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ExperimentAxisQuery - to_anndata obsp/varp as sparse matrices #3387

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merged 2 commits into from
Nov 25, 2024

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@bkmartinjr bkmartinjr commented Nov 25, 2024

Issue and/or context:

Fixes #3360

Changes:

obsp/varp slots in the AnnData returned by ExperimentAxisQuery.to_anndata will be sparse matrices. Previously they were dense NDArray.

Notes for Reviewer:

  1. this required a bit of refactoring
  2. as part of this, obsp/varp will be read using the partitioned reader (same as X layers)

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codecov bot commented Nov 25, 2024

Codecov Report

Attention: Patch coverage is 97.14286% with 1 line in your changes missing coverage. Please review.

Project coverage is 85.97%. Comparing base (d1178ae) to head (83e778f).
Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3387      +/-   ##
==========================================
+ Coverage   85.87%   85.97%   +0.09%     
==========================================
  Files          55       55              
  Lines        6143     6144       +1     
==========================================
+ Hits         5275     5282       +7     
+ Misses        868      862       -6     
Flag Coverage Δ
python 85.97% <97.14%> (+0.09%) ⬆️

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Components Coverage Δ
python_api 85.97% <97.14%> (+0.09%) ⬆️
libtiledbsoma ∅ <ø> (∅)

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🚢

@bkmartinjr bkmartinjr merged commit 1a3ee19 into main Nov 25, 2024
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@bkmartinjr bkmartinjr deleted the bkmartinjr/3360-sparse-obsp branch November 25, 2024 21:42
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Successfully merging this pull request may close these issues.

[python] Inconsistency in to_anndata density/sparsity of obsp/varp
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