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Fix pandas and plotting warning #1065

Merged
merged 18 commits into from
May 31, 2023
Merged

Fix pandas and plotting warning #1065

merged 18 commits into from
May 31, 2023

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michalk8
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@michalk8 michalk8 commented May 23, 2023 •
edited by WeilerP
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Changes

Bug fixes

Fixes pandas>=2, removes setting attributes in get_df, Colorbar.draw() (deprecated; doesn't seem to have any effect) and uses scanpy.pp.log1p in log1p implementation. Also fixes some tests and ignores warning in tests.

Also incorporates the changes from #1059

Related issues

Closes #958
Closes #1037
Closes #1058
Closes theislab/cellrank#1018
Closes #1071

@michalk8 michalk8 added the bugfix Fixes a bug label May 23, 2023
@michalk8 michalk8 self-assigned this May 23, 2023
@michalk8 michalk8 changed the title Fix/pandas2.0 Fix pandas and plotting warning May 23, 2023
@michalk8 michalk8 requested a review from WeilerP May 23, 2023 15:15
WeilerP
WeilerP reviewed May 25, 2023
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Thanks, @michalk8. I only left minor comments (mainly moving unnecessary changes to separate PRs).

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@WeilerP WeilerP merged commit e8fa7a1 into theislab:master May 31, 2023
@michalk8 michalk8 deleted the fix/pandas2.0 branch June 7, 2023 19:09
@WeilerP WeilerP mentioned this pull request Jun 8, 2023
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@michalk8 michalk8 mentioned this pull request Jun 28, 2023
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@hiraksarkar
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hiraksarkar commented Aug 28, 2023 •
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Getting the same error with the below version

>  pd.__version__
'2.0.3'
> scv.__version__
'0.2.5'

@zhanghao-njmu zhanghao-njmu mentioned this pull request Aug 31, 2023
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