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theislab / scgen

Single cell perturbation prediction
https://scgen.readthedocs.io
GNU General Public License v3.0
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Update depreciated `AnnData.concatenate` #82

Open quentinblampey opened 1 year ago

quentinblampey commented 1 year ago

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 commented 1 year ago

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

Sophon-0 commented 1 year ago

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