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Update depreciated AnnData.concatenate #82

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quentinblampey opened this issue Jun 21, 2023 · 2 comments
Open

Update depreciated AnnData.concatenate #82

quentinblampey opened this issue Jun 21, 2023 · 2 comments

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@quentinblampey
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Hello,

The depreciated method AnnData.concatenate is used when running batch_removal (see here).

This only throws a warning with anndata==0.9 and pandas<2.0, but it crashes when using pandas==2.0.

I downgraded to pandas==1.5.2 and it works fine, but it could be great to use anndata.concat instead of AnnData.concatenate, as it would fix the bug for pandas==2.0!
@quentinblampey
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Oh I wanted to make a pull request for this, but I just shown this open PR (#77) that tries to solve this

@Sophon-0
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It would be nice to have the exact version of all modules.

@Koncopd Koncopd mentioned this issue Aug 10, 2023
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@Sophon-0 @quentinblampey