updated scib version

[danielStrobl]

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
• [x] 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]

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

[danielStrobl]

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

[danielStrobl]

Scib is updated now, this should hopefully work now

[codecov[bot]]

Codecov Report

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

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

Additional details and impacted files

```diff @@ 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%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio) | Coverage Δ | | |---|---|---| | [...on/batch\_integration\_graph/metrics/iso\_label\_f1.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9ncmFwaC9tZXRyaWNzL2lzb19sYWJlbF9mMS5weQ==) | `100.00% <ø> (ø)` | | | [...enproblems/tasks/\_batch\_integration/\_common/api.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9fY29tbW9uL2FwaS5weQ==) | `95.45% <0.00%> (-4.55%)` | :arrow_down: | | [...batch\_integration/batch\_integration\_feature/api.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9mZWF0dXJlL2FwaS5weQ==) | `100.00% <0.00%> (ø)` | | | [...integration/batch\_integration\_embed/metrics/nmi.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL25taS5weQ==) | `100.00% <0.00%> (ø)` | | | [...batch\_integration\_feature/metrics/iso\_label\_sil.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9mZWF0dXJlL21ldHJpY3MvaXNvX2xhYmVsX3NpbC5weQ==) | `100.00% <0.00%> (ø)` | | | [...\_integration\_feature/metrics/graph\_connectivity.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9mZWF0dXJlL21ldHJpY3MvZ3JhcGhfY29ubmVjdGl2aXR5LnB5) | `100.00% <0.00%> (ø)` | | | [...egration/batch\_integration\_feature/metrics/kBET.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9mZWF0dXJlL21ldHJpY3Mva0JFVC5weQ==) | `100.00% <0.00%> (ø)` | | | [...integration/batch\_integration\_embed/metrics/ari.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL2FyaS5weQ==) | `100.00% <0.00%> (ø)` | | | [...ion/batch\_integration\_feature/metrics/sil\_batch.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9mZWF0dXJlL21ldHJpY3Mvc2lsX2JhdGNoLnB5) | `100.00% <0.00%> (ø)` | | | [...tion/batch\_integration\_feature/metrics/cc\_score.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9mZWF0dXJlL21ldHJpY3MvY2Nfc2NvcmUucHk=) | `100.00% <0.00%> (ø)` | | | ... and [7 more](https://codecov.io/gh/openproblems-bio/openproblems/pull/793?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio) | | Help us with your feedback. 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[scottgigante-immunai]

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

[github-actions[bot]]

[danielStrobl]

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

[scottgigante-immunai]

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]

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]

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

[scottgigante-immunai]

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