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docs: switch to sphinx-exec-jupyter#4182

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flying-sheep wants to merge 6 commits into
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docs: switch to sphinx-exec-jupyter#4182
flying-sheep wants to merge 6 commits into
mainfrom
pa/scverse-misc

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@flying-sheep

@flying-sheep flying-sheep commented Jun 25, 2026

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It’s a bit slower (212 sec → 274 sec) but all docs pages are run in isolation and the docs logs aren’t spammed with warnings that happen during plot execution.

Also it locally caches the plot code execution, so things should be faster locally with a populated cache.

  • Closes #
  • Tests included or not required because:

TODO:

  • add mode that only runs each page in isolation, not each code block

@codecov

codecov Bot commented Jun 25, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.72%. Comparing base (68eeb6a) to head (07c29d0).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #4182   +/-   ##
=======================================
  Coverage   79.72%   79.72%           
=======================================
  Files         120      120           
  Lines       12833    12833           
=======================================
  Hits        10231    10231           
  Misses       2602     2602           
Flag Coverage Δ
hatch-test.low-vers 78.78% <ø> (ø)
hatch-test.pre 79.59% <ø> (+0.01%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/metrics/_metrics.py 97.14% <ø> (ø)
src/scanpy/plotting/_anndata.py 85.42% <ø> (ø)
src/scanpy/plotting/_dotplot.py 94.87% <ø> (ø)
src/scanpy/plotting/_matrixplot.py 96.51% <ø> (ø)
src/scanpy/plotting/_preprocessing.py 86.27% <ø> (ø)
src/scanpy/plotting/_qc.py 86.11% <ø> (ø)
src/scanpy/plotting/_stacked_violin.py 85.78% <ø> (ø)
src/scanpy/plotting/_tools/__init__.py 76.17% <ø> (ø)
src/scanpy/plotting/_tools/paga.py 64.26% <ø> (ø)
src/scanpy/plotting/_tools/scatterplots.py 83.41% <ø> (ø)
... and 2 more

@flying-sheep flying-sheep added this to the 1.13.0 milestone Jun 26, 2026
@flying-sheep flying-sheep marked this pull request as ready for review June 26, 2026 12:46
@flying-sheep flying-sheep requested a review from ilan-gold June 26, 2026 12:55
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