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chore: remove external tests and deprecate sc.external - #3645

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chore: remove external tests and deprecate sc.external#3645
flying-sheep wants to merge 6 commits into
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pa/deprecate-external

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@flying-sheep

@flying-sheep flying-sheep commented May 26, 2025

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I’m not sure I’m happy with the recommendations, e.g. are the named ones really replacements for mnnpy?

Docs currently fail since we haven’t moved the functions we want to move yet

  • Release notes not necessary because:

@flying-sheep flying-sheep added this to the 1.12.0 milestone May 26, 2025
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codecov Bot commented May 26, 2025

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Codecov Report

❌ Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.32%. Comparing base (6b5405d) to head (e0ac683).
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/__init__.py 60.00% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3645      +/-   ##
==========================================
+ Coverage   80.01%   81.32%   +1.31%     
==========================================
  Files         132      132              
  Lines       13397    13036     -361     
==========================================
- Hits        10719    10602     -117     
+ Misses       2678     2434     -244     
Flag Coverage Δ
hatch-test.low-vers 79.50% <88.88%> (+1.26%) ⬆️
hatch-test.pre 81.19% <88.88%> (+1.31%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/external/pl.py 100.00% <ø> (+70.78%) ⬆️
src/scanpy/external/pp/_bbknn.py 100.00% <100.00%> (+54.54%) ⬆️
src/scanpy/external/pp/_hashsolo.py 14.47% <100.00%> (-73.57%) ⬇️
src/scanpy/external/pp/_magic.py 100.00% <100.00%> (+73.80%) ⬆️
src/scanpy/external/pp/_mnn_correct.py 100.00% <100.00%> (+77.77%) ⬆️
src/scanpy/external/pp/_scanorama_integrate.py 100.00% <100.00%> (+77.77%) ⬆️
src/scanpy/external/tl/_harmony_timeseries.py 100.00% <100.00%> (+71.42%) ⬆️
src/scanpy/external/tl/_palantir.py 58.33% <100.00%> (+31.86%) ⬆️
src/scanpy/external/tl/_phate.py 100.00% <100.00%> (+66.66%) ⬆️
src/scanpy/external/tl/_phenograph.py 100.00% <100.00%> (+74.35%) ⬆️
... and 5 more

@flying-sheep flying-sheep modified the milestones: 1.12.0, 1.13.0 Jan 23, 2026
@flying-sheep flying-sheep changed the title Remove external tests and deprecate sc.external chore: remove external tests and deprecate sc.external Aug 14, 2026
@flying-sheep
flying-sheep requested a review from Zethson August 14, 2026 14:28

@Zethson Zethson left a comment

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Sorry, I don't know more here than you do.

@deprecated(
Deprecation(
"1.13.0",
# TODO: better suggestion?

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Probably #4302 then.

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deprecate sc.external

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