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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
1.88k stars 594 forks source link

Backport PR #3264 on branch 1.10.x (Fix compat typing and old_positionals usage) #3265

Closed meeseeksmachine closed 3 days ago

meeseeksmachine commented 3 days ago

Backport PR #3264: Fix compat typing and old_positionals usage

codecov[bot] commented 3 days ago

Codecov Report

Attention: Patch coverage is 92.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 76.91%. Comparing base (7ccf96d) to head (bd99e6d). Report is 1 commits behind head on 1.10.x.

Files with missing lines Patch % Lines
src/scanpy/_compat.py 81.81% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## 1.10.x #3265 +/- ## ========================================== - Coverage 76.93% 76.91% -0.02% ========================================== Files 109 109 Lines 12454 12451 -3 ========================================== - Hits 9581 9577 -4 - Misses 2873 2874 +1 ``` | [Flag](https://app.codecov.io/gh/scverse/scanpy/pull/3265/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/3265/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | `76.91% <92.00%> (-0.02%)` | :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=scverse#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files with missing lines](https://app.codecov.io/gh/scverse/scanpy/pull/3265?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/neighbors/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?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=) | `81.06% <100.00%> (-0.06%)` | :arrow_down: | | [src/scanpy/plotting/\_baseplot\_class.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?src=pr&el=tree&filepath=src%2Fscanpy%2Fplotting%2F_baseplot_class.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wbG90dGluZy9fYmFzZXBsb3RfY2xhc3MucHk=) | `91.59% <100.00%> (-0.03%)` | :arrow_down: | | [src/scanpy/plotting/\_preprocessing.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?src=pr&el=tree&filepath=src%2Fscanpy%2Fplotting%2F_preprocessing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wbG90dGluZy9fcHJlcHJvY2Vzc2luZy5weQ==) | `87.50% <100.00%> (-0.22%)` | :arrow_down: | | [src/scanpy/preprocessing/\_deprecated/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?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)` | | | [...preprocessing/\_deprecated/highly\_variable\_genes.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?src=pr&el=tree&filepath=src%2Fscanpy%2Fpreprocessing%2F_deprecated%2Fhighly_variable_genes.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wcmVwcm9jZXNzaW5nL19kZXByZWNhdGVkL2hpZ2hseV92YXJpYWJsZV9nZW5lcy5weQ==) | `95.50% <100.00%> (ø)` | | | [src/scanpy/preprocessing/\_simple.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?src=pr&el=tree&filepath=src%2Fscanpy%2Fpreprocessing%2F_simple.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9wcmVwcm9jZXNzaW5nL19zaW1wbGUucHk=) | `88.63% <100.00%> (-0.04%)` | :arrow_down: | | [src/scanpy/readwrite.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?src=pr&el=tree&filepath=src%2Fscanpy%2Freadwrite.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9yZWFkd3JpdGUucHk=) | `77.53% <100.00%> (-0.06%)` | :arrow_down: | | [src/scanpy/tools/\_ingest.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?src=pr&el=tree&filepath=src%2Fscanpy%2Ftools%2F_ingest.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS90b29scy9faW5nZXN0LnB5) | `77.67% <100.00%> (-0.10%)` | :arrow_down: | | [src/scanpy/\_compat.py](https://app.codecov.io/gh/scverse/scanpy/pull/3265?src=pr&el=tree&filepath=src%2Fscanpy%2F_compat.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9fY29tcGF0LnB5) | `77.08% <81.81%> (-0.70%)` | :arrow_down: |