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Fix layers parameter in score_genes with .raw #3155

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Merged
merged 12 commits into from
Jul 25, 2024
Merged

Fix layers parameter in score_genes with .raw #3155

merged 12 commits into from
Jul 25, 2024

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Intron7
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@Intron7 Intron7 commented Jul 12, 2024 •
edited by flying-sheep
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This would fix this interaction

sc.tl.score_genes(adata, layer="counts", gene_list=adata.var.index[:5])

This requires #3154

@Intron7 Intron7 added this to the 1.11.0 milestone Jul 12, 2024
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codecov bot commented Jul 12, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.52%. Comparing base (71fd59a) to head (7c8ccc2).
Report is 54 commits behind head on main.

Additional details and impacted files 
@@           Coverage Diff           @@
##             main    #3155   +/-   ##
=======================================
  Coverage   76.52%   76.52%           
=======================================
  Files         109      109           
  Lines       12483    12483           
=======================================
  Hits         9553     9553           
  Misses       2930     2930
Files with missing lines Coverage Δ
src/scanpy/_utils/__init__.py 74.89% <100.00%> (+0.10%) ⬆️
src/scanpy/plotting/_anndata.py 84.98% <100.00%> (-0.04%) ⬇️
src/scanpy/tools/_score_genes.py 85.10% <100.00%> (ø)

@Intron7 Intron7 requested a review from flying-sheep July 25, 2024 08:56
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flying-sheep requested changes Jul 25, 2024
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Looks good, aside from the duplicated test code.

#3154 still needs to be backported before we can merge this, please do that or ask me for help doing it!

@Intron7 Intron7 requested a review from flying-sheep July 25, 2024 11:01
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@flying-sheep flying-sheep enabled auto-merge (squash) July 25, 2024 11:50
@flying-sheep flying-sheep disabled auto-merge July 25, 2024 11:50
@flying-sheep flying-sheep changed the title Check use raw Fix layers parameter in score_genes with .raw Jul 25, 2024
@flying-sheep flying-sheep enabled auto-merge (squash) July 25, 2024 11:51
@flying-sheep flying-sheep merged commit 208115d into main Jul 25, 2024
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@flying-sheep flying-sheep deleted the _check_use_raw branch July 25, 2024 12:21
kaushalprasadhial pushed a commit to sanchit-misra/scanpy that referenced this pull request Feb 4, 2025
@Intron7
Fix layers parameter in score_genes with .raw (scverse#3155)
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