ATOMICA/environment.yml at main · mims-harvard/ATOMICA · GitHub

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name: atomica-env
channels:
  - pytorch
  - nvidia
  - conda-forge
  - defaults

dependencies:
  # Python version
  - python=3.11

  # PyTorch with CUDA 11.8
  - pytorch==2.1.1
  - pytorch-cuda=11.8

  # Core scientific computing (faster from conda)
  - numpy==1.26.4
  - scipy==1.13.1
  - pandas==2.2.3
  - scikit-learn==1.5.2

  # Visualization
  - matplotlib==3.9.2
  - seaborn==0.13.2
  - plotly==5.24.1

  # Utilities
  - networkx==3.2.1
  - tqdm==4.66.5
  - joblib==1.4.2
  - sympy==1.13.3

  # Development tools
  - pytest
  - jupyter
  - ipywidgets

  # pip dependencies (packages not available or better from pip)
  - pip
  - pip:
      # PyTorch Geometric dependencies (need special wheel index)
      - torch-scatter==2.1.2 --find-links https://pytorch-geometric.com/whl/torch-2.1.1+cu118.html
      - torch-cluster==1.6.3 --find-links https://pytorch-geometric.com/whl/torch-2.1.1+cu118.html

      # Chemistry and structure libraries (not in conda or better from pip)
      - rdkit-pypi==2022.9.5
      - openbabel-wheel==3.1.1.20
      - biopython==1.84
      - biotite==0.40.0
      - e3nn==0.5.1

      # Data processing
      - pyarrow==21.0.0
      - orjson==3.10.16

      # ML utilities
      - umap-learn==0.5.6

      # Logging and experiment tracking
      - wandb==0.18.2
      - tensorboard==2.18.0

      # ATOMICA package (installed separately as editable)
      # -e .