==1.1.1
+    - coverage==7.6.1
+    - matplotlib==3.7.5
+    - pytest-cov==5.0.0
+    - scipy==1.10.1
+    - six==1.17.0
+    - typing-extensions==4.13.2
+    - unittest-xml-reporting==3.2.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_44864_5_test
diff --git a/configs/s41467_024_44864_5_test/explicit.txt b/configs/s41467_024_44864_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02b4be2b60dfa8c8da5ce1c495713b7519b9c208
--- /dev/null
+++ b/configs/s41467_024_44864_5_test/explicit.txt
@@ -0,0 +1,80 @@
+# 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/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_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/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
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
+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-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/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
+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/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614
+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/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7
+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/libfreetype6-2.14.1-h73754d4_0.conda#8e7251989bca326a28f4a5ffbd74557a
+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/libtiff-4.7.1-h8261f1e_0.conda#72b531694ebe4e8aa6f5745d1015c1b4
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda#000e85703f0fd9594c81710dd5066471
+https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda#f4084e4e6577797150f9b04a4560ceb0
+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/openjpeg-2.5.4-h55fea9a_0.conda#11b3379b191f63139e29c0d19dee24cd
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333
+https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441
+https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda#4afc585cd97ba8a23809406cd8a9eda8
+https://repo.anaconda.com/pkgs/main/linux-64/kiwisolver-1.4.4-py38h6a678d5_0.conda#7424aa335d22974192800ec19a68486e
+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
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+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
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diff --git a/configs/s41467_024_44864_5_test/meta.json b/configs/s41467_024_44864_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..30ad5a7548a6bd31986af0d57df84cd92cd0d4e8
--- /dev/null
+++ b/configs/s41467_024_44864_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_44864_5_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_44864_5_test",
+  "exported_at": "2026-05-17T04:04:32Z"
+}
diff --git a/configs/s41467_024_44864_5_test/pip-clean.txt b/configs/s41467_024_44864_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb37361129b6b57aab6b37132adbf663dfd040d6
--- /dev/null
+++ b/configs/s41467_024_44864_5_test/pip-clean.txt
@@ -0,0 +1,444 @@
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diff --git a/configs/s41467_024_44864_5_test/pip-freeze.txt b/configs/s41467_024_44864_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aea741df7208175f5b62487d46263558bcd1f12f
--- /dev/null
+++ b/configs/s41467_024_44864_5_test/pip-freeze.txt
@@ -0,0 +1,453 @@
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+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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+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
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+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
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+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
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+iniconfig==1.1.1
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+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 @ file:///croot/kiwisolver_1672387140495/work
+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 @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1632416634429/work
+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
+pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
+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 @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
+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==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
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
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+tensorboardX==2.4.1
+text-unidecode==1.3
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+thefuzz==0.22.1
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+tifffile==2023.7.10
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+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
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+typing-inspect==0.9.0
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+tzdata==2024.1
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+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
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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_024_44907_x_test/editable.txt b/configs/s41467_024_44907_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_44907_x_test/env.yml b/configs/s41467_024_44907_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0e9429e334866fafad457b56783e1916389ef070
--- /dev/null
+++ b/configs/s41467_024_44907_x_test/env.yml
@@ -0,0 +1,41 @@
+name: s41467_024_44907_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:
+    - coverage==7.6.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - pytest-cov==5.0.0
+    - scipy==1.10.1
+    - six==1.17.0
+    - unittest-xml-reporting==3.2.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_44907_x_test
diff --git a/configs/s41467_024_44907_x_test/explicit.txt b/configs/s41467_024_44907_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_44907_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_44907_x_test/meta.json b/configs/s41467_024_44907_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a9a6e2585352d73e8579a249e33e24a7799fc960
--- /dev/null
+++ b/configs/s41467_024_44907_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_44907_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_44907_x_test",
+  "exported_at": "2026-05-17T04:04:32Z"
+}
diff --git a/configs/s41467_024_44907_x_test/pip-clean.txt b/configs/s41467_024_44907_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_024_44907_x_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
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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_44907_x_test/pip-freeze.txt b/configs/s41467_024_44907_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_024_44907_x_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
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+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
+astunparse==1.6.3
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+attrs==25.3.0
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+dataclasses==0.6
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+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
+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_45059_8_test/editable.txt b/configs/s41467_024_45059_8_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_45059_8_test/env.yml b/configs/s41467_024_45059_8_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d6976cd9c9886e81718486690b8d0754cb617500
--- /dev/null
+++ b/configs/s41467_024_45059_8_test/env.yml
@@ -0,0 +1,111 @@
+name: s41467_024_45059_8_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2026.4.22
+  - certifi=2024.2.2
+  - 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
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.25
+  - libpng=1.6.50
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.7.1
+  - libuuid=2.38.1
+  - 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
+  - openjpeg=2.5.4
+  - openssl=3.6.2
+  - packaging=25.0
+  - pandas=2.0.3
+  - patsy=0.5.6
+  - pillow=10.4.0
+  - pip=22.1.2
+  - 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
+  - seaborn=0.13.2
+  - seaborn-base=0.13.2
+  - setuptools=70.3.0
+  - statsmodels=0.13.5
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - tornado=6.2
+  - 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:
+    - contourpy==1.1.1
+    - coverage==7.6.1
+    - filelock==3.16.1
+    - fsspec==2025.3.0
+    - h5py==3.11.0
+    - jinja2==3.1.6
+    - 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
+    - opencv-python==4.13.0.92
+    - pyfirmata==1.1.0
+    - pyserial==3.5
+    - pytest-cov==5.0.0
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - unittest-xml-reporting==3.2.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45059_8_test
diff --git a/configs/s41467_024_45059_8_test/explicit.txt b/configs/s41467_024_45059_8_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44aac9464caaf5b25268c46ad13f2c6b585a681c
--- /dev/null
+++ b/configs/s41467_024_45059_8_test/explicit.txt
@@ -0,0 +1,80 @@
+# 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/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_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/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
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
+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-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0
+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-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/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
+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/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614
+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/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7
+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/libfreetype6-2.14.1-h73754d4_0.conda#8e7251989bca326a28f4a5ffbd74557a
+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/libtiff-4.7.1-h8261f1e_0.conda#72b531694ebe4e8aa6f5745d1015c1b4
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda#000e85703f0fd9594c81710dd5066471
+https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda#f4084e4e6577797150f9b04a4560ceb0
+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/openjpeg-2.5.4-h55fea9a_0.conda#11b3379b191f63139e29c0d19dee24cd
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333
+https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441
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diff --git a/configs/s41467_024_45059_8_test/meta.json b/configs/s41467_024_45059_8_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..17a48123accd0074a9daf8036a48d3d32b2c9c0f
--- /dev/null
+++ b/configs/s41467_024_45059_8_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_45059_8_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_45059_8_test",
+  "exported_at": "2026-05-17T04:04:39Z"
+}
diff --git a/configs/s41467_024_45059_8_test/pip-clean.txt b/configs/s41467_024_45059_8_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..815cc15801fec8e6171f37100346f5367480815e
--- /dev/null
+++ b/configs/s41467_024_45059_8_test/pip-clean.txt
@@ -0,0 +1,463 @@
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diff --git a/configs/s41467_024_45059_8_test/pip-freeze.txt b/configs/s41467_024_45059_8_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78b0ba487e8b301f72619e1cb50ba9649330d4ee
--- /dev/null
+++ b/configs/s41467_024_45059_8_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
+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 @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
+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 @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
+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
+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 @ file:///croot/kiwisolver_1672387140495/work
+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 @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1632416634429/work
+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 @ 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-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
+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 @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
+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
+pyFirmata==1.1.0
+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 @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
+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
+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-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_45514_6_test/meta.json b/configs/s41467_024_45514_6_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..48b81735c916c9718f59a3e1f1ac2f4ab725ada6
--- /dev/null
+++ b/configs/s41467_024_45514_6_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_45514_6_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_45514_6_test",
+  "exported_at": "2026-05-17T04:04:36Z"
+}
diff --git a/configs/s41467_024_45599_z_test/editable.txt b/configs/s41467_024_45599_z_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_45599_z_test/env.yml b/configs/s41467_024_45599_z_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bb74189f66f7353a542e1666b9c19e1ad0e004e0
--- /dev/null
+++ b/configs/s41467_024_45599_z_test/env.yml
@@ -0,0 +1,65 @@
+name: s41467_024_45599_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:
+    - charset-normalizer==3.4.3
+    - coverage==7.6.1
+    - 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-nccl-cu12==2.20.5
+    - nvidia-nvjitlink-cu12==12.9.86
+    - nvidia-nvtx-cu12==12.1.105
+    - packaging==25.0
+    - pytest-cov==5.0.0
+    - requests==2.32.4
+    - scipy==1.10.1
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.1.2+cpu
+    - triton==3.0.0
+    - typing-extensions==4.13.2
+    - unittest-xml-reporting==3.2.0
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45599_z_test
diff --git a/configs/s41467_024_45599_z_test/explicit.txt b/configs/s41467_024_45599_z_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_45599_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
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diff --git a/configs/s41467_024_45599_z_test/meta.json b/configs/s41467_024_45599_z_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2c1b8ff049535fdac2de955f6cc2a1db442497d7
--- /dev/null
+++ b/configs/s41467_024_45599_z_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_45599_z_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_45599_z_test",
+  "exported_at": "2026-05-17T04:04:43Z"
+}
diff --git a/configs/s41467_024_45599_z_test/pip-clean.txt b/configs/s41467_024_45599_z_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..279ad12ed0ef03585785e50ac4bd7cab609c350d
--- /dev/null
+++ b/configs/s41467_024_45599_z_test/pip-clean.txt
@@ -0,0 +1,462 @@
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diff --git a/configs/s41467_024_45599_z_test/pip-freeze.txt b/configs/s41467_024_45599_z_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..279ad12ed0ef03585785e50ac4bd7cab609c350d
--- /dev/null
+++ b/configs/s41467_024_45599_z_test/pip-freeze.txt
@@ -0,0 +1,462 @@
+absl-py==2.3.1
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+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
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+future==0.18.2
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+gdown==5.2.0
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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
+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
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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
+idna==3.10
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
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+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
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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
+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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+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
+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
+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_024_45772_4_test/editable.txt b/configs/s41467_024_45772_4_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_45772_4_test/env.yml b/configs/s41467_024_45772_4_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bfb991196db9db8aeb36a289017735d8b93a7a6e
--- /dev/null
+++ b/configs/s41467_024_45772_4_test/env.yml
@@ -0,0 +1,88 @@
+name: s41467_024_45772_4_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - certifi=2024.2.2
+  - 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
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libopenblas=0.3.25
+  - libpng=1.6.50
+  - libsqlite=3.50.4
+  - libstdcxx=15.1.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.7.1
+  - libuuid=2.38.1
+  - 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
+  - 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
+  - pthread-stubs=0.4
+  - pyparsing=3.1.4
+  - python=3.8.20
+  - python-tzdata=2025.2
+  - python_abi=3.8
+  - pytz=2024.2
+  - readline=8.2
+  - scikit-learn=1.3.2
+  - seaborn=0.13.2
+  - seaborn-base=0.13.2
+  - setuptools=70.3.0
+  - statsmodels=0.13.5
+  - threadpoolctl=3.3.0
+  - tk=8.6.13
+  - tornado=6.2
+  - 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:
+    - contourpy==1.1.1
+    - coverage==7.6.1
+    - matplotlib==3.7.5
+    - pytest-cov==5.0.0
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+    - unittest-xml-reporting==3.2.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45772_4_test
diff --git a/configs/s41467_024_45772_4_test/explicit.txt b/configs/s41467_024_45772_4_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02b4be2b60dfa8c8da5ce1c495713b7519b9c208
--- /dev/null
+++ b/configs/s41467_024_45772_4_test/explicit.txt
@@ -0,0 +1,80 @@
+# 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/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_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/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
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
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diff --git a/configs/s41467_024_45772_4_test/meta.json b/configs/s41467_024_45772_4_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..16bab8e63ff7b588f167b7bc6076dea2f42f1ead
--- /dev/null
+++ b/configs/s41467_024_45772_4_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_45772_4_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_45772_4_test",
+  "exported_at": "2026-05-17T04:04:46Z"
+}
diff --git a/configs/s41467_024_45772_4_test/pip-clean.txt b/configs/s41467_024_45772_4_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb37361129b6b57aab6b37132adbf663dfd040d6
--- /dev/null
+++ b/configs/s41467_024_45772_4_test/pip-clean.txt
@@ -0,0 +1,444 @@
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+rdkit==2024.3.5
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+regex==2022.4.24
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+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
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+sse-starlette==1.8.2
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+statsmodels==0.14.1
+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
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+weasel==0.3.4
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+Werkzeug==2.0.2
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+xlrd==2.0.1
+XlsxWriter==3.0.2
+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_45772_4_test/pip-freeze.txt b/configs/s41467_024_45772_4_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aea741df7208175f5b62487d46263558bcd1f12f
--- /dev/null
+++ b/configs/s41467_024_45772_4_test/pip-freeze.txt
@@ -0,0 +1,453 @@
+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
+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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+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
+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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+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 @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
+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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+jiter==0.9.1
+jmespath==0.10.0
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+jsonnet==0.17.0
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+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver @ file:///croot/kiwisolver_1672387140495/work
+kubernetes==29.0.0
+langchain==0.1.16
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+linear-operator==0.4.0
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+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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+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 @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1632416634429/work
+mdtex2html==1.3.0
+mdurl==0.1.2
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+networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work
+neuroHarmonize==2.4.5
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+nltk==3.8.1
+numba==0.58.1
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+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
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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
+pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
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+pooch==1.8.2
+portalocker==2.4.0
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+preshed==3.0.9
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+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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+pyfaidx==0.9.0.1
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+PyMuPDFb==1.23.9
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+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
+pypdf==4.2.0
+pypdfium2==4.29.0
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+pyro-ppl==1.9.1
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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
+PyWavelets==1.4.1
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+sacrebleu==2.1.0
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+scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work
+scipy==1.10.1
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+sentence-transformers==2.2.2
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+session_info==1.0.1
+sgmllib3k==1.0.0
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+sphinxcontrib-devhelp==1.0.2
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+sphinxcontrib-jsmath==1.0.1
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+streamlit-chatbox==1.1.11
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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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+toolz==0.12.1
+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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+typing_extensions==4.13.2
+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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+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
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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/s41467_024_46399_1_test/env.yml b/configs/s41467_024_46399_1_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..3f97593be4fe9ca258ae324f977c0e5cca583e00
--- /dev/null
+++ b/configs/s41467_024_46399_1_test/env.yml
@@ -0,0 +1,52 @@
+name: s41467_024_46399_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:
+    - contourpy==1.1.1
+    - coverage==7.6.1
+    - imageio==2.35.1
+    - lazy-loader==0.4
+    - matplotlib==3.7.5
+    - natsort==8.4.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - pandas==2.0.3
+    - pytest-cov==5.0.0
+    - python-dateutil==2.9.0.post0
+    - pytz==2025.2
+    - pywavelets==1.4.1
+    - scikit-image==0.21.0
+    - scipy==1.10.1
+    - six==1.17.0
+    - tifffile==2023.7.10
+    - unittest-xml-reporting==3.2.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46399_1_test
diff --git a/configs/s41467_024_46399_1_test/pip-freeze.txt b/configs/s41467_024_46399_1_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db7455f93c5a63b0465aa2622166f3964e3e7420
--- /dev/null
+++ b/configs/s41467_024_46399_1_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
+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
+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
+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
+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
+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_46523_1_test/env.yml b/configs/s41467_024_46523_1_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ba4b464af9bd4c3afe449e5ee270737cbd844a5b
--- /dev/null
+++ b/configs/s41467_024_46523_1_test/env.yml
@@ -0,0 +1,53 @@
+name: s41467_024_46523_1_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.10.5
+  - joblib=1.4.2
+  - ld_impl_linux-64=2.44
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libffi=3.5.2
+  - libgcc=15.2.0
+  - libgcc-ng=15.2.0
+  - libgfortran=15.2.0
+  - libgfortran-ng=15.2.0
+  - libgfortran5=15.2.0
+  - libgomp=15.2.0
+  - 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=15.2.0
+  - libstdcxx-ng=15.2.0
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - numpy=1.24.4
+  - openssl=3.5.4
+  - 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
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46523_1_test
diff --git a/configs/s41467_024_46523_1_test/explicit.txt b/configs/s41467_024_46523_1_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f813c7ced4a310f0a6db11f1e5829a03719e6e32
--- /dev/null
+++ b/configs/s41467_024_46523_1_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-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
+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-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+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-15.2.0-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/libgfortran5-15.2.0-hcd61629_7.conda#f116940d825ffc9104400f0d7f1a4551
+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
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+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-15.2.0-h4852527_7.conda#f627678cf829bd70bccf141a19c3ad3e
+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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+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-15.2.0-h69a702a_7.conda#beeb74a6fe5ff118451cf0581bfe2642
+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/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
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+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
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+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-20_linux64_openblas.conda#6fabc51f5e647d09cc010c40061557e0
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+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_46523_1_test/meta.json b/configs/s41467_024_46523_1_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3547eb7d387ac51055c9fd53be536baeb55934da
--- /dev/null
+++ b/configs/s41467_024_46523_1_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46523_1_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46523_1_test",
+  "exported_at": "2026-05-17T04:04:55Z"
+}
diff --git a/configs/s41467_024_46700_2_test/editable.txt b/configs/s41467_024_46700_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_46700_2_test/env.yml b/configs/s41467_024_46700_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..8823cb4f1c3f9528033ed44586bfd384f6540c27
--- /dev/null
+++ b/configs/s41467_024_46700_2_test/env.yml
@@ -0,0 +1,67 @@
+name: s41467_024_46700_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:
+    - asttokens==3.0.0
+    - backcall==0.2.0
+    - cloudpickle==3.1.1
+    - 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
+    - opencv-python-headless==4.13.0.92
+    - packaging==25.0
+    - parso==0.8.5
+    - pexpect==4.9.0
+    - pickleshare==0.7.5
+    - pillow==10.4.0
+    - ptyprocess==0.7.0
+    - pure-eval==0.2.3
+    - pyparsing==3.1.4
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - shap==0.44.1
+    - six==1.17.0
+    - slicer==0.0.7
+    - stack-data==0.6.3
+    - traitlets==5.14.3
+    - typing-extensions==4.13.2
+    - wcwidth==0.2.14
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46700_2_test
diff --git a/configs/s41467_024_46700_2_test/explicit.txt b/configs/s41467_024_46700_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_46700_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
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+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
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+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
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+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_46700_2_test/meta.json b/configs/s41467_024_46700_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4864cf73101694cdf6d008039c9f722ee9dd98f7
--- /dev/null
+++ b/configs/s41467_024_46700_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_46700_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46700_2_test",
+  "exported_at": "2026-05-17T04:04:57Z"
+}
diff --git a/configs/s41467_024_46700_2_test/pip-clean.txt b/configs/s41467_024_46700_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7962ab2c26dc3c76a0b652732a1655a5a5a922cb
--- /dev/null
+++ b/configs/s41467_024_46700_2_test/pip-clean.txt
@@ -0,0 +1,471 @@
+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
+asttokens==3.0.0
+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
+backcall==0.2.0
+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
+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
+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
+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
+executing==2.2.1
+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
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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
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
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+h11==0.14.0
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+httpcore==1.0.5
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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
+importlib_resources==6.4.5
+inequalipy==1.0.5
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+jaxlib==0.4.13
+jaxtyping==0.2.19
+jedi==0.19.2
+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
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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
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+vllm==0.2.7
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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
+zstandard==0.23.0
diff --git a/configs/s41467_024_46700_2_test/pip-freeze.txt b/configs/s41467_024_46700_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7962ab2c26dc3c76a0b652732a1655a5a5a922cb
--- /dev/null
+++ b/configs/s41467_024_46700_2_test/pip-freeze.txt
@@ -0,0 +1,471 @@
+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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+attrs==25.3.0
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+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
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+azure-storage-blob==12.26.0
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+backcall==0.2.0
+backoff==2.2.1
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+beartype==0.14.1
+better-abc==0.0.3
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+chaospy==3.3.9
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+ConfigArgParse==1.5.3
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+sgmllib3k==1.0.0
+shap==0.44.1
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+slicer==0.0.7
+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
+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
+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
+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_47569_x_test/editable.txt b/configs/s41467_024_47569_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_47569_x_test/env.yml b/configs/s41467_024_47569_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..77266f2514e3e4626c94f836875ebd3672732815
--- /dev/null
+++ b/configs/s41467_024_47569_x_test/env.yml
@@ -0,0 +1,37 @@
+name: s41467_024_47569_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_47569_x_test
diff --git a/configs/s41467_024_47569_x_test/explicit.txt b/configs/s41467_024_47569_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_47569_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_47569_x_test/meta.json b/configs/s41467_024_47569_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..31dbddc55448e5e33b9a4ef5a9526c51207c08f6
--- /dev/null
+++ b/configs/s41467_024_47569_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_47569_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_47569_x_test",
+  "exported_at": "2026-05-17T04:05:06Z"
+}
diff --git a/configs/s41467_024_47569_x_test/pip-clean.txt b/configs/s41467_024_47569_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_47569_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
+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
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+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
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+multipledispatch==1.0.0
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+narwhals==1.42.1
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+nest-asyncio==1.6.0
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+nh3==0.2.17
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+python-dateutil==2.9.0.post0
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+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_47569_x_test/pip-freeze.txt b/configs/s41467_024_47569_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_47569_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_47661_2_test/editable.txt b/configs/s41467_024_47661_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_47661_2_test/env.yml b/configs/s41467_024_47661_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f88d1b860242bd6a50b70c37598fc7376a59d836
--- /dev/null
+++ b/configs/s41467_024_47661_2_test/env.yml
@@ -0,0 +1,59 @@
+name: s41467_024_47661_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:
+    - 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
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - 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_47661_2_test
diff --git a/configs/s41467_024_47661_2_test/explicit.txt b/configs/s41467_024_47661_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_47661_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_024_47661_2_test/meta.json b/configs/s41467_024_47661_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..eadedb6ca32db9741ba77b0289941c9182047457
--- /dev/null
+++ b/configs/s41467_024_47661_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_47661_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_47661_2_test",
+  "exported_at": "2026-05-17T04:05:12Z"
+}
diff --git a/configs/s41467_024_47661_2_test/pip-clean.txt b/configs/s41467_024_47661_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1c37e9116c791f01fa1bf3dc7a3e0b55de8d2a3
--- /dev/null
+++ b/configs/s41467_024_47661_2_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
+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
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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
+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
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+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_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
+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
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+snowballstemmer==2.2.0
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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
+sphinxcontrib-jsmath==1.0.1
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+stdlib-list==0.10.0
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+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
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+strsimpy==0.2.1
+svgwrite==1.4.3
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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
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.4.1+cpu
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+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
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+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_47661_2_test/pip-freeze.txt b/configs/s41467_024_47661_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1c37e9116c791f01fa1bf3dc7a3e0b55de8d2a3
--- /dev/null
+++ b/configs/s41467_024_47661_2_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
+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
+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+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_49261_6_test/editable.txt b/configs/s41467_024_49261_6_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_49261_6_test/env.yml b/configs/s41467_024_49261_6_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..40d21ae72b28bf4da1ff7113ec848a9030499144
--- /dev/null
+++ b/configs/s41467_024_49261_6_test/env.yml
@@ -0,0 +1,47 @@
+name: s41467_024_49261_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:
+    - 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_49261_6_test
diff --git a/configs/s41467_024_49261_6_test/explicit.txt b/configs/s41467_024_49261_6_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_49261_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
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diff --git a/configs/s41467_024_49261_6_test/meta.json b/configs/s41467_024_49261_6_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..55c345899905cd921408d078583d00d56e8f4ef7
--- /dev/null
+++ b/configs/s41467_024_49261_6_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_49261_6_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_49261_6_test",
+  "exported_at": "2026-05-17T04:05:21Z"
+}
diff --git a/configs/s41467_024_49261_6_test/pip-clean.txt b/configs/s41467_024_49261_6_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_49261_6_test/pip-clean.txt
@@ -0,0 +1,451 @@
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diff --git a/configs/s41467_024_49261_6_test/pip-freeze.txt b/configs/s41467_024_49261_6_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644
--- /dev/null
+++ b/configs/s41467_024_49261_6_test/pip-freeze.txt
@@ -0,0 +1,451 @@
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+faiss-cpu==1.7.4
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+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
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+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
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+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
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+smart-open==6.4.0
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+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
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+soupsieve==2.5
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+sphinxcontrib-devhelp==1.0.2
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+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
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+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
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+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
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+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-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/editable.txt b/configs/s41467_024_49516_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_49516_2_test/explicit.txt b/configs/s41467_024_49516_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_49516_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_024_49516_2_test/meta.json b/configs/s41467_024_49516_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..af4aa9b41d6f866f5c55eca94306883c8dd68f43
--- /dev/null
+++ b/configs/s41467_024_49516_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_49516_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_49516_2_test",
+  "exported_at": "2026-05-17T04:05:23Z"
+}
diff --git a/configs/s41467_024_49516_2_test/pip-clean.txt b/configs/s41467_024_49516_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..450d5cd28eb88d9985e3a6377eff713de06e0bb5
--- /dev/null
+++ b/configs/s41467_024_49516_2_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
+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
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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_49516_2_test/pip-freeze.txt b/configs/s41467_024_49516_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..450d5cd28eb88d9985e3a6377eff713de06e0bb5
--- /dev/null
+++ b/configs/s41467_024_49516_2_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
+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
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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
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+better-abc==0.0.3
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+blessed==1.20.0
+blis==0.7.11
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+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
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+datasets==2.19.0
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+Deprecated==1.2.14
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+editdistance==0.6.0
+effdet==0.4.1
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+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
+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
+torch_scatter==2.1.2
+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_50043_3_test/editable.txt b/configs/s41467_024_50043_3_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_50043_3_test/env.yml b/configs/s41467_024_50043_3_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..5f0348d09b41b4ab90845e100b6e09708bc7d35e
--- /dev/null
+++ b/configs/s41467_024_50043_3_test/env.yml
@@ -0,0 +1,61 @@
+name: s41467_024_50043_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:
+    - antlr4-python3-runtime==4.9.3
+    - braceexpand==0.1.7
+    - certifi==2026.4.22
+    - decord==0.6.0
+    - 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
+    - omegaconf==2.3.0
+    - opencv-python==4.13.0.92
+    - packaging==25.0
+    - pillow==10.4.0
+    - python-dateutil==2.9.0.post0
+    - pyyaml==6.0.3
+    - requests==2.32.4
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - torchvision==0.19.1+cpu
+    - tqdm==4.67.1
+    - typing-extensions==4.12.2
+    - urllib3==2.2.3
+    - webdataset==0.2.100
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_50043_3_test
diff --git a/configs/s41467_024_50043_3_test/explicit.txt b/configs/s41467_024_50043_3_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_50043_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_50043_3_test/meta.json b/configs/s41467_024_50043_3_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f8783287e8902df2c648e7ca625992a01b9c881b
--- /dev/null
+++ b/configs/s41467_024_50043_3_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_50043_3_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_50043_3_test",
+  "exported_at": "2026-05-17T04:05:29Z"
+}
diff --git a/configs/s41467_024_50043_3_test/pip-clean.txt b/configs/s41467_024_50043_3_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03f1d02550911be742a121bcc63feec2b71e42d9
--- /dev/null
+++ b/configs/s41467_024_50043_3_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
+antlr4-python3-runtime==4.9.3
+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
+braceexpand==0.1.7
+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
+decord==0.6.0
+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==3.11
+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==3.0
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
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+numba==0.58.1
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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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+tzdata==2024.1
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+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+webdataset==0.2.100
+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
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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_50043_3_test/pip-freeze.txt b/configs/s41467_024_50043_3_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03f1d02550911be742a121bcc63feec2b71e42d9
--- /dev/null
+++ b/configs/s41467_024_50043_3_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
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+alabaster==0.7.12
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+altair==5.3.0
+annotated-types==0.6.0
+antlr4-python3-runtime==4.9.3
+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
+biopython==1.83
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+chaospy==3.3.9
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+confection==0.1.4
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
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+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
+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
+webdataset==0.2.100
+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_50114_5_test/editable.txt b/configs/s41467_024_50114_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_50114_5_test/env.yml b/configs/s41467_024_50114_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..5c5d81ffdf6a31ebc6672a54066b5aaabfaae929
--- /dev/null
+++ b/configs/s41467_024_50114_5_test/env.yml
@@ -0,0 +1,62 @@
+name: s41467_024_50114_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:
+    - certifi==2026.2.25
+    - flatbuffers==25.9.23
+    - fonttools==4.57.0
+    - gast==0.7.0
+    - google-auth==2.42.0
+    - google-auth-oauthlib==1.0.0
+    - idna==3.11
+    - keras==2.13.1
+    - kiwisolver==1.4.7
+    - libclang==18.1.1
+    - numpy==1.24.3
+    - packaging==25.0
+    - protobuf==4.25.8
+    - pyasn1==0.6.1
+    - pyasn1-modules==0.4.2
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - requests==2.32.4
+    - 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
+    - urllib3==2.2.3
+    - wrapt==2.0.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_50114_5_test
diff --git a/configs/s41467_024_50114_5_test/explicit.txt b/configs/s41467_024_50114_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_50114_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_50114_5_test/meta.json b/configs/s41467_024_50114_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3c9b0fa8f455cc3db6fd5bc6ae86429c7929b152
--- /dev/null
+++ b/configs/s41467_024_50114_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_50114_5_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_50114_5_test",
+  "exported_at": "2026-05-17T04:05:31Z"
+}
diff --git a/configs/s41467_024_50114_5_test/pip-clean.txt b/configs/s41467_024_50114_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a5f337b85e008080434b4df2c381b5f4ce1f9c1
--- /dev/null
+++ b/configs/s41467_024_50114_5_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==2026.2.25
+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
+flatbuffers==25.9.23
+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
+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==2.42.0
+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==3.11
+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==2.13.1
+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
+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
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+marshmallow==3.21.1
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+overrides==7.7.0
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+pdf2image==1.17.0
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+pikepdf==8.4.1
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+pyfaidx==0.9.0.1
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+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
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+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
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+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
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+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==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/configs/s41467_024_50114_5_test/pip-freeze.txt b/configs/s41467_024_50114_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a5f337b85e008080434b4df2c381b5f4ce1f9c1
--- /dev/null
+++ b/configs/s41467_024_50114_5_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
+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
+flatbuffers==25.9.23
+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
+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==2.42.0
+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==3.11
+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==2.13.1
+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
+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
+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==1.24.3
+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
+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
+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
+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/configs/s41467_024_51560_x_test/editable.txt b/configs/s41467_024_51560_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_51560_x_test/env.yml b/configs/s41467_024_51560_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6b08bc913a7940c30e29c744e70946cf8b39ca30
--- /dev/null
+++ b/configs/s41467_024_51560_x_test/env.yml
@@ -0,0 +1,48 @@
+name: s41467_024_51560_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:
+    - 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
+    - pyfftw==0.13.1
+    - 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_51560_x_test
diff --git a/configs/s41467_024_51560_x_test/explicit.txt b/configs/s41467_024_51560_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_51560_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_51560_x_test/meta.json b/configs/s41467_024_51560_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f1e0b7575e03ec700379df04ae5476b8f9f2bd55
--- /dev/null
+++ b/configs/s41467_024_51560_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_51560_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_51560_x_test",
+  "exported_at": "2026-05-17T04:05:37Z"
+}
diff --git a/configs/s41467_024_51560_x_test/pip-clean.txt b/configs/s41467_024_51560_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb81f0a4b8ffe782939c31033ffe850bfd4a2a00
--- /dev/null
+++ b/configs/s41467_024_51560_x_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
+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
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+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
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+pyFFTW==0.13.1
+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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+pypdfium2==4.29.0
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+pyro-api==0.1.2
+pyro-ppl==1.9.1
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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
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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
+pytz==2025.2
+pyvista==0.44.2
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+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
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+smart-open==6.4.0
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+sobol-seq==0.2.0
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+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
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+sse-starlette==1.8.2
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+stdlib-list==0.10.0
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+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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+tzdata==2024.1
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+unstructured==0.11.0
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+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
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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
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+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_51560_x_test/pip-freeze.txt b/configs/s41467_024_51560_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb81f0a4b8ffe782939c31033ffe850bfd4a2a00
--- /dev/null
+++ b/configs/s41467_024_51560_x_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
+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
+pyFFTW==0.13.1
+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_53200_w_test/editable.txt b/configs/s41467_024_53200_w_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_53200_w_test/env.yml b/configs/s41467_024_53200_w_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e58ab219b50d21fcf0c64d1dffb9151ac3b76504
--- /dev/null
+++ b/configs/s41467_024_53200_w_test/env.yml
@@ -0,0 +1,37 @@
+name: s41467_024_53200_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
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_53200_w_test
diff --git a/configs/s41467_024_53200_w_test/explicit.txt b/configs/s41467_024_53200_w_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_53200_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
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diff --git a/configs/s41467_024_53200_w_test/meta.json b/configs/s41467_024_53200_w_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9c79b0a6b8eb519b30048a08f2b7febba296047a
--- /dev/null
+++ b/configs/s41467_024_53200_w_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_53200_w_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_53200_w_test",
+  "exported_at": "2026-05-17T04:05:49Z"
+}
diff --git a/configs/s41467_024_53200_w_test/pip-clean.txt b/configs/s41467_024_53200_w_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_53200_w_test/pip-clean.txt
@@ -0,0 +1,443 @@
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diff --git a/configs/s41467_024_53200_w_test/pip-freeze.txt b/configs/s41467_024_53200_w_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_024_53200_w_test/pip-freeze.txt
@@ -0,0 +1,443 @@
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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
+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_53818_w_test/editable.txt b/configs/s41467_024_53818_w_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_53818_w_test/explicit.txt b/configs/s41467_024_53818_w_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_53818_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_024_53818_w_test/meta.json b/configs/s41467_024_53818_w_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..741e287679723ae1d0cfb3c0df020a34f0c2b68a
--- /dev/null
+++ b/configs/s41467_024_53818_w_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_53818_w_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_53818_w_test",
+  "exported_at": "2026-05-17T04:05:52Z"
+}
diff --git a/configs/s41467_024_53818_w_test/pip-clean.txt b/configs/s41467_024_53818_w_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_024_53818_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
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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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+unstructured==0.11.0
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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
+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_53818_w_test/pip-freeze.txt b/configs/s41467_024_53818_w_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_024_53818_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
+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
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+Brotli==1.1.0
+bs4==0.0.2
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+chaospy==3.3.9
+charset-normalizer==3.4.7
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+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
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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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+equinox==0.10.4
+et-xmlfile==1.1.0
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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
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+GitPython==3.1.43
+google-pasta==0.2.0
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+litellm==1.77.4
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+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_54738_5_test/editable.txt b/configs/s41467_024_54738_5_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_024_54738_5_test/env.yml b/configs/s41467_024_54738_5_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..113e4967527c7270dda8c2587cdeda678d0e9690
--- /dev/null
+++ b/configs/s41467_024_54738_5_test/env.yml
@@ -0,0 +1,47 @@
+name: s41467_024_54738_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:
+    - filelock==3.13.1
+    - fsspec==2024.6.1
+    - jinja2==3.1.6
+    - 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
+    - torchvision==0.19.1+cpu
+    - typing-extensions==4.12.2
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_54738_5_test
diff --git a/configs/s41467_024_54738_5_test/explicit.txt b/configs/s41467_024_54738_5_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_024_54738_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_54738_5_test/meta.json b/configs/s41467_024_54738_5_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f838b0ceddc2cf52fe3fe36aa3373cecdc4f3b18
--- /dev/null
+++ b/configs/s41467_024_54738_5_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_54738_5_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_54738_5_test",
+  "exported_at": "2026-05-17T04:06:00Z"
+}
diff --git a/configs/s41467_024_54738_5_test/pip-clean.txt b/configs/s41467_024_54738_5_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21080465f89cf1aec1e86fb2a2531c4c23282db4
--- /dev/null
+++ b/configs/s41467_024_54738_5_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
+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
+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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+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
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+nltk==3.8.1
+numba==0.58.1
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+nvidia-ml-py==12.535.133
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+onnxruntime==1.15.1
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+overrides==7.7.0
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+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
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+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
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+pydeck==0.9.0b1
+pyDOE2==1.3.0
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+pyfaidx==0.9.0.1
+Pygments==2.19.2
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+PyMuPDFb==1.23.9
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+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
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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
+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_024_54738_5_test/pip-freeze.txt b/configs/s41467_024_54738_5_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21080465f89cf1aec1e86fb2a2531c4c23282db4
--- /dev/null
+++ b/configs/s41467_024_54738_5_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
+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
+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
+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
+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_55594_z_test/pip-clean.txt b/configs/s41467_024_55594_z_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5acfec541568e356c83667aefd1ae39befc8cf8
--- /dev/null
+++ b/configs/s41467_024_55594_z_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
+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
+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
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+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
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+scooby==0.10.1
+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
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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
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+spacy-loggers==1.0.5
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+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
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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
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+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
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+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+cpu
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+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_56078_4_test/editable.txt b/configs/s41467_025_56078_4_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_56078_4_test/explicit.txt b/configs/s41467_025_56078_4_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_56078_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_56078_4_test/meta.json b/configs/s41467_025_56078_4_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..34c65842b2a3bc212961652f26ffa835152bda09
--- /dev/null
+++ b/configs/s41467_025_56078_4_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_56078_4_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56078_4_test",
+  "exported_at": "2026-05-17T04:06:12Z"
+}
diff --git a/configs/s41467_025_56078_4_test/pip-clean.txt b/configs/s41467_025_56078_4_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce674b75930e9128d5370fd0a86d430f19aedd99
--- /dev/null
+++ b/configs/s41467_025_56078_4_test/pip-clean.txt
@@ -0,0 +1,475 @@
+absl-py==2.3.1
+accelerate==0.24.1
+addict==2.4.0
+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
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+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
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+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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+python-multipart==0.0.18
+python-pptx==0.6.23
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+pytorch-pretrained-bert==0.6.2
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+rapidocr-onnxruntime==1.3.8
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+rdkit==2024.3.5
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+sphinxcontrib-devhelp==1.0.2
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+streamlit-antd-components==0.3.1
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+streamlit-modal==0.1.0
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+tenacity==8.2.3
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+tensorboard-plugin-wit==1.8.0
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+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
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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
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+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
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+triton==3.0.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
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+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
+yapf==0.43.0
+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/pip-freeze.txt b/configs/s41467_025_56078_4_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce674b75930e9128d5370fd0a86d430f19aedd99
--- /dev/null
+++ b/configs/s41467_025_56078_4_test/pip-freeze.txt
@@ -0,0 +1,475 @@
+absl-py==2.3.1
+accelerate==0.24.1
+addict==2.4.0
+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
+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
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+get-annotations==0.1.2
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+google-auth-oauthlib==1.0.0
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+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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+jsonpickle==2.0.0
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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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+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
+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
+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==5.29.5
+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
+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
+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
+tb-nightly==2.14.0a20230808
+tenacity==8.2.3
+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
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+yapf==0.43.0
+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_57867_7_test/editable.txt b/configs/s41467_025_57867_7_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_57867_7_test/env.yml b/configs/s41467_025_57867_7_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..8f9604764adfd75e1c7c4df1704bedb8ce7ba209
--- /dev/null
+++ b/configs/s41467_025_57867_7_test/env.yml
@@ -0,0 +1,53 @@
+name: s41467_025_57867_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
+    - joblib==1.4.2
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - neurocombat==0.2.12
+    - nibabel==5.2.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - pandas==2.0.3
+    - patsy==1.0.1
+    - pyparsing==3.1.4
+    - pyqt5==5.15.11
+    - pyqt5-qt5==5.15.17
+    - pyqt5-sip==12.15.0
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+    - statsmodels==0.14.1
+    - threadpoolctl==3.5.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_57867_7_test
diff --git a/configs/s41467_025_57867_7_test/explicit.txt b/configs/s41467_025_57867_7_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_57867_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_57867_7_test/meta.json b/configs/s41467_025_57867_7_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a3e1dd25c4431499d5a224563d2224e805b7d849
--- /dev/null
+++ b/configs/s41467_025_57867_7_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_57867_7_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_57867_7_test",
+  "exported_at": "2026-05-17T04:06:27Z"
+}
diff --git a/configs/s41467_025_57867_7_test/pip-clean.txt b/configs/s41467_025_57867_7_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e124b92cc551c8a61c478f43013586612f434de1
--- /dev/null
+++ b/configs/s41467_025_57867_7_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
+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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+jmespath==0.10.0
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+pysqlite3-binary==0.5.2.post3
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+python-iso639==2024.4.27
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+python-multipart==0.0.18
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+pytorch-pretrained-bert==0.6.2
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+sentry-sdk==2.39.0
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+streamlit-antd-components==0.3.1
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+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
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+svgwrite==1.4.3
+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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+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_57867_7_test/pip-freeze.txt b/configs/s41467_025_57867_7_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e124b92cc551c8a61c478f43013586612f434de1
--- /dev/null
+++ b/configs/s41467_025_57867_7_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
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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
+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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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+fuzzywuzzy==0.18.0
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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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+huggingface_hub==0.36.1
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+icetk==0.0.4
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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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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
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+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
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+langsmith==0.1.51
+language_data==1.2.0
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+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
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+madoka==0.7.1
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+opentelemetry-sdk==1.24.0
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+ordered-set==4.1.0
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+overrides==7.7.0
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+parsimonious==0.8.1
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+referencing==0.35.1
+regex==2022.4.24
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+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_58741_2_test/editable.txt b/configs/s41467_025_58741_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_58741_2_test/env.yml b/configs/s41467_025_58741_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..07b5c2d5799a9aac6c576d8f2a24503f179833a9
--- /dev/null
+++ b/configs/s41467_025_58741_2_test/env.yml
@@ -0,0 +1,58 @@
+name: s41467_025_58741_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
+  - 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
+  - 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=0.3.30
+  - 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=3.5.4
+  - packaging=25.0
+  - pip=22.1.2
+  - python=3.8.20
+  - python_abi=3.8
+  - 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
+    - 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
+    - tqdm==4.67.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58741_2_test
diff --git a/configs/s41467_025_58741_2_test/explicit.txt b/configs/s41467_025_58741_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..238f83bee03a41d6e7a1f46201b7338deaf291f9
--- /dev/null
+++ b/configs/s41467_025_58741_2_test/explicit.txt
@@ -0,0 +1,42 @@
+# 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-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
+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/libopenblas-0.3.30-pthreads_h94d23a6_2.conda#dfc5aae7b043d9f56ba99514d5e60625
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-35_h4a7cf45_openblas.conda#6da7e852c812a84096b68158574398d0
+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/libcblas-3.9.0-35_h0358290_openblas.conda#8aa3389d36791ecd31602a247b1f3641
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-35_h47877c9_openblas.conda#aa0b36b71d44f74686f13b9bfabec891
+https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda#58335b26c38bf4a20f399384c33cbcf9
+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/linux-64/numpy-1.24.4-py38h59b608b_0.conda#8c3e050afeeb2b32575bdb8955cc67b2
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
diff --git a/configs/s41467_025_58741_2_test/meta.json b/configs/s41467_025_58741_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c3ac353d493dcdadaf198d7282a728c82f170c75
--- /dev/null
+++ b/configs/s41467_025_58741_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58741_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58741_2_test",
+  "exported_at": "2026-05-17T04:06:38Z"
+}
diff --git a/configs/s41467_025_58741_2_test/pip-clean.txt b/configs/s41467_025_58741_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9458ab30ce10c4b6b07d7bf2fba5fb970af82bb2
--- /dev/null
+++ b/configs/s41467_025_58741_2_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
+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
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+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
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diff --git a/configs/s41467_025_58741_2_test/pip-freeze.txt b/configs/s41467_025_58741_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f9eb7ca1921a25a5858817f4a648d42c7c7c2e1
--- /dev/null
+++ b/configs/s41467_025_58741_2_test/pip-freeze.txt
@@ -0,0 +1,451 @@
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+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_59099_1_test/editable.txt b/configs/s41467_025_59099_1_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_59099_1_test/env.yml b/configs/s41467_025_59099_1_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e8dcb76e891257b088b7b3d3b15629b2e6f8e347
--- /dev/null
+++ b/configs/s41467_025_59099_1_test/env.yml
@@ -0,0 +1,48 @@
+name: s41467_025_59099_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:
+    - 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
+    - pandas==2.0.3
+    - 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
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_59099_1_test
diff --git a/configs/s41467_025_59099_1_test/explicit.txt b/configs/s41467_025_59099_1_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_59099_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_59099_1_test/meta.json b/configs/s41467_025_59099_1_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3323d4277ac7fe90e94de2104df0c99fbe0eebef
--- /dev/null
+++ b/configs/s41467_025_59099_1_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_59099_1_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_59099_1_test",
+  "exported_at": "2026-05-17T04:06:40Z"
+}
diff --git a/configs/s41467_025_59099_1_test/pip-clean.txt b/configs/s41467_025_59099_1_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecaaa038f8a14af671a3ebd3d0001a97bd679ec9
--- /dev/null
+++ b/configs/s41467_025_59099_1_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
+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
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+narwhals==1.42.1
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+nest-asyncio==1.6.0
+netCDF4==1.7.2
+neuroHarmonize==2.4.5
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+nltk==3.8.1
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+onnxruntime==1.15.1
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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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+pfzy==0.3.4
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+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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+pondpond==1.4.1
+pooch==1.8.2
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+pulsar-client==3.5.0
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+Pyomo==6.8.2
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+pysqlite3-binary==0.5.2.post3
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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
+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
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+regex==2022.4.24
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+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
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+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_59099_1_test/pip-freeze.txt b/configs/s41467_025_59099_1_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecaaa038f8a14af671a3ebd3d0001a97bd679ec9
--- /dev/null
+++ b/configs/s41467_025_59099_1_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
+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
+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_59198_z_test/editable.txt b/configs/s41467_025_59198_z_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_59198_z_test/env.yml b/configs/s41467_025_59198_z_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ee8cf7f71ef16d2193a16864d5f104f35abf31cc
--- /dev/null
+++ b/configs/s41467_025_59198_z_test/env.yml
@@ -0,0 +1,48 @@
+name: s41467_025_59198_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:
+    - appdirs==1.4.4
+    - certifi==2026.4.22
+    - h5py==3.11.0
+    - idna==3.13
+    - networkx==3.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - pennylane==0.33.1
+    - pennylane-lightning==0.34.0
+    - requests==2.32.4
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_59198_z_test
diff --git a/configs/s41467_025_59198_z_test/explicit.txt b/configs/s41467_025_59198_z_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_59198_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
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diff --git a/configs/s41467_025_59198_z_test/meta.json b/configs/s41467_025_59198_z_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2cb9d00758d76d6735913f24257b887cc6bada8e
--- /dev/null
+++ b/configs/s41467_025_59198_z_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_59198_z_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_59198_z_test",
+  "exported_at": "2026-05-17T04:06:42Z"
+}
diff --git a/configs/s41467_025_59198_z_test/pip-clean.txt b/configs/s41467_025_59198_z_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..560668525b761dfb8117ba76854b6131850e9525
--- /dev/null
+++ b/configs/s41467_025_59198_z_test/pip-clean.txt
@@ -0,0 +1,453 @@
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diff --git a/configs/s41467_025_59198_z_test/pip-freeze.txt b/configs/s41467_025_59198_z_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..560668525b761dfb8117ba76854b6131850e9525
--- /dev/null
+++ b/configs/s41467_025_59198_z_test/pip-freeze.txt
@@ -0,0 +1,453 @@
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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
+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
+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==3.13
+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
+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
+PennyLane==0.33.1
+PennyLane-Lightning==0.34.0
+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
+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_59847_3_test/editable.txt b/configs/s41467_025_59847_3_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_59847_3_test/env.yml b/configs/s41467_025_59847_3_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f2eaf172ab6de1a7c3d2aa673076d2e5a59c56b6
--- /dev/null
+++ b/configs/s41467_025_59847_3_test/env.yml
@@ -0,0 +1,56 @@
+name: s41467_025_59847_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
+    - filelock==3.16.1
+    - fonttools==4.57.0
+    - fsspec==2025.3.0
+    - h5py==3.11.0
+    - 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
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - scipy==1.10.1
+    - 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_59847_3_test
diff --git a/configs/s41467_025_59847_3_test/explicit.txt b/configs/s41467_025_59847_3_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_59847_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_59847_3_test/meta.json b/configs/s41467_025_59847_3_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3f2a13f28b2064c41cf76b2a874ce0bac5d3b481
--- /dev/null
+++ b/configs/s41467_025_59847_3_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_59847_3_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_59847_3_test",
+  "exported_at": "2026-05-17T04:06:53Z"
+}
diff --git a/configs/s41467_025_59847_3_test/pip-clean.txt b/configs/s41467_025_59847_3_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ce1be6530c684bb9642b5d63c844305218bd5ac
--- /dev/null
+++ b/configs/s41467_025_59847_3_test/pip-clean.txt
@@ -0,0 +1,457 @@
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diff --git a/configs/s41467_025_59847_3_test/pip-freeze.txt b/configs/s41467_025_59847_3_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ce1be6530c684bb9642b5d63c844305218bd5ac
--- /dev/null
+++ b/configs/s41467_025_59847_3_test/pip-freeze.txt
@@ -0,0 +1,457 @@
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+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
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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
+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-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
+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
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+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_59917_6_test/editable.txt b/configs/s41467_025_59917_6_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_59917_6_test/env.yml b/configs/s41467_025_59917_6_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0a39a1dd11a57392aad0434a474f5cbdcffc17b1
--- /dev/null
+++ b/configs/s41467_025_59917_6_test/env.yml
@@ -0,0 +1,46 @@
+name: s41467_025_59917_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:
+    - 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_59917_6_test
diff --git a/configs/s41467_025_59917_6_test/explicit.txt b/configs/s41467_025_59917_6_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_59917_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_025_59917_6_test/meta.json b/configs/s41467_025_59917_6_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2878bd00e92f055844650ae7775238b7d9c23dc8
--- /dev/null
+++ b/configs/s41467_025_59917_6_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_59917_6_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_59917_6_test",
+  "exported_at": "2026-05-17T04:06:53Z"
+}
diff --git a/configs/s41467_025_59917_6_test/pip-clean.txt b/configs/s41467_025_59917_6_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_59917_6_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
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+torchaudio==2.1.2+cu118
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+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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+word2number==1.1
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+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/s41467_025_59917_6_test/pip-freeze.txt b/configs/s41467_025_59917_6_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09370617fe1b88cd427bed865d3a16a9cc519bfb
--- /dev/null
+++ b/configs/s41467_025_59917_6_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
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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
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+better-abc==0.0.3
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+chaospy==3.3.9
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+click==8.1.7
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+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
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+cryptography==42.0.5
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+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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+editdistance==0.6.0
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+et-xmlfile==1.1.0
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+fairseq==0.10.2
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+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+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_60306_2_test/editable.txt b/configs/s41467_025_60306_2_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_60306_2_test/env.yml b/configs/s41467_025_60306_2_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..886b84df266551fbf066d37930243b30bfefd1f3
--- /dev/null
+++ b/configs/s41467_025_60306_2_test/env.yml
@@ -0,0 +1,38 @@
+name: s41467_025_60306_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:
+    - numpy==1.24.4
+    - packaging==25.0
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_60306_2_test
diff --git a/configs/s41467_025_60306_2_test/explicit.txt b/configs/s41467_025_60306_2_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_60306_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_60306_2_test/meta.json b/configs/s41467_025_60306_2_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0d665e876b6dbad93e784f398560773f4ed0c2da
--- /dev/null
+++ b/configs/s41467_025_60306_2_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_60306_2_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_60306_2_test",
+  "exported_at": "2026-05-17T04:06:52Z"
+}
diff --git a/configs/s41467_025_60306_2_test/pip-clean.txt b/configs/s41467_025_60306_2_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_025_60306_2_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
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+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
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+numpoly==1.0.6
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+openpyxl==3.0.9
+opentelemetry-api==1.24.0
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+packaging==26.2
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+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
+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_60306_2_test/pip-freeze.txt b/configs/s41467_025_60306_2_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7
--- /dev/null
+++ b/configs/s41467_025_60306_2_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
+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
+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
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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
+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
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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
+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
+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_60898_9_test/editable.txt b/configs/s41467_025_60898_9_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_60898_9_test/env.yml b/configs/s41467_025_60898_9_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6914fb6c1e735a90524f3c750cfa81dabeb51c9b
--- /dev/null
+++ b/configs/s41467_025_60898_9_test/env.yml
@@ -0,0 +1,56 @@
+name: s41467_025_60898_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:
+    - attrs==25.3.0
+    - certifi==2026.2.25
+    - charset-normalizer==3.4.3
+    - 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
+    - packaging==25.0
+    - psutil==7.2.2
+    - pyparsing==3.1.4
+    - 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+cpu
+    - typing-extensions==4.13.2
+    - urllib3==2.2.3
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_60898_9_test
diff --git a/configs/s41467_025_60898_9_test/explicit.txt b/configs/s41467_025_60898_9_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_60898_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_60898_9_test/meta.json b/configs/s41467_025_60898_9_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..fef744fb140ba86c1f61ef83150ced564d9e295b
--- /dev/null
+++ b/configs/s41467_025_60898_9_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_60898_9_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_60898_9_test",
+  "exported_at": "2026-05-17T04:07:04Z"
+}
diff --git a/configs/s41467_025_60898_9_test/pip-clean.txt b/configs/s41467_025_60898_9_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15f922a6c3dc0a18c3e7d31475e623c34a6c4f29
--- /dev/null
+++ b/configs/s41467_025_60898_9_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
+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==3.16.1
+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
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+mrcfile==1.5.4
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+msg-parser==1.2.0
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+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
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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
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+PICOS==2.6.1
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+python-dateutil==2.9.0.post0
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+referencing==0.35.1
+regex==2022.4.24
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+responses==0.16.0
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+rouge-score==0.1.2
+rpds-py==0.20.1
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+sentence-transformers==2.2.2
+sentencepiece==0.1.91
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+session_info==1.0.1
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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==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/s41467_025_60898_9_test/pip-freeze.txt b/configs/s41467_025_60898_9_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15f922a6c3dc0a18c3e7d31475e623c34a6c4f29
--- /dev/null
+++ b/configs/s41467_025_60898_9_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
+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==3.16.1
+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-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
+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+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/s41467_025_61628_x_test/editable.txt b/configs/s41467_025_61628_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_61628_x_test/env.yml b/configs/s41467_025_61628_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e5ebed325711b5227e6f493e8d60dd8debc1b94d
--- /dev/null
+++ b/configs/s41467_025_61628_x_test/env.yml
@@ -0,0 +1,51 @@
+name: s41467_025_61628_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:
+    - anndata==0.9.2
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - h5py==3.11.0
+    - 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
+    - scanpy==1.9.8
+    - scikit-learn==1.3.2
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_61628_x_test
diff --git a/configs/s41467_025_61628_x_test/explicit.txt b/configs/s41467_025_61628_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_61628_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
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diff --git a/configs/s41467_025_61628_x_test/meta.json b/configs/s41467_025_61628_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..74059819f37d6475f967ceee954b666ac3b4a6f7
--- /dev/null
+++ b/configs/s41467_025_61628_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_61628_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_61628_x_test",
+  "exported_at": "2026-05-17T04:07:08Z"
+}
diff --git a/configs/s41467_025_61628_x_test/pip-clean.txt b/configs/s41467_025_61628_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cd52baa032c7c19f779427459a3247274eb69fe
--- /dev/null
+++ b/configs/s41467_025_61628_x_test/pip-clean.txt
@@ -0,0 +1,456 @@
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diff --git a/configs/s41467_025_61628_x_test/pip-freeze.txt b/configs/s41467_025_61628_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cd52baa032c7c19f779427459a3247274eb69fe
--- /dev/null
+++ b/configs/s41467_025_61628_x_test/pip-freeze.txt
@@ -0,0 +1,456 @@
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+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
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+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
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+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
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+icetk==0.0.4
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+iniconfig==1.1.1
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+jaxtyping==0.2.19
+Jinja2==3.1.6
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+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
+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
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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
+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
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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-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
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+requests-oauthlib==1.3.0
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+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
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+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
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+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scanpy==1.9.8
+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
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+streamlit-aggrid==0.3.4.post3
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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
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+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
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+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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+tzdata==2024.1
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+vtk==9.3.1
+wandb==0.22.0
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+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
+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/s41467_025_62292_x_test/editable.txt b/configs/s41467_025_62292_x_test/editable.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/configs/s41467_025_62292_x_test/env.yml b/configs/s41467_025_62292_x_test/env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..ae509e602bd750127ca4a6d0ed96653a0f87d5fb
--- /dev/null
+++ b/configs/s41467_025_62292_x_test/env.yml
@@ -0,0 +1,37 @@
+name: s41467_025_62292_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_025_62292_x_test
diff --git a/configs/s41467_025_62292_x_test/explicit.txt b/configs/s41467_025_62292_x_test/explicit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc
--- /dev/null
+++ b/configs/s41467_025_62292_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_62292_x_test/meta.json b/configs/s41467_025_62292_x_test/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5e8f004f2cd53b2c12ee5d919bd21b66128a452e
--- /dev/null
+++ b/configs/s41467_025_62292_x_test/meta.json
@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_62292_x_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_62292_x_test",
+  "exported_at": "2026-05-17T04:07:10Z"
+}
diff --git a/configs/s41467_025_62292_x_test/pip-clean.txt b/configs/s41467_025_62292_x_test/pip-clean.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_025_62292_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
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+tzdata==2024.1
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+unstructured==0.11.0
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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
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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/s41467_025_62292_x_test/pip-freeze.txt b/configs/s41467_025_62292_x_test/pip-freeze.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb
--- /dev/null
+++ b/configs/s41467_025_62292_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
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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
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+async-timeout==4.0.3
+attrs==25.3.0
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+Babel==2.9.1
+backoff==2.2.1
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+coloredlogs==15.0.1
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+dataclasses==0.6
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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