numpy
scipy
pandas
torch
pydantic
pydantic-settings
pyyaml
rich
rootutils
tqdm
python-dotenv>=1.2.2
safetensors
polars
cloudpickle
submitit
biotite
atomworks[catcif,ml]<4,>=3.0.1
peppr
catcif-tools
absl-py
hpccm

[all]
chaperone-pipelines[cli,dev,docs,notebook,pyrosetta,rna]

[cli]

[cloud]
modal<2,>=1.6.1

[dev]
setuptools>=77.0.3
pytest
pytest-xdist
ruff==0.6.2
pre-commit==3.7.*
ipython
icecream
ipdb
wandb

[docs]
mkdocs>=1.6.0
mkdocs-material>=9.5.0
mkdocstrings[python]>=0.26.0
mkdocs-gen-files>=0.5.0
mkdocs-literate-nav>=0.6.1

[ligand]
dimorphite-dl

[notebook]
matplotlib
seaborn
ipykernel
jupytext
papermill

[plip]
plip

[pyrosetta]
pyrosetta-installer

[rna]
ViennaRNA
tmtools
