.environment.yml

name: TRILL_RTD
channels:
  - conda-forge
  - defaults
  - pytorch
  - pyg
  - nvidia
dependencies:
  - python=3.8
  - pip=24.0
  - openmm
  - swig
  - pdbfixer
  - llvm-openmp
  - pytorch=2.3.0=py3.8_cpu_0
  - cuda-cudart=11.8
  - cpuonly
  - pyg=2.6.1=py38_torch_2.3.0_cpu 
  - pytorch-cluster=1.6.3=py38_torch_2.3.0_cpu 
  - pytorch-sparse=0.6.18=py38_torch_2.3.0_cpu 
  - pytorch-scatter=2.1.2=py38_torch_2.3.0_cpu
  # - mkl=2024.1.0
  - pip:
    - torchmetrics==0.11.4
    - setuptools==69.5.1
    - lightning-fabric==2.3.0
    - h5py
    - loguru
    - setuptools
    - pytorch-lightning==1.7.7
    - transformers
    - datasets
    - biotite
    - bokeh
    - umap-learn
    - pyfiglet
    - fair-esm
    - GitPython
    - xgboost
    - pandas
    - rdkit
    - e3nn
    - biopython==1.81
    - spyrmsd
    - SentencePiece
    - omegaconf
    - hydra-core
    - icecream
    - chardet
    - cchardet
    - skops
    - fairscale
    # - deepspeed
    - sphinx-argparse
    - myst-parser
    - sphinx-rtd-dark-mode
    - sphinx-copybutton
    - biobb_vs
    - scikit-optimize