h5py>=3.11
hnswlib>=0.8
leidenalg>=0.12
loguru>=0.7
networkx>=3
numba>=0.60
numcodecs>=0.16
numpy>=2
packaging
pandas>=2.2.2
scikit-learn>=1.5
scipy!=1.17.0,>=1.13
setuptools>=61
statsmodels>=0.14.2
threadpoolctl
tqdm>=4.60
umap-learn>=0.5.12
zarr>=3.2.0
obstore>=0.5.1
sgtsnepi
huggingface-hub>=1.24.0
zstandard>=0.25.0

[docs]
jinja2
jedi
myst-parser
myst-nb
sphinx
sphinx_autodoc_typehints
sphinx-book-theme
sphinx-copybutton
sphinx-external-toc
sphinx-tabs
topacedo
nbclient
jupyter-cache>=1.0.1
sphinx-reredirects>=1.1.0
sphinxcontrib-mermaid>=2.1.0

[extra]
anndata>=0.12
kneed>=0.8
matplotlib>=3.9
seaborn>=0.13
ipython-autotime>=0.3
ipywidgets>=8

[test]
pytest>=7.0
pytest-cov>=4
pytest-xdist>=3
topacedo>=0.2.10
anndata>=0.12
scikit-network>=0.33.1
rdata>=1.1.0
