foldtree2/environment-dev.yml at main · DessimozLab/foldtree2 · GitHub

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name: foldtree2-dev
channels:
  - pytorch
  - pyg
  - conda-forge
  - bioconda
  - defaults

dependencies:
  - python=3.10

  # Build tools
  - conda-build
  - anaconda-client
  - setuptools
  - wheel
  - pip

  # Core scientific computing
  - numpy>=1.21.0
  - pandas>=1.3.0
  - scipy>=1.7.0
  - matplotlib-base>=3.4.0

  # PyTorch ecosystem
  - pytorch>=2.0.0
  - pytorch-cuda=11.8  # or cpuonly for CPU-only builds
  - pytorch-geometric>=2.3.0

  # Bioinformatics tools
  - biopython>=1.79
  - prody>=2.0.0
  - pydssp>=1.0.0

  # Deep learning utilities
  - pytorch-lightning>=2.0.0
  - tensorboard>=2.10.0
  - einops>=0.6.0

  # Phylogenetics
  - ete3>=3.1.2
  - raxml-ng>=1.1.0
  - mafft>=7.450

  # Utilities
  - colour>=0.1.5
  - datasketch>=1.5.0
  - pebble>=5.0.0
  - tqdm>=4.62.0
  - h5py>=3.6.0
  - pyyaml>=5.4.0

  # Optional dependencies
  - transformers>=4.20.0

  # Development tools
  - pytest
  - pytest-cov
  - black
  - flake8
  - mypy
  - sphinx
  - sphinx_rtd_theme