setuptools<81,>=80.9.0
packaging<26,>=24.0
snakemake-interface-common==1.20.2
spatialdata<0.6,>=0.5.0
spatialdata-io<0.4,>=0.3.0
spatialdata-plot<0.3,>=0.2.11
dask<2025,>=2024.11.2
dask-expr<2,>=1.1.19
dask-image<2025,>=2024.5.3
xarray<2026,>=2025.1.2
pims<0.8,>=0.7
pooch<1.9,>=1.8.2
numpy<2.3,>=2.2.6
scanpy<1.11,>=1.10.4
anndata<0.13,>=0.12.0
umap-learn>=0.5.7
pandas<2.3,>=2.2.3
scipy<1.15,>=1.13.1
scikit-learn<1.8,>=1.7.2
numba<0.63,>=0.62.1
llvmlite<0.46,>=0.45.1
shapely<2.2,>=2.1.1
matplotlib<3.10,>=3.9.4
seaborn>=0.13.2
plotnine>=0.15.0
Pillow<12,>=11.3.0
zarr<3,>=2.18.7
h5py>=3.14.0
tifffile>=2025.8.28
imageio>=2.37.0
ome-zarr<0.12,>=0.11.1
statsmodels>=0.14.5
Pint>=0.25
pyarrow<22,>=21.0.0
click>=8.3.0
typer>=0.16.0
docopt>=0.6.2
PyYAML>=6.0.3
geosketch>=1.3
geopandas<1.1.2,>=1.1.1
pyogrio<0.13,>=0.12.1
pydeseq2>=0.5.2
harmonypy<0.1,>=0.0.10
bbknn<1.7,>=1.6.0
python-igraph<0.12,>=0.11.9
louvain>=0.8.2

[extended]
cell2location<0.2,>=0.1.5
opencv-python<4.14,>=4.13.0.92
scvi-tools<1.5,>=1.4.0
squidpy<1.7,>=1.6.5
napari-spatialdata<0.6,>=0.5.7
PyQt5==5.15.11
scikit-misc>=0.5.2
ipython<10,>=9.5.0
pyro-ppl<1.9.2,>=1.9.1
pyro-api<0.2,>=0.1.1
opt-einsum<4,>=3.3.0
cellphonedb<5.1,>=5.0.1
torch<2.9,>=2.8.0
pytorch-lightning<2.6,>=2.5.5
cellcharter<0.4,>=0.3.5
cytoolz<2,>=1.0.1
ktplotspy<0.4,>=0.3.3
liana<1.7,>=1.6.1
loompy<3.1,>=3.0.8
pyscenic<0.13,>=0.12.1
distributed<2025,>=2024.11.2
leidenalg<0.11,>=0.10.2
