# configuration and utilities
hydra-core
pandas==2.0
# swifter
pandarallel
tensorboard
biopython
apscheduler
tinydb
email-validator

# deep learning
# Install with conda
torch==2.1
torch_geometric
lightning==2.1
torchdata==0.7.0
torchmetrics
transformers
scikit-learn
dgl
dgllife

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

# feature extraction
rdkit
py3Dmol
mordred
networkx
mhfp
panel==1.3.6
bokeh
plotly
seaborn
# tmap