requirements.txt

# 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