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Update depreciated `AnnData.concatenate`

Open quentinblampey opened this issue 2 years ago • 2 comments

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 avatar Jun 21 '23 12:06 quentinblampey

Oh I wanted to make a pull request for this, but I just shown this open PR (https://github.com/theislab/scgen/pull/77) that tries to solve this

quentinblampey avatar Jun 21 '23 12:06 quentinblampey

It would be nice to have the exact version of all modules.

Sophon-0 avatar Jul 19 '23 21:07 Sophon-0