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scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
1.92k stars 602 forks source link

Add `SIM` checks #3258

Closed flying-sheep closed 1 month ago

flying-sheep commented 1 month ago

See #1241

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 79.24528% with 22 lines in your changes missing coverage. Please review.

Project coverage is 76.96%. Comparing base (8b2088d) to head (1b1fbc9). Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/scanpy/plotting/_tools/__init__.py 44.44% 5 Missing :warning:
src/scanpy/tools/_sim.py 58.33% 5 Missing :warning:
src/scanpy/plotting/_anndata.py 81.25% 3 Missing :warning:
src/scanpy/plotting/_baseplot_class.py 71.42% 2 Missing :warning:
src/scanpy/_utils/compute/is_constant.py 0.00% 1 Missing :warning:
src/scanpy/external/pl.py 50.00% 1 Missing :warning:
src/scanpy/plotting/_tools/scatterplots.py 75.00% 1 Missing :warning:
src/scanpy/preprocessing/_simple.py 66.66% 1 Missing :warning:
src/scanpy/tools/_ingest.py 75.00% 1 Missing :warning:
src/scanpy/tools/_paga.py 50.00% 1 Missing :warning:
... and 1 more
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #3258 +/- ## ========================================== + Coverage 76.85% 76.96% +0.11% ========================================== Files 109 109 Lines 12554 12469 -85 ========================================== - Hits 9648 9597 -51 + Misses 2906 2872 -34 ``` | [Flag](https://app.codecov.io/gh/scverse/scanpy/pull/3258/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | Coverage Δ | | |---|---|---| | [](https://app.codecov.io/gh/scverse/scanpy/pull/3258/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | `76.96% <79.24%> (+0.11%)` | :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=scverse#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files with missing lines](https://app.codecov.io/gh/scverse/scanpy/pull/3258?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | Coverage Δ | | |---|---|---| | [src/scanpy/\_settings.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2F_settings.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9fc2V0dGluZ3MucHk=) | `90.20% <100.00%> (ø)` | | | [src/scanpy/\_utils/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2F_utils%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9fdXRpbHMvX19pbml0X18ucHk=) | `75.51% <100.00%> (+0.26%)` | :arrow_up: | | [src/scanpy/datasets/\_datasets.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fdatasets%2F_datasets.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9kYXRhc2V0cy9fZGF0YXNldHMucHk=) | `100.00% <ø> (ø)` | | | [src/scanpy/datasets/\_ebi\_expression\_atlas.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fdatasets%2F_ebi_expression_atlas.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9kYXRhc2V0cy9fZWJpX2V4cHJlc3Npb25fYXRsYXMucHk=) | `93.97% <100.00%> (+1.03%)` | :arrow_up: | | [src/scanpy/get/get.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fget%2Fget.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9nZXQvZ2V0LnB5) | `92.06% <100.00%> (-0.17%)` | :arrow_down: | | [src/scanpy/neighbors/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fneighbors%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9uZWlnaGJvcnMvX19pbml0X18ucHk=) | `81.11% <100.00%> (-0.15%)` | :arrow_down: | | [src/scanpy/plotting/\_tools/paga.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fplotting%2F_tools%2Fpaga.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wbG90dGluZy9fdG9vbHMvcGFnYS5weQ==) | `68.47% <100.00%> (ø)` | | | [src/scanpy/plotting/\_utils.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fplotting%2F_utils.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wbG90dGluZy9fdXRpbHMucHk=) | `56.64% <100.00%> (ø)` | | | [src/scanpy/preprocessing/\_combat.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fpreprocessing%2F_combat.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wcmVwcm9jZXNzaW5nL19jb21iYXQucHk=) | `91.47% <100.00%> (+0.63%)` | :arrow_up: | | [src/scanpy/preprocessing/\_deprecated/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree&filepath=src%2Fscanpy%2Fpreprocessing%2F_deprecated%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wcmVwcm9jZXNzaW5nL19kZXByZWNhdGVkL19faW5pdF9fLnB5) | `90.47% <100.00%> (ø)` | | | ... and [22 more](https://app.codecov.io/gh/scverse/scanpy/pull/3258?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | |