openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
MIT License
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change multimodal data integration task name to matching modalities #778

Closed LuckyMD closed 1 year ago

LuckyMD commented 1 year ago

Just changed the folder name and README title for the task. Anything else that would need to be changed @scottgigante-immunai ? Website should pull directly from this, no?

codecov[bot] commented 1 year ago

Codecov Report

Base: 94.93% // Head: 94.98% // Increases project coverage by +0.04% :tada:

Coverage data is based on head (3066a43) compared to base (5f8fd17). Patch has no changes to coverable lines.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #778 +/- ## ========================================== + Coverage 94.93% 94.98% +0.04% ========================================== Files 157 157 Lines 4288 4288 Branches 227 227 ========================================== + Hits 4071 4073 +2 + Misses 142 141 -1 + Partials 75 74 -1 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `94.98% <ø> (+0.04%)` | :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/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio) | Coverage Δ | | |---|---|---| | [openproblems/tasks/matching\_modalities/api.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvYXBpLnB5) | `100.00% <ø> (ø)` | | | [...lems/tasks/matching\_modalities/datasets/citeseq.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvZGF0YXNldHMvY2l0ZXNlcS5weQ==) | `100.00% <ø> (ø)` | | | [...blems/tasks/matching\_modalities/datasets/scicar.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvZGF0YXNldHMvc2NpY2FyLnB5) | `100.00% <ø> (ø)` | | | [...lems/tasks/matching\_modalities/methods/baseline.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvbWV0aG9kcy9iYXNlbGluZS5weQ==) | `100.00% <ø> (ø)` | | | [.../matching\_modalities/methods/harmonic\_alignment.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvbWV0aG9kcy9oYXJtb25pY19hbGlnbm1lbnQucHk=) | `90.24% <ø> (ø)` | | | [...nproblems/tasks/matching\_modalities/methods/mnn.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvbWV0aG9kcy9tbm4ucHk=) | `100.00% <ø> (ø)` | | | [...ms/tasks/matching\_modalities/methods/procrustes.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvbWV0aG9kcy9wcm9jcnVzdGVzLnB5) | `100.00% <ø> (ø)` | | | [...blems/tasks/matching\_modalities/metrics/knn\_auc.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvbWV0cmljcy9rbm5fYXVjLnB5) | `100.00% <ø> (ø)` | | | [...nproblems/tasks/matching\_modalities/metrics/mse.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL21hdGNoaW5nX21vZGFsaXRpZXMvbWV0cmljcy9tc2UucHk=) | `82.35% <ø> (ø)` | | | [...l\_cell\_communication/\_common/metrics/odds\_ratio.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/778?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19jZWxsX2NlbGxfY29tbXVuaWNhdGlvbi9fY29tbW9uL21ldHJpY3Mvb2Rkc19yYXRpby5weQ==) | `100.00% <0.00%> (+7.40%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio)

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scottgigante-immunai commented 1 year ago

The diff in this PR doesn't look right... you should be renaming the entire task folder and everything in it, instead I just see a single new markdown file.

LuckyMD commented 1 year ago

hmm, it looks like the stuff wasn't added when i renamed the folder.

LuckyMD commented 1 year ago

should be fixed now

LuckyMD commented 1 year ago

there, now it looks better ^^.

scottgigante-immunai commented 1 year ago

All tests failing (: Fixed with 8c8c769

scottgigante-immunai commented 1 year ago

Website should pull directly from this, no?

We will probably need to rename the image file corresponding with this task on the website, but that's a TODO for the website PR that will result from this change.

Also, we probably shouldn't merge this until we're ready to rerun the benchmark, as the resulting content PR will break due to out of date results files.

LuckyMD commented 1 year ago

Ah, right... thx for catching the import change. Makes sense to keep this here until the benchmark rerun.

github-actions[bot] commented 1 year ago

Current build status