| name: dnabind3 | |
| channels: | |
| - conda-forge | |
| - defaults | |
| dependencies: | |
| - python=3.10 | |
| - pip>=24 | |
| # compiled / heavy libs via conda-forge | |
| - numpy>=2.0,<3.0 | |
| - scikit-learn>=1.5,<1.7 | |
| - pandas>=2.2,<2.3 | |
| - matplotlib>=3.8,<3.11 | |
| - lxml>=5.2,<6 | |
| - lightning=2.5.1 | |
| - torchmetrics>=1.3 | |
| - dask | |
| - distributed | |
| - dask-ml | |
| # toolchain for JIT/building CUDA extensions (mamba-ssm, Triton kernels) | |
| - cuda-toolkit=12.4 | |
| - cmake | |
| - ninja | |
| - pip: | |
| # Force CUDA wheels and keep them from being overwritten by CPU builds | |
| - --index-url=https://download.pytorch.org/whl/cu124 | |
| - torch==2.6.0+cu124 | |
| # HF stack + hard deps used at runtime | |
| - transformers==4.53.0 | |
| - tokenizers>=0.21,<0.22 | |
| - safetensors>=0.4.3 | |
| - huggingface-hub==0.34.4 | |
| - regex | |
| # Your libs | |
| - rootutils==1.0.7 | |
| - hydra-core==1.3.2 | |
| - hydra-colorlog==1.2.0 | |
| - omegaconf==2.3.0 | |
| - pymex==0.9.31 | |
| - gitpython==3.1.44 | |
| - black==25.1.0 | |
| - tqdm==4.67.1 | |
| - biopython==1.85 | |
| - ortools==9.14.6206 | |
| - fair-esm==2.0.0 | |
| - rich==14.1.0 | |
| - wandb==0.21.1 | |
| # Mamba + Triton (for CUDA kernels) | |
| - mamba-ssm==2.2.4 | |
| - triton>=3.0,<3.5 | |
| # your package | |
| - -e . | |