docs: docstrings for core metrics (D1, part 1) - #29
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Full NumPy-style docstrings (summary, parameters, returns with shapes/units, math definitions, examples) for the core analysis API in tcri.metrics: clonotypic_entropy, phenotypic_entropy, clonality, mutual_information, flux. These flow into the D11 autodoc reference and mirror the D2 concepts page. Docstring-only (no behavior change); docs build clean (0 warnings); math and cross-references render. Part of Notion D1 (public API docstrings). Remaining chunks: preprocessing (register_model, joint_distribution*), model (TCRIModel), then plotting/utils. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
First chunk of D1 (public API docstrings): full NumPy-style docstrings for the core
tcri.tlanalysis API —clonotypic_entropy,phenotypic_entropy— normalized entropies with shapes/unitsclonality— clonal concentration per phenotypemutual_information— clone–phenotype coupling (with the MI formula)flux— phenotypic movement between two covariatesEach has a one-line summary, full parameter table,
Returnswith shapes + units, mathNotes,See Also, and a runnableExamplesblock. They render straight into the D11 autodoc reference and mirror the D2 concepts page.Verification
python -m py_compileclean; docstring-only, no behavior change.python -m sphinx -b html docs <out>→ build succeeded, 0 warnings; the metrics page now shows Parameters/Returns/math (cross-refs toregister_modelresolve).Scope
This is part 1. Remaining D1 chunks, in priority order:
register_model,joint_distribution,joint_distribution_posteriorTCRIModel(setup_anndata,__init__, train)tcri.plfunctions are internal helpers)🤖 Generated with Claude Code