scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Updated Harmony Integrate Docs to better match interface to Harmonypy package #3362

Closed DaminK closed 3 days ago

DaminK commented 1 week ago

Fixed harmony documentation where a crucial feature of Harmony, namely the integration w.r.t. multiple covariates was not mentioned despite being supported by the interface. Harmony can take strings and lists of strings as its "vars_use" parameter which is named "key" in the Scanpy interface.

Small non-breaking change to docs. However, pre-commit throws:

ruff.....................................................................Failed
- hook id: ruff
- files were modified by this hook

Will wait if some maintainer know an easy fix for this before trying to debug this myself. Guess its more related to incorrect flags somewhere than the code.

codecov[bot] commented 1 week ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 76.49%. Comparing base (0f32b08) to head (99aa9da). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #3362 +/- ## ======================================= Coverage 76.49% 76.49% ======================================= Files 111 111 Lines 12866 12867 +1 ======================================= + Hits 9842 9843 +1 Misses 3024 3024 ``` | [Files with missing lines](https://app.codecov.io/gh/scverse/scanpy/pull/3362?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/external/pp/\_harmony\_integrate.py](https://app.codecov.io/gh/scverse/scanpy/pull/3362?src=pr&el=tree&filepath=src%2Fscanpy%2Fexternal%2Fpp%2F_harmony_integrate.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NjYW5weS9leHRlcm5hbC9wcC9faGFybW9ueV9pbnRlZ3JhdGUucHk=) | `87.50% <100.00%> (+0.83%)` | :arrow_up: |

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flying-sheep commented 3 days ago

Thanks!