Fix #4008: Opinionated defaults for 2.0#4063
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JiwaniZakir wants to merge 1 commit into
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #4063 +/- ##
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- Coverage 78.62% 78.61% -0.01%
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Files 117 117
Lines 12727 12713 -14
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- Hits 10006 9994 -12
+ Misses 2721 2719 -2
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Hi, that issue isn’t actionable yet, we’re still deciding what the defaults are going to be |
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Closes #4008
test_v2preview_preset_mask_varintests/test_rank_genes_groups.pySets
mask_var="highly_variable"as the default forRankGenesGroupsPresetunder theScanpyV2Previewpreset insrc/scanpy/_settings/presets.py. Previously bothScanpyV1andScanpyV2Previewusedmask_var=None; nowScanpyV2Previewautomatically restricts differential expression to highly variable genes by default, aligning with the opinionated v2.0 conventions described in #4008.The new unit test
test_v2preview_preset_mask_vardirectly asserts:Preset.ScanpyV2Preview.rank_genes_groups.mask_var == "highly_variable"Preset.ScanpyV1.rank_genes_groups.mask_var is NoneThis PR was created with AI assistance (Claude). The changes were reviewed by quality gates and a critic model before submission.