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Use `scanpy` for reading matrixes

Open LucaMarconato opened this issue 8 months ago • 0 comments

We currently have a the custom implementation for reading matrices (copied from scanpy) in https://github.com/scverse/spatialdata-io/blob/main/src/spatialdata_io/readers/_utils/_read_10x_h5.py.

I would remove that code and use directly scanpy, which is already a dependency. I think initially the code was copied to minimize the number of dependencies (@giovp what this the case?) but then we chose to add scanpy anyway.

LucaMarconato avatar Mar 15 '25 13:03 LucaMarconato