`squidpy==1.6.1` not compatible with `anndata>=0.11.0`

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

BSD 3-Clause "New" or "Revised" License

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`squidpy==1.6.1` not compatible with `anndata>=0.11.0` #890

Closed alam-shahul closed 1 month ago

alam-shahul commented 2 months ago

Due to changes in how AnnData handles sparse arrays/matrices, squidpy==1.6.1 is not compatible with anndata>=0.11.0. A simple fix would be to keep using sparse matrices instead of sparse arrays, and change the names in SquidPy accordingly.