refactor: retire unused QCPipeline and ReferencePanel abstractions - #248
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Brainstormed design for removing two confirmed-orphaned Python abstractions (QCPipeline + QCResult/QCStepProtocol, and the unadopted ReferencePanel module). Deletion-only cleanup; targets refactor/main. genotools/container/ is intentionally retained as a historical reference for rebuilding containerized inference later. See the spec for evidence, per-commit plan, and verification.
QCPipeline (qc/pipeline.py) plus QCResult and QCStepProtocol were an orchestration API the CLI runner never used (it reimplements orchestration in _run_single_step/_run_qc_pipeline). Their golden coverage was redundant with the direct step-function golden tests, which remain. Removes the class, its QCResult return type, their exports, and their self-tests. FilterResult (returned by every step) is kept.
ancestry/reference.py (ReferencePanel + get_default_model_path + validate_model_files) was a public export referenced only in docstrings, never constructed in shipped code, with zero test coverage. The new-ancestry path uses AncestryModel directly, and the runner registered ReferencePanel in _new_modules but never read it. Removes the module, its exports, and the dead registration. Also fixes the AncestryModel docstrings, which showed a stale ReferencePanel-based workflow (fit() actually takes a DataFrame + labels).
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Summary
QCPipeline(qc/pipeline.py) + itsQCResultreturn type +QCStepProtocol: an orchestration API the CLI runner never used (it reimplements orchestration in_run_single_step/_run_qc_pipeline). Its golden regression coverage was redundant with the direct step-function golden tests, which remain.FilterResult(returned by every step) is kept.ReferencePanel(ancestry/reference.py, incl.get_default_model_path/validate_model_files): a public export referenced only in docstrings, never constructed in shipped code, zero test coverage. The new-ancestry path usesAncestryModeldirectly; the runner registered it in_new_modulesbut never read it. Also corrects theAncestryModeldocstrings, which showed a staleReferencePanel-based workflow (fit()actually takes a DataFrame + labels).Intentionally NOT touched
genotools/container/— orphaned, but kept as a historical reference for rebuilding containerized ancestry inference later (maintainer decision).ancestry/results.py,qc/results.py::FilterResult,gwas/results.py— all live and tested.What changed
genotools/qc/pipeline.py(deleted),genotools/qc/results.py(dropQCResult),genotools/qc/__init__.py(exports + docstring).genotools/ancestry/reference.py(deleted),genotools/ancestry/__init__.py(exports + docstring),genotools/ancestry/model.py(docstrings),genotools/cli/runner.py(import + dead_new_modulesregistration).tests/unit/test_qc/test_pipeline.py(deleted),TestQCResultremoved fromtests/unit/test_qc/test_results.py,TestQCPipeline*removed fromtests/regression/test_qc_steps.py. All direct step/CLI golden tests retained.Test plan
grepconfirms zero remaining references to every removed symbol.import genotools{,.qc,.ancestry,.cli,.gwas}OK.tests/unit tests/regression: 374 passed (was 397; the 23 removed are the deleted QCPipeline/QCResult self-tests, not failures). Parity suite green with.venv-stable.python -m genotools --helpexits 0.Notes
refactor/main, notmain.docs/superpowers/specs/2026-07-16-retire-dead-abstractions-design.md,docs/superpowers/plans/2026-07-16-retire-dead-abstractions.md.