openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
MIT License
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DR baseline: just use true features but smaller in test #712

Closed scottgigante-immunai closed 1 year ago

scottgigante-immunai commented 1 year ago

We had a brainwave that we should just use the full features as we originally wanted to, but we can subset in test.

scottgigante-immunai commented 1 year ago

Passing tests at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/LYKh1vgvWRGBL

codecov[bot] commented 1 year ago

Codecov Report

Base: 95.07% // Head: 95.04% // Decreases project coverage by -0.03% :warning:

Coverage data is based on head (2e9391c) compared to base (4ac6faf). Patch coverage: 100.00% of modified lines in pull request are covered.

:exclamation: Current head 2e9391c differs from pull request most recent head 486df99. Consider uploading reports for the commit 486df99 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #712 +/- ## ========================================== - Coverage 95.07% 95.04% -0.04% ========================================== Files 154 154 Lines 4085 4076 -9 Branches 206 207 +1 ========================================== - Hits 3884 3874 -10 Misses 131 131 - Partials 70 71 +1 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `95.04% <100.00%> (-0.04%)` | :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/712?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio) | Coverage Δ | | |---|---|---| | [...tasks/dimensionality\_reduction/methods/baseline.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/712/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL2RpbWVuc2lvbmFsaXR5X3JlZHVjdGlvbi9tZXRob2RzL2Jhc2VsaW5lLnB5) | `93.75% <100.00%> (-6.25%)` | :arrow_down: | | [.../\_cell\_cell\_communication/\_common/methods/liana.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/712/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19jZWxsX2NlbGxfY29tbXVuaWNhdGlvbi9fY29tbW9uL21ldGhvZHMvbGlhbmEucHk=) | `100.00% <0.00%> (ø)` | | 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

Code looks fine to me. You didn't want to keep the PCA as another baseline or was the idea that this should be better in all cases?

This should be better in all cases :)