environment.yml

name: allogen
channels:
  - pytorch
  - nvidia
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python=3.10
  - pip
  # Core scientific stack
  - numpy>=1.24
  - scipy>=1.10
  - pandas>=2.0
  - scikit-learn>=1.3
  - pyyaml>=6.0
  - tqdm>=4.65
  - matplotlib>=3.7
  # PyTorch (CUDA 11.8; change pytorch-cuda to match your driver, or drop for CPU-only)
  - pytorch>=2.0
  - pytorch-cuda=11.8
  # Protein structure
  - biopython>=1.80
  - mdtraj>=1.9
  # pip-only extras
  - pip:
      - einops>=0.6.0
      - wandb>=0.12.0
      - fair-esm>=2.0.0