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chore: use memory store in tests - #2634

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flying-sheep merged 5 commits into
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ig/memory_store_for_tests
Sep 8, 2026
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chore: use memory store in tests#2634
flying-sheep merged 5 commits into
mainfrom
ig/memory_store_for_tests

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@ilan-gold

@ilan-gold ilan-gold commented Sep 4, 2026

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I try to resolve the problem "what if our zarr tests didn't take so long and we also didn't write SO much data during testing" by moving to memory stores where possible - there is still a test explicitly for local storage in tests/test_readwrite.py::test_readwrite_equivalent_h5ad_zarr (or where appropriate to not change) but otherwise, this should provide a big speedup!

  • Closes #
  • Tests added
  • Release note not necessary because: testing change

@ilan-gold ilan-gold added this to the 0.13.4 milestone Sep 4, 2026
@ilan-gold ilan-gold changed the title perf: use memory store in tests chore: use memory store in tests Sep 4, 2026
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codecov Bot commented Sep 4, 2026

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Codecov Report

❌ Patch coverage is 96.15385% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 85.84%. Comparing base (d75540e) to head (d4f8a71).
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/anndata/tests/helpers.py 92.85% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2634      +/-   ##
==========================================
- Coverage   87.66%   85.84%   -1.82%     
==========================================
  Files          49       49              
  Lines        8121     8138      +17     
==========================================
- Hits         7119     6986     -133     
- Misses       1002     1152     +150     
Files with missing lines Coverage Δ
src/anndata/experimental/merge.py 88.70% <100.00%> (+0.37%) ⬆️
src/anndata/tests/helpers.py 83.92% <92.85%> (-8.86%) ⬇️

... and 7 files with indirect coverage changes

@ilan-gold

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Not too shabby! https://github.com/scverse/anndata/actions/runs/33877901352/job/101039244161 for example took 13min but now it runs in 9min!

@ilan-gold
ilan-gold marked this pull request as ready for review September 4, 2026 15:42

@flying-sheep flying-sheep left a comment

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very nice! I tried doing the same for HDF5, but it seems to give no advantage, so I just backported the helper from there.

@flying-sheep
flying-sheep merged commit 26ba98f into main Sep 8, 2026
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flying-sheep deleted the ig/memory_store_for_tests branch September 8, 2026 09:37
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2 participants