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,>=1.15
statsmodels>=0.14.5
threadpoolctl>=3.5.0
tqdm>=4.60
umap-learn>=0.5.12
zarr>=3.2.0
obstore>=0.5.1
huggingface-hub>=2.0.0
zstandard>=0.25.0
igraph>=1.0.0

[agent]
pydantic-ai-slim[openai]>=2.51.0

[cytebase]
duckdb>=1.5.5
httpx>=0.28.1
matplotlib>=3.9
pytz>=2026.3.post1
seaborn>=0.13

[docs]
mystmd>=1.11.0
jupytext>=1.19.6
ipykernel>=7.3.0
nbclient
myst-parser
sphinx
sphinx_autodoc_typehints
sphinx-book-theme
sphinx-copybutton

[docs:sys_platform == "linux" and platform_machine == "x86_64"]
sgtsnepi>=0.7

[extra]
anndata>=0.12
kneed>=0.8.1
matplotlib>=3.9
seaborn>=0.13
ipython-autotime>=0.3
ipywidgets>=8

[test]
pytest>=7.0
pytest-cov>=4
pytest-xdist>=3
anndata>=0.12
scikit-network>=0.33.1
rdata>=1.1.0
pydantic-ai-slim[openai]>=2.51.0

[test:sys_platform == "linux" and platform_machine == "x86_64"]
sgtsnepi>=0.7

[tsne]
sgtsnepi>=0.7
