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chore!: remove old positional compat#3984

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flying-sheep wants to merge 6 commits intomainfrom
pa/rm-old-positionals
Open

chore!: remove old positional compat#3984
flying-sheep wants to merge 6 commits intomainfrom
pa/rm-old-positionals

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@flying-sheep flying-sheep commented Feb 23, 2026

  • Closes #
  • Tests included or not required because:

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codecov bot commented Feb 23, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.94%. Comparing base (e8dc05d) to head (c4ca288).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3984      +/-   ##
==========================================
- Coverage   78.28%   77.94%   -0.34%     
==========================================
  Files         117      117              
  Lines       12635    12506     -129     
==========================================
- Hits         9891     9748     -143     
- Misses       2744     2758      +14     
Flag Coverage Δ
hatch-test.low-vers 77.22% <100.00%> (-0.35%) ⬇️
hatch-test.pre 76.88% <100.00%> (-0.35%) ⬇️

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

Files with missing lines Coverage Δ
src/scanpy/_compat.py 70.93% <100.00%> (-0.67%) ⬇️
src/scanpy/_settings/__init__.py 86.03% <100.00%> (-0.06%) ⬇️
src/scanpy/datasets/_datasets.py 90.90% <100.00%> (-0.08%) ⬇️
src/scanpy/external/exporting.py 12.28% <ø> (-1.11%) ⬇️
src/scanpy/external/pl.py 30.00% <100.00%> (-1.53%) ⬇️
src/scanpy/external/pp/_bbknn.py 45.45% <ø> (-8.40%) ⬇️
src/scanpy/external/pp/_dca.py 40.00% <ø> (-10.00%) ⬇️
src/scanpy/external/pp/_harmony_integrate.py 42.85% <ø> (-7.15%) ⬇️
src/scanpy/external/pp/_hashsolo.py 88.03% <ø> (-0.21%) ⬇️
src/scanpy/external/pp/_scanorama_integrate.py 22.22% <ø> (-5.37%) ⬇️
... and 43 more

... and 1 file with indirect coverage changes

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Is this Scanpy 2.0 or you want to do this right now?

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flying-sheep commented Feb 24, 2026

right now, these all existed for some time.

there’s going to be enough complexity around parameters in the time leading up to 2.0, I won’t drag around years old deprecations.

@flying-sheep flying-sheep marked this pull request as ready for review February 24, 2026 09:13
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