Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly
Appearance settings

updated scib version #793

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
Merged
scottgigante-immunai merged 10 commits into from
Feb 1, 2023
Merged

updated scib version #793

scottgigante-immunai merged 10 commits into from
Feb 1, 2023

Conversation

@danielStrobl
Copy link
Collaborator

@danielStrobl danielStrobl commented Jan 30, 2023

New scib version due to isolated label ASW score bug.

Submission type

  • This submission adds a new dataset
  • This submission adds a new method
  • This submission adds a new metric
  • This submission adds a new task
  • This submission adds a new Docker image
  • This submission fixes a bug (link to related issue: #685 )
  • This submission adds a new feature not listed above

Testing

  • This submission was written on a forked copy of openproblems
  • Nextflow test pipeline is passing on this base branch of this pull
    request (include link to passed test on NF Tower found in GitHub Actions summary: )
  • If this pull request is not ready for review (including passing the Nextflow test
    pipeline), I will open this PR as a draft (click on the down arrow next to the
    "Create Pull Request" button)

Submission guidelines

  • This submission follows the guidelines in our
    Contributing document
  • I have checked to ensure there aren't other open Pull Requests for the
    same update/change

PR review checklist

This PR will be evaluated on the basis of the following checks:

  • The task addresses a valid open problem in single-cell analysis
  • The latest version of master is merged and tested
  • The methods/metrics are imported to __init__.py and were tested in the pipeline
  • Method and metric decorators are annotated with paper title, year, author, code
    version, and date
  • The README gives an outline of the methods, metrics and datasets in the folder
  • The README provides a satisfactory task explanation (for new tasks)
  • The sample test data is appropriate to test implementation of all methods and
    metrics (for new tasks)

@scottgigante-immunai
Copy link
Collaborator

scottgigante-immunai commented Jan 30, 2023

Tests failing: https://github.com/danielStrobl/SingleCellOpenProblems/actions/runs/4046320867/jobs/6958959663#step:8:2649

@danielStrobl
Copy link
Collaborator Author

danielStrobl commented Jan 30, 2023

The tests can't pass here yet as the new scib version doesn't exist yet

@danielStrobl
Copy link
Collaborator Author

danielStrobl commented Jan 31, 2023

Scib is updated now, this should hopefully work now

@danielStrobl danielStrobl marked this pull request as ready for review January 31, 2023 15:38
@codecov
Copy link

codecov bot commented Jan 31, 2023 •
edited
Loading

Codecov Report

Base: 94.95% // Head: 95.03% // Increases project coverage by +0.08% 🎉

Coverage data is based on head (9e0aa8c) compared to base (61be1cf).
Patch has no changes to coverable lines.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #793      +/-   ##
==========================================
+ Coverage   94.95%   95.03%   +0.08%     
==========================================
  Files         157      171      +14     
  Lines        4298     4408     +110     
  Branches      228      228              
==========================================
+ Hits         4081     4189     +108     
  Misses        142      142              
- Partials       75       77       +2
Flag Coverage Δ
unittests 95.03% <ø> (+0.08%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
...on/batch_integration_graph/metrics/iso_label_f1.py 100.00% <ø> (ø)
...enproblems/tasks/_batch_integration/_common/api.py 95.45% <0.00%> (-4.55%) ⬇️
...batch_integration/batch_integration_feature/api.py 100.00% <0.00%> (ø)
...integration/batch_integration_embed/metrics/nmi.py 100.00% <0.00%> (ø)
...batch_integration_feature/metrics/iso_label_sil.py 100.00% <0.00%> (ø)
..._integration_feature/metrics/graph_connectivity.py 100.00% <0.00%> (ø)
...egration/batch_integration_feature/metrics/kBET.py 100.00% <0.00%> (ø)
...integration/batch_integration_embed/metrics/ari.py 100.00% <0.00%> (ø)
...ion/batch_integration_feature/metrics/sil_batch.py 100.00% <0.00%> (ø)
...tion/batch_integration_feature/metrics/cc_score.py 100.00% <0.00%> (ø)
... and 7 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

@scottgigante-immunai scottgigante-immunai marked this pull request as draft January 31, 2023 17:19
@scottgigante-immunai
Copy link
Collaborator

scottgigante-immunai commented Jan 31, 2023

Converting to draft until tests pass on fork. Added another commit as scib is installed on two images

@github-actions
Copy link
Contributor

github-actions bot commented Jan 31, 2023

Current build status

@danielStrobl
Copy link
Collaborator Author

danielStrobl commented Feb 1, 2023

passing tests: https://github.com/danielStrobl/SingleCellOpenProblems/actions/runs/4063040131

@scottgigante-immunai
Copy link
Collaborator

scottgigante-immunai commented Feb 1, 2023

Looks like a test failure to me. A version of something you changed has caused spatial decomp to fail. I'm going to see if upgrading scvi-tools fixes it

@danielStrobl
Copy link
Collaborator Author

danielStrobl commented Feb 1, 2023

Sorry, I thought this might be a general spatial decomp error as it' also failing here without changing any packages: https://github.com/danielStrobl/SingleCellOpenProblems/actions/runs/4062456961

@danielStrobl
Copy link
Collaborator Author

danielStrobl commented Feb 1, 2023

yeah, this also fails on main (in my fork): https://github.com/danielStrobl/SingleCellOpenProblems/actions/runs/4063611749

@scottgigante-immunai
Copy link
Collaborator

scottgigante-immunai commented Feb 1, 2023

Yep, just discovered that myself. I'm on it.

@scottgigante-immunai scottgigante-immunai marked this pull request as ready for review February 1, 2023 19:07
scottgigante-immunai
scottgigante-immunai approved these changes Feb 1, 2023
View reviewed changes
Copy link
Collaborator

@scottgigante-immunai scottgigante-immunai left a comment

Choose a reason for hiding this comment

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

Passing at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/1zq0QqSDGxwez5

@scottgigante-immunai scottgigante-immunai merged commit 32b46e6 into openproblems-bio:main Feb 1, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@scottgigante-immunai scottgigante-immunai scottgigante-immunai 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

@danielStrobl @scottgigante-immunai
Morty Proxy This is a proxified and sanitized view of the page, visit original site.