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♻️ Refactor CellxGeneAnnDataCatManager #2555

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merged 10 commits into from
Mar 14, 2025
Merged

♻️ Refactor CellxGeneAnnDataCatManager #2555

merged 10 commits into from
Mar 14, 2025

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sunnyosun
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@sunnyosun sunnyosun commented Mar 13, 2025

  • Removed exclude in CatManager classes
  • Refactored source fetching in CellxGeneAnnDataCatManager so the previous test passes: 🚚 Move Curator to lamindb cellxgene-lamin#120
  • save_ulabels_parentsave_ulabels_type
  • Deprecated _get_categoricals_defaults()categoricals_defaults
  • Removed support of adata=path to be consistent with AnnDataCurator, also backed access of obs doesn't allow mutations

@sunnyosun sunnyosun changed the title ♻️ Refactored CellxGeneAnnDataCatManager ♻️ Refactored CellxGeneAnnDataCatManager Mar 13, 2025
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codecov bot commented Mar 13, 2025

Codecov Report

Attention: Patch coverage is 85.32110% with 16 lines in your changes missing coverage. Please review.

Project coverage is 92.19%. Comparing base (cbe457a) to head (8918904).
Report is 10 commits behind head on main.

Files with missing lines Patch % Lines
lamindb/curators/__init__.py 75.00% 14 Missing ⚠️
lamindb/curators/_cellxgene_schemas/__init__.py 96.22% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2555      +/-   ##
==========================================
+ Coverage   92.15%   92.19%   +0.04%     
==========================================
  Files          60       60              
  Lines        9988     9960      -28     
==========================================
- Hits         9204     9183      -21     
+ Misses        784      777       -7     

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github-actions bot commented Mar 13, 2025

@github-actions github-actions bot temporarily deployed to pull request March 13, 2025 20:24 Inactive
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Awesome! Much better!

Moving much of this logic from a CatManager to a Schema(name="CellxGene v5.1.2") object can come in another PR.

We shouldn't need a CellxGeneCatManager; all its logic should be persisted in a schema object and then understood by the AnnDataCurator().

@falexwolf falexwolf changed the title ♻️ Refactored CellxGeneAnnDataCatManager ♻️ Refactore CellxGeneAnnDataCatManager Mar 13, 2025
@falexwolf falexwolf changed the title ♻️ Refactore CellxGeneAnnDataCatManager ♻️ Refactor CellxGeneAnnDataCatManager Mar 13, 2025
@sunnyosun sunnyosun merged commit 5734ae7 into main Mar 14, 2025
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@sunnyosun sunnyosun deleted the refactor-cxg branch March 14, 2025 12:44
@github-actions github-actions bot temporarily deployed to pull request March 14, 2025 12:48 Inactive
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2 participants