Skip to content

chore: update API for anndata 0.12 #186

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
Open
wants to merge 6 commits into
base: main
Choose a base branch
from
Open

chore: update API for anndata 0.12 #186

wants to merge 6 commits into from

Conversation

ilan-gold
Copy link
Contributor

No description provided.

@review-notebook-app Review Notebook App
Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

@ilan-gold ilan-gold requested a review from flying-sheep July 29, 2025 11:13
flying-sheep
flying-sheep approved these changes Jul 29, 2025
View reviewed changes
Copy link
Member

@flying-sheep flying-sheep left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

looks good, but I’d install ipywidgets to get rid of the two warnings related to it missing. (no need to rerun other stuff and wait 2 more hours)

also any idea why the umap looks completely different?

@ilan-gold
Copy link
Contributor Author

also any idea why the umap looks completely different?

I would guess the neighbors changed. The clustering is also different.

@ilan-gold
Copy link
Contributor Author

It's possible something in sklearn but I'm not sure! scikit-learn-contrib/sklearn-ann#101

@flying-sheep
Copy link
Member

yeah, I’m just wondering because it’s much more detailed now, and implies much more structure.

which could just be some visual setting, but idk.

anyway, could you please fix the ipywidget warnings if you still have the environment available?

@ilan-gold
Copy link
Contributor Author

which could just be some visual setting, but idk.

It just changed again, so I think there is something going on with annoy

@ilan-gold
Copy link
Contributor Author

Potentially related: spotify/annoy#679

@flying-sheep
Copy link
Member

at least the umap you committed in 449a344 looks extremely similar to the one you committed last.

as said, the level of detail in the umap is what I’m talking about and that didn’t change again.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@flying-sheep flying-sheep flying-sheep approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@ilan-gold @flying-sheep