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Fix #4008: Opinionated defaults for 2.0 #4063

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Fix #4008: Opinionated defaults for 2.0 #4063

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2 changes: 1 addition & 1 deletion src/scanpy/_settings/presets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ def rank_genes_groups() -> Mapping[Preset, RankGenesGroupsPreset]:
return {
Preset.ScanpyV1: RankGenesGroupsPreset(method="t-test", mask_var=None),
Preset.ScanpyV2Preview: RankGenesGroupsPreset(
method="wilcoxon", mask_var=None
method="wilcoxon", mask_var="highly_variable"
),
}

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8 changes: 8 additions & 0 deletions tests/test_rank_genes_groups.py
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Expand Up @@ -311,3 +311,11 @@ def test_mask_not_equal():
with_mask = pbmc.uns["rank_genes_groups"]["names"]

assert not np.array_equal(no_mask, with_mask)


def test_v2preview_preset_mask_var() -> None:
"""Test that ScanpyV2Preview preset sets mask_var='highly_variable'."""
from scanpy import Preset

assert Preset.ScanpyV2Preview.rank_genes_groups.mask_var == "highly_variable"
assert Preset.ScanpyV1.rank_genes_groups.mask_var is None
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