anndata>=0.9
matplotlib>=3.6
numba>=0.57
numpy>=1.22
pandas>=1.5
POT==0.9.5
PyYAML>=6.0
scanpy>=1.9
statsmodels>=0.14.1
scikit-image>=0.20
scikit-learn>=1.2
scipy>=1.9
seaborn>=0.12
squidpy>=1.2
tqdm>=4.64
igraph
leidenalg
scikit-misc

[cci]
cellphonedb<6,>=5
omicverse==1.7.5
torch-geometric
torch
setuptools<81
transformers<5

[dev]
black
ruff
pytest
pytest-cov

[dev:python_version < "3.11"]
tomli

[pathway]
gseapy
networkx
omicverse==1.7.5
torch-geometric
torch
setuptools<81
transformers<5

[spatialdata]
spatialdata>=0.2

[tacco]
tacco==0.5.0

[trajectory]
omicverse==1.7.5
torch-geometric
torch
setuptools<81
transformers<5
