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Catplot fix #2739

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merged 5 commits into from Nov 13, 2023
Merged

Catplot fix #2739

merged 5 commits into from Nov 13, 2023

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eroell
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@eroell eroell commented Nov 9, 2023

  • Release notes not necessary because:

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codecov bot commented Nov 9, 2023

Codecov Report

Merging #2739 (22e75c6) into master (8369414) will increase coverage by 0.20%.
The diff coverage is n/a.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #2739      +/-   ##
==========================================
+ Coverage   72.92%   73.13%   +0.20%     
==========================================
  Files         111      111              
  Lines       12134    12134              
==========================================
+ Hits         8849     8874      +25     
+ Misses       3285     3260      -25     
Files Coverage Δ
scanpy/plotting/_anndata.py 85.02% <ø> (+1.78%) ⬆️

... and 3 files with indirect coverage changes

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eroell commented Nov 9, 2023

test_pca failing here and here?

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To see tracebacks, you need to scroll up from the end past the enormous warnings list (I’m working on that), then you see the actual error

E           UserWarning: The problem size 5 minus the constraints size 0 is too small relative to the block size 4. Using a dense eigensolver instead of LOBPCG iterations.No output of the history of the iterations.

/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/scipy/sparse/linalg/_eigen/lobpcg/lobpcg.py:493: UserWarning

This test has stared to become flaky some time ago, needs some investigation to make this work reliably again.

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eroell commented Nov 9, 2023

Yeah noted there is an issue with scipy... Not related to this the single-line update?

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flying-sheep commented Nov 9, 2023

Not related to your changes, no.

You can see that e.g. the “PyTest anndata_dev” job succeeded

@eroell eroell added this to the 1.9.7 milestone Nov 9, 2023
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eroell commented Nov 10, 2023

thx!

@flying-sheep flying-sheep merged commit e8b6b00 into scverse:master Nov 13, 2023
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meeseeksmachine pushed a commit to meeseeksmachine/scanpy that referenced this pull request Nov 13, 2023
flying-sheep pushed a commit that referenced this pull request Nov 13, 2023
Co-authored-by: Eljas Roellin <65244425+eroell@users.noreply.github.com>
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Plotting with using scanpy.pl gives attribute error.
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