theislab / scib

Benchmarking analysis of data integration tools
MIT License
294 stars 63 forks source link

Make rpy2 and anndata2ri optional #339

Closed mumichae closed 1 year ago

codecov[bot] commented 1 year ago

Codecov Report

Merging #339 (4f16990) into main (e578d84) will decrease coverage by 1.94%. The diff coverage is 15.85%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #339 +/- ## ========================================== - Coverage 56.70% 54.76% -1.95% ========================================== Files 38 38 Lines 1984 2027 +43 ========================================== - Hits 1125 1110 -15 - Misses 859 917 +58 ``` | Flag | Coverage Δ | | |---|---|---| | unittest | `54.76% <15.85%> (-1.95%)` | :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=theislab#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/theislab/scib/pull/339?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) | Coverage Δ | | |---|---|---| | [tests/metrics/rpy2/test\_kbet.py](https://codecov.io/gh/theislab/scib/pull/339/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-dGVzdHMvbWV0cmljcy9ycHkyL3Rlc3Rfa2JldC5weQ==) | `100.00% <ø> (ø)` | | | [scib/metrics/lisi.py](https://codecov.io/gh/theislab/scib/pull/339/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL2xpc2kucHk=) | `41.82% <5.55%> (-3.49%)` | :arrow_down: | | [scib/preprocessing.py](https://codecov.io/gh/theislab/scib/pull/339/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9wcmVwcm9jZXNzaW5nLnB5) | `18.95% <8.82%> (-2.35%)` | :arrow_down: | | [scib/integration.py](https://codecov.io/gh/theislab/scib/pull/339/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9pbnRlZ3JhdGlvbi5weQ==) | `32.71% <15.38%> (-1.63%)` | :arrow_down: | | [scib/metrics/kbet.py](https://codecov.io/gh/theislab/scib/pull/339/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL2tiZXQucHk=) | `20.56% <37.50%> (-2.12%)` | :arrow_down: | | [scib/exceptions.py](https://codecov.io/gh/theislab/scib/pull/339/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9leGNlcHRpb25zLnB5) | `50.00% <100.00%> (ø)` | |
LuckyMD commented 1 year ago

Before mergeable then only need:

mumichae commented 1 year ago

For scib-pipeline, I don't think we need to change anything, since rpy2 is added as a dependency in the conda environments, regardless of the scib dependencies

mumichae commented 1 year ago

scib-pipeline CI is running through using the dependencies https://github.com/theislab/scib-pipeline/pull/45