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Backport categorical ComBat reference coding to 1.12.x - #4496
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sylvesterkaczmarek wants to merge 2 commits into
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sylvesterkaczmarek wants to merge 2 commits into
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## 1.12.x #4496 +/- ##
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+ Coverage 78.73% 78.76% +0.03%
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Files 121 121
Lines 12760 12760
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+ Hits 10046 10051 +5
+ Misses 2714 2709 -5
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Refs #4454. Targets 1.12.x, not main.
Backport the categorical-covariate reference coding already accepted in #4389. The current 1.12 maintenance branch still constructs a full set of categorical dummy columns alongside all batch indicators, introducing a redundant column. Use the same treatment coding as main and remove its intercept before combining the matrices.
This is a targeted backport of the existing correction, with new regression coverage. No solver, numerical threshold, dependency or unrelated function changes are included. Main and 1.11.x are not changed. Designs confounded for other reasons are outside this fix.
Validation
Validation ran on the exact pinned source in the contributor fork's Linux/Python 3.12 workflow. The validation helpers and workflow are on a separate branch and are not included in this proposed diff. This is not upstream CI. The full repository suite, documentation build, other platforms and the reporter's dataset were not tested.
Fork evidence: https://github.com/sylvesterkaczmarek/scanpy/actions/runs/42367545452
Post-submission verification
The release-note fragment has been renamed to 4496.fix.md. The targeted tests were independently rerun after the filename change and passed: 12 tests. Human review of the latest changes remains pending.
LLM usage
LLM or coding agent used: GPT-6 via ChatGPT and Codex CLI v0.166.0 assisted with code, tests, documentation, and review. The Codex model version used for the original implementation was not independently recorded.
If one was used, I, a human, have reviewed, understood and tested every changed line.
Tests included.
Issue reference included above; this change is limited to the 1.12 maintenance branch.
Release notes not necessary because:
A release note is included as
4496.fix.md, matching the assigned PR number.