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Update for cope with issue introduced in umap-learn 0.5.2 #2028

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merged 4 commits into from
Nov 3, 2021

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lmcinnes
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As of umap-learn 0.5.2 an n_epochs value of 0 is now a valid value and None is used instead to indicate a value should be generated. To maintain forward compatability and backward compatibility with older umap-learn versions we instead make use of the epch setting criterion internal to umap-learn here directly. This should resolve issue #2026 and lmcinnes/umap#798

As of umap-learn 0.5.2 an ``n_epochs`` value of 0 is now a valid value and None is used instead to indicate a value should be generated. To maintain forward compatability and backward compatibility with older umap-learn versions we instead make use of the epch setting criterion internal to umap-learn here directly. This should resolve issue scverse#2026 and lmcinnes/umap#798
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codecov bot commented Oct 29, 2021

Codecov Report

Merging #2028 (a7d60e0) into master (1b74015) will increase coverage by 0.01%.
The diff coverage is 100.00%.

❗ Current head a7d60e0 differs from pull request most recent head 91aa733. Consider uploading reports for the commit 91aa733 to get more accurate results

@@            Coverage Diff             @@
##           master    #2028      +/-   ##
==========================================
+ Coverage   71.63%   71.64%   +0.01%     
==========================================
  Files          92       92              
  Lines       11248    11252       +4     
==========================================
+ Hits         8057     8062       +5     
+ Misses       3191     3190       -1     
Impacted Files Coverage Δ
scanpy/tools/_ingest.py 68.33% <100.00%> (+0.12%) ⬆️
scanpy/tools/_score_genes.py 85.71% <100.00%> (+1.56%) ⬆️
scanpy/tools/_umap.py 74.24% <100.00%> (+0.39%) ⬆️

@Zethson
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Zethson commented Nov 1, 2021

Thanks!
@ivirshup umap-learn 0.52 was released 3 days ago. Maybe we should even push out a patch release? I expect that many people will run into this issue and be left confused.

@ivirshup ivirshup linked an issue Nov 3, 2021 that may be closed by this pull request
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@ivirshup ivirshup added this to the 1.8.2 milestone Nov 3, 2021
@ivirshup ivirshup enabled auto-merge (squash) November 3, 2021 13:35
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ivirshup commented Nov 3, 2021

Thanks for the fix!

I've just added a release note.

@ivirshup ivirshup merged commit cfcc5b0 into scverse:master Nov 3, 2021
meeseeksmachine pushed a commit to meeseeksmachine/scanpy that referenced this pull request Nov 3, 2021
ivirshup pushed a commit that referenced this pull request Nov 3, 2021
…n 0.5.2 (#2033)

Co-authored-by: Leland McInnes <leland.mcinnes@gmail.com>
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umap embedding not working as expected in umap-learn 0.5.2
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