openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
MIT License
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Split torch from non-torch dependencies #733

Closed scottgigante-immunai closed 1 year ago

scottgigante-immunai commented 1 year ago

Reverts openproblems-bio/openproblems#732

This needs work; something in here breaks rpy2.

codecov[bot] commented 1 year ago

Codecov Report

Base: 94.70% // Head: 94.70% // No change to project coverage :thumbsup:

Coverage data is based on head (40eb0f6) compared to base (7ffc855). Patch coverage: 100.00% of modified lines in pull request are covered.

:exclamation: Current head 40eb0f6 differs from pull request most recent head 43cb370. Consider uploading reports for the commit 43cb370 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #733 +/- ## ======================================= Coverage 94.70% 94.70% ======================================= Files 154 154 Lines 4097 4097 Branches 207 207 ======================================= Hits 3880 3880 Misses 144 144 Partials 73 73 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `94.70% <100.00%> (ø)` | | 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/733?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/733/diff?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/733/diff?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)` | | | [...integration/batch\_integration\_embed/metrics/pcr.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/733/diff?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/733/diff?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/733/diff?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/733/diff?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/733/diff?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/733/diff?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)` | | | [...integration/batch\_integration\_graph/methods/mnn.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/733/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9ncmFwaC9tZXRob2RzL21ubi5weQ==) | `100.00% <ø> (ø)` | | | [...egration/batch\_integration\_graph/methods/scalex.py](https://codecov.io/gh/openproblems-bio/openproblems/pull/733/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openproblems-bio#diff-b3BlbnByb2JsZW1zL3Rhc2tzL19iYXRjaF9pbnRlZ3JhdGlvbi9iYXRjaF9pbnRlZ3JhdGlvbl9ncmFwaC9tZXRob2RzL3NjYWxleC5weQ==) | `100.00% <ø> (ø)` | | | ... and [18 more](https://codecov.io/gh/openproblems-bio/openproblems/pull/733/diff?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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