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feat: Allow using accessors in sc.get.aggregate#4199

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flying-sheep wants to merge 19 commits into
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aggregate-dim
Open

feat: Allow using accessors in sc.get.aggregate#4199
flying-sheep wants to merge 19 commits into
mainfrom
aggregate-dim

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  • Closes #
  • Tests included or not required because:

@codecov

codecov Bot commented Jul 6, 2026

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Codecov Report

❌ Patch coverage is 95.55556% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.03%. Comparing base (dde009a) to head (82bb6ad).
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/get/get.py 91.66% 8 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4199      +/-   ##
==========================================
+ Coverage   79.91%   80.03%   +0.12%     
==========================================
  Files         121      121              
  Lines       12949    13030      +81     
==========================================
+ Hits        10348    10429      +81     
  Misses       2601     2601              
Flag Coverage Δ
hatch-test.low-vers 78.98% <82.22%> (-0.06%) ⬇️
hatch-test.pre 79.94% <91.66%> (+0.07%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/_settings/presets.py 90.97% <100.00%> (+0.12%) ⬆️
...c/scanpy/experimental/pp/_highly_variable_genes.py 94.23% <100.00%> (ø)
src/scanpy/experimental/pp/_normalization.py 94.56% <100.00%> (ø)
src/scanpy/get/__init__.py 100.00% <ø> (ø)
src/scanpy/get/_aggregated.py 96.60% <100.00%> (+2.68%) ⬆️
src/scanpy/metrics/_gearys_c.py 100.00% <100.00%> (ø)
src/scanpy/metrics/_morans_i.py 100.00% <100.00%> (ø)
src/scanpy/preprocessing/_highly_variable_genes.py 94.63% <100.00%> (ø)
src/scanpy/preprocessing/_normalization.py 94.66% <100.00%> (ø)
src/scanpy/preprocessing/_pca/__init__.py 91.92% <100.00%> (ø)
... and 7 more

@flying-sheep flying-sheep changed the title WIP aggregate AdRef Aggregate AdRef Jul 7, 2026
@flying-sheep flying-sheep requested a review from ilan-gold July 7, 2026 06:37
@flying-sheep flying-sheep marked this pull request as ready for review July 7, 2026 06:37
@flying-sheep flying-sheep changed the title Aggregate AdRef feat: Allow using accessors in sc.get.aggregate Jul 7, 2026
Comment thread src/scanpy/get/_aggregated.py Outdated
@flying-sheep flying-sheep added this to the 1.13.0 milestone Jul 7, 2026

@ilan-gold ilan-gold left a comment

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I don't see any tests for the added behavior i.e., around by=A.obsm["foo"][:, 1]

Comment thread tests/test_aggregated.py Outdated
Comment thread src/scanpy/get/_aggregated.py Outdated
@flying-sheep flying-sheep requested a review from ilan-gold July 7, 2026 13:11
Comment thread tests/test_aggregated.py
@flying-sheep flying-sheep requested review from ilan-gold and removed request for ilan-gold July 9, 2026 07:05
@flying-sheep flying-sheep requested a review from ilan-gold July 14, 2026 12:47
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2 participants