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Rename DistanceTest alpha to padj_threshold - #1062

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Zethson merged 2 commits into
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rename/distance-test-padj-threshold
Aug 4, 2026
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Rename DistanceTest alpha to padj_threshold#1062
Zethson merged 2 commits into
mainfrom
rename/distance-test-padj-threshold

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@Zethson

@Zethson Zethson commented Aug 4, 2026

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Closes #1002

Aligns DistanceTest with the significance threshold naming introduced in #974, where alpha became padj_threshold in Milo, the DGE base and enrichment.
alpha stays accepted via deprecated_arg and now emits a FutureWarning.

DIALOGUE is left alone, as requested in the issue.

Two things worth a look:

  • The attribute DistanceTest.alpha became DistanceTest.padj_threshold without an alias, since only the constructor argument is deprecated.
  • The distance tests tutorial passes alpha=0.0015; it lives in the pertpy-tutorials submodule, so it keeps working through the deprecation and needs a separate update there.

Closes #1002

Aligns DistanceTest with the significance threshold naming introduced in
 #974, where alpha became padj_threshold in Milo, the DGE base and
enrichment. alpha stays accepted and now emits a FutureWarning.

DIALOGUE is left alone as requested in the issue.
@Zethson
Zethson merged commit 7dc796b into main Aug 4, 2026
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@Zethson
Zethson deleted the rename/distance-test-padj-threshold branch August 4, 2026 15:20
@Zethson Zethson mentioned this pull request Aug 4, 2026
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Codecov Report

❌ Patch coverage is 87.50000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 78.72%. Comparing base (40dfeb6) to head (d8ee95e).
⚠️ Report is 6 commits behind head on main.

Files with missing lines Patch % Lines
src/pertpy/tools/_distances/_distance_tests.py 87.50% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1062      +/-   ##
==========================================
+ Coverage   74.15%   78.72%   +4.56%     
==========================================
  Files          52       52              
  Lines        7291     7290       -1     
==========================================
+ Hits         5407     5739     +332     
+ Misses       1884     1551     -333     
Files with missing lines Coverage Δ
src/pertpy/tools/_distances/_distance_tests.py 92.74% <87.50%> (-0.60%) ⬇️

... and 8 files with indirect coverage changes

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Consistent significance threshold naming

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