notebook>=7.0.6
markov-clustering>=0.0.6.dev0
tensorboard>=0.9.0
protobuf>=3.20.1
dill>=0.3.8
pyarrow>=15.0.0
tables>=3.8.0
numpy<2.0,>=1.25
scipy>=1.13.1
h5py>=3.6.0
networkx>=2.6.3
matplotlib>=3.5.1
scikit-learn>=1.0.2
chart-studio>=1.1.0
pdb2sql>=0.5.1
python-louvain>=0.16
tqdm>=4.63.0
freesasa>=2.1.0
biopython>=1.81

[notebooks]
nbmake

[publishing]
build
twine
wheel

[test]
pytest>=7.4.0
bump2version
coverage
pycodestyle
pytest-cov
pytest-runner
coveralls
ruff>=0.3.0
