hvg flavors seurat and cellranger with batch: bug in subset #3042
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #3042 +/- ##
=======================================
Coverage 75.80% 75.80%
=======================================
Files 110 110
Lines 12502 12504 +2
=======================================
+ Hits 9477 9479 +2
Misses 3025 3025
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Looks simple enough! Please deduplicate the tests though, they have too many identical lines. |
To do so did across-setting tests with for loop on top of former test... Would you prefer one separate test with that for loop for the across-settings check? |
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This PR fixes the bug reported in the linked issue.
A new test which spots the erroneous computations has been added.
I would use this chance to refactor the
_highly_variable_genes.py, rather than using the 2-lines fix suggested in the first commit:Doing the multi-batch hvg flagging differently for seurat_v3 and seurat/cell_ranger is what made this bug hard to spot in the first place I think.