| # BoltzGen 0.3.2 on OneScience / Python 3.11 / DTK 25.04 / PyTorch 2.5.1 |
| # Install only after OneScience is installed: |
| # python -m pip install --no-deps -r requirements.txt |
|
|
| # Additional dependencies absent from the OneScience base inventory. |
| hydride |
| pydssp |
| logomaker |
| frozendict |
|
|
| # Compatibility upgrade validated on SCNet. Lightning 1.8.6 rejects the |
| # precision=bf16-mixed value used by BoltzGen. Install with --no-deps so this |
| # upgrade does not replace the OneScience/DTK PyTorch build. |
| pytorch-lightning==2.5.6 |
|
|
| # Supplied by OneScience; retained as the complete dependency inventory. |
| # Do not reinstall these packages over OneScience/DTK builds. |
| # torch==2.5.1 # DTK/DCU build supplied by OneScience |
| # numpy==1.26.3 # validated despite upstream pinning 2.0.2 |
| # numba |
| # matplotlib |
| # biotite==1.0.1 |
| # gemmi |
| # mashumaro==3.16 |
| # einx==0.3.0 |
| # einops>=0.7.0 |
| # scikit-learn>=1.2.2,<=1.6.0 |
| # hydra-core>=1.2.0 |
| # omegaconf>=2.3.0 |
| # rdkit>=2025.3.5 |
| # pandas>=2.2.2 |
| # biopython==1.84 |
| # huggingface_hub |
| # pyyaml>=6.0 |
| # scipy==1.14.1 |
| # tqdm>=4.60.0 |
| # torchmetrics |
| # pytorch-lightning==2.0.6 # OneScience inventory; upgraded above for BoltzGen |
| # wandb>=0.13.7 # training logging; disabled in smoke tests |
| # redis==7.0.0 |
| # nvidia-ml-py>=12.535.133 # NVIDIA monitoring only; not needed on DCU |
|
|
| # Declared upstream but not imported by the validated paths. |
| # edit-distance |
| # pdbeccdutils |
|
|
| # Optional: antibody/nanobody CDR logo generation during filtering only. |
| # abnumber |
|
|
| # NVIDIA CUDA 12-only extensions: intentionally disabled on DCU. |
| # cuequivariance_ops_cu12>=0.5.0 |
| # cuequivariance_ops_torch_cu12>=0.5.0 |
| # cuequivariance_torch>=0.5.0 |
|
|
