[kkkklck]

LLM usage

• LLM or coding agent used: GPT-5.6 Sol via ChatGPT
• If one was used, I, a human, have reviewed, understood and tested every changed line

PR Checklist

• If you've fixed a bug or added code that should be tested, add tests!

Description of changes

Mixscape.mixscape() currently uses min_de_genes for two independent thresholds:

1. the minimum number of DE genes required to classify a perturbation, and
2. the minimum number of cells that must remain assigned to the perturbed class during the iterative KO/NP classification.

The current Seurat reference implementation separates these concepts as min.de.genes and min.cells. Seurat fixed the same coupling in satijalab/seurat#10299 in February 2026.

This PR adds min_cells=5 to Mixscape.mixscape() and uses it for the cell-count safeguard while leaving min_de_genes responsible only for the DE-gene threshold. The default is 5, matching Seurat, so default behavior is unchanged.

A regression test deliberately sets min_de_genes and min_cells to different values and verifies that changing one no longer changes the semantics of the other.

Technical details

The behavioral change is limited to calls that explicitly use a non-default min_de_genes value. Previously, for example, min_de_genes=10 also implicitly required at least 10 cells to remain classified as perturbed. After this change, the cell threshold is controlled independently through min_cells.

Validation completed:

• upstream CI test matrix passes on Python 3.13 stable, Python 3.14 stable, and Python 3.14 pre-release dependencies
• Codecov reports all modified and coverable lines are covered by tests
• ruff check passes
• ruff format passes
• build and tutorial workflows pass

The remaining Pre-commit checks failure is unrelated to this PR: mypy currently fails while parsing PyQt6/QtGui.pyi with 16 syntax errors. The same failure is present on the current main branch scheduled Test workflow at commit 9b5c53b.

Additional context

Reference fix in Seurat: satijalab/seurat#10299.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.12%. Comparing base (e4f0802) to head (d81224a).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1189      +/-   ##
==========================================
+ Coverage   74.06%   74.12%   +0.05%     
==========================================
  Files          57       57              
  Lines        8895     8895              
==========================================
+ Hits         6588     6593       +5     
+ Misses       2307     2302       -5     

Files with missing lines	Coverage Δ
...c/pertpy/tools/_perturbation_efficacy/_mixscape.py	66.78% <100.00%> (+1.39%)	⬆️

... and 1 file with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Zethson]

Thank you very much!