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feat: add anndata.acc support to mask params - #4333

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flying-sheep wants to merge 5 commits into
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mask-acc
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feat: add anndata.acc support to mask params#4333
flying-sheep wants to merge 5 commits into
mainfrom
mask-acc

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@flying-sheep

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TODO:

  • probably good to unify _mask_arg with _check_mask?
  • think about if it makes sense to rename from mask_{obs,var} to mask:
    • not explicit from param name anymore which dim is masked
    • but explicit through argument (e.g. mask="obs.xy")
    • also good fit for functions that can operate on either axis (sample, aggregate) or allow to mask either or both axes (e.g. pca could be fit on a subset or scale could be called on a subset)

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Codecov Report

❌ Patch coverage is 96.82540% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.93%. Comparing base (a656a33) to head (dd09b9f).
⚠️ Report is 3 commits behind head on main.
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/get/get.py 94.11% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4333      +/-   ##
==========================================
- Coverage   81.98%   81.93%   -0.06%     
==========================================
  Files         134      134              
  Lines       13235    13028     -207     
==========================================
- Hits        10851    10674     -177     
+ Misses       2384     2354      -30     
Flag Coverage Δ
hatch-test.low-vers 78.80% <84.12%> (-0.27%) ⬇️
hatch-test.pre 81.80% <96.82%> (-0.06%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
src/scanpy/_docs.py 100.00% <100.00%> (ø)
src/scanpy/_settings/presets.py 93.15% <100.00%> (ø)
src/scanpy/_utils/__init__.py 75.57% <100.00%> (ø)
src/scanpy/experimental/pp/_normalization.py 92.75% <100.00%> (-1.93%) ⬇️
src/scanpy/get/_aggregated.py 95.28% <100.00%> (+0.03%) ⬆️
src/scanpy/preprocessing/_docs.py 100.00% <100.00%> (ø)
src/scanpy/preprocessing/_highly_variable_genes.py 94.63% <ø> (ø)
src/scanpy/preprocessing/_pca/__init__.py 90.76% <100.00%> (-0.75%) ⬇️
src/scanpy/preprocessing/_scale.py 100.00% <100.00%> (+10.41%) ⬆️
src/scanpy/preprocessing/_simple.py 90.99% <100.00%> (ø)
... and 3 more

@flying-sheep flying-sheep added this to the 1.13.0 milestone Sep 1, 2026
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anndata.acc based API for mask/mask_{obs,var}

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