# deep learning
# Install with conda
torch>=2.1.0
torch_geometric
lightning>=2.1.0
torchmetrics
transformers
scikit-learn
dgl
dglgo
dgllife

# configuration and utilities
hydra-core
# hydra-colorlog
# hydra-optuna-sweeper
# hydra-submitit-launcher
pandas
swifter
# pre-commit
# rich
# pytest
# tensorboard

# feature extraction
biopython
rdkit
networkx>=3.2.0
mhfp
# tmap

# model-specific requirements
# subword-nmt  # MONN
tape_proteins  # TransformerCPI2
gensim # TransformerCPI
fair-esm  # CoaDTI-pro
# apex # recommended by TAPE-BERT

# data visualization utilities
seaborn
plotly