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scverse / mudata

Multimodal Data (.h5mu) implementation for Python
https://mudata.rtfd.io
BSD 3-Clause "New" or "Revised" License
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MuData is incompatible with AnnData v0.10.9 #77

Closed canergen closed 2 months ago

canergen commented 2 months ago

Import broken with AnnData version 0.10.9

System

  File "/home/cane/.local/share/hatch/env/virtual/scvi-tools/E5IuCX_W/scvi-tools/lib/python3.12/site-packages/mudata/_core/mudata.py", line 18, in <module>
    from anndata._core.aligned_mapping import (
ImportError: cannot import name 'AlignedViewMixin' from 'anndata._core.aligned_mapping' (/home/cane/.local/share/hatch/env/virtual/scvi-tools/E5IuCX_W/scvi-tools/lib/python3.12/site-packages/anndata/_core/aligned_mapping.py). Did you mean: 'AlignedView'?
ilan-gold commented 2 months ago

Before looking into this, I would like to point out that this is not part of our public API

ilan-gold commented 2 months ago

Also @gtca maybe worth adding a test for the latest AnnData branch as a CI job like scanpy does?

https://github.com/scverse/scanpy/blob/b6193502e11b84fc1b4a011ee9cf08a19da22ebf/.azure-pipelines.yml#L69-L74

gtca commented 2 months ago

@ilan-gold, there has been one already that pulls the version from https://github.com/scverse/anndata.

ilan-gold commented 2 months ago

@ilan-gold, there has been one already that pulls the version from https://github.com/scverse/anndata.

Great! I looked into this, but the issue isn't just exporting. Our API also changed, so just re-exporting hte AxisArraysView = AxisArrays doesn't seem to solve this