Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update depreciated AnnData.concatenate #82

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

Update depreciated AnnData.concatenate #82

quentinblampey opened this issue Jun 21, 2023 · 2 comments

Comments

@quentinblampey
Copy link

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
Copy link
Author

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
Copy link

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

@Koncopd Koncopd mentioned this issue Aug 10, 2023
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@Sophon-0 @quentinblampey