[label projection] scVI+scArches+XGBoost

scottgigante-immunai commented 1 year ago

Submission type

[X] This submission adds a new method

Testing

[X] This submission was written in 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: )

Submission guidelines

[X] 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 (closes #494)

PR review checklist

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

[X] The task addresses a valid open problem in single-cell analysis

github-actions[bot] commented 1 year ago

scottgigante-immunai commented 1 year ago

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

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 97.29% and project coverage change: -0.12 :warning:

Comparison is base (9d16650) 95.60% compared to head (d67bada) 95.48%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #853 +/- ## ========================================== - Coverage 95.60% 95.48% -0.12% ========================================== Files 187 188 +1 Lines 4980 5055 +75 Branches 273 279 +6 ========================================== + Hits 4761 4827 +66 - Misses 141 148 +7 - Partials 78 80 +2 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `95.48% <97.29%> (-0.12%)` | :arrow_down: | 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/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio) | Coverage Δ | | |---|---|---| | [...ration/batch\_integration\_embed/metrics/cc\_score.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL2NjX3Njb3JlLnB5) | `100.00% <ø> (ø)` | | | [...n/batch\_integration\_embed/metrics/iso\_label\_sil.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL2lzb19sYWJlbF9zaWwucHk=) | `100.00% <ø> (ø)` | | | [...ntegration/batch\_integration\_embed/metrics/kBET.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL2tCRVQucHk=) | `100.00% <ø> (ø)` | | | [...integration/batch\_integration\_embed/metrics/pcr.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL3Bjci5weQ==) | `100.00% <ø> (ø)` | | | [...ation/batch\_integration\_embed/metrics/sil\_batch.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL3NpbF9iYXRjaC5weQ==) | `100.00% <ø> (ø)` | | | [...tion/batch\_integration\_embed/metrics/silhouette.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9lbWJlZC9tZXRyaWNzL3NpbGhvdWV0dGUucHk=) | `100.00% <ø> (ø)` | | | [...ch\_integration\_feature/metrics/hvg\_conservation.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9mZWF0dXJlL21ldHJpY3MvaHZnX2NvbnNlcnZhdGlvbi5weQ==) | `100.00% <ø> (ø)` | | | [...tegration/batch\_integration\_graph/methods/bbknn.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9ncmFwaC9tZXRob2RzL2Jia25uLnB5) | `100.00% <ø> (ø)` | | | [...egration/batch\_integration\_graph/methods/combat.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9ncmFwaC9tZXRob2RzL2NvbWJhdC5weQ==) | `100.00% <ø> (ø)` | | | [...gration/batch\_integration\_graph/methods/fastmnn.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9ncmFwaC9tZXRob2RzL2Zhc3Rtbm4ucHk=) | `100.00% <ø> (ø)` | | | ... and [82 more](https://codecov.io/gh/openproblems-bio/openproblems/pull/853?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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mxposed commented 1 year ago

Thank you, Scott!

openproblems-bio / openproblems