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fix: support umap-learn 0.6 - #4480

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fix-umap-0.6
Nov 4, 2026
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fix: support umap-learn 0.6#4480
flying-sheep merged 1 commit into
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fix-umap-0.6

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@flying-sheep flying-sheep commented Nov 4, 2026

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LLM usage

  • LLM or coding agent used:
  • If one was used, I, a human, have reviewed, understood and tested every changed line

@flying-sheep flying-sheep added this to the 1.12.6 milestone Nov 4, 2026
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Documentation build overview

📚 scanpy | 🛠️ Build #4671369 | 📁 Comparing 35d8ca0 against latest (a0f08da)

  🔍 Preview build  

3 files changed
± release-notes/index.html
± api/generated/scanpy.pp.calculate_qc_metrics.html
± api/generated/scanpy.settings.html

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codecov Bot commented Nov 4, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.41%. Comparing base (a0f08da) to head (35d8ca0).
✅ All tests successful. No failed tests found.

Additional details and impacted files 
@@           Coverage Diff           @@
##             main    #4480   +/-   ##
=======================================
  Coverage   84.41%   84.41%           
=======================================
  Files         134      134           
  Lines       12768    12770    +2     
=======================================
+ Hits        10778    10780    +2     
  Misses       1990     1990
Flag Coverage Δ
hatch-test.low-vers 81.19% <100.00%> (+<0.01%) ⬆️
hatch-test.pre 84.22% <100.00%> (+<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/neighbors/_connectivity.py 88.23% <ø> (ø)
src/scanpy/tools/_ingest.py 85.41% <100.00%> (+0.12%) ⬆️

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flying-sheep merged commit c1f5350 into main Nov 4, 2026
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flying-sheep deleted the fix-umap-0.6 branch November 4, 2026 13:02
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flying-sheep added a commit that referenced this pull request Nov 5, 2026
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Backport PR #4480: fix: support umap-learn 0.6
87e6050
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flying-sheep added a commit that referenced this pull request Nov 5, 2026
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docs: generate 1.12.6 release notes (and backport #4480) (#4485)
f044749
@jan-glx jan-glx mentioned this pull request Nov 11, 2026
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@LouisFaure LouisFaure mentioned this pull request Nov 11, 2026
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LouisFaure added a commit to LouisFaure/scFates that referenced this pull request Nov 11, 2026
@LouisFaure @claude
Release notes for v1.2.6
58084ca 
- Pin umap-learn<0.6 in the package dependencies (scanpy <=1.12.5 is
  incompatible with umap-learn 0.6, see scverse/scanpy#4480).
- Register the :issue: role via sphinx.ext.extlinks so issue references
  in the release notes render as links.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Integration Testing CI Test Failure on python 3.14 with prerelease dependencies

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