docs: fix fabricated API in README + quickstart - #28
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Both the README and docs/usage/quickstart.md documented an API that does not exist or is wrong: global_joint_distribution, probability_ternary, polar_plot (deprecation path), register_model phenotype_prob_slot="X_tcri_phenotypes", clonotypic_entropy(adata, cov, "phenotype"), n_latent=10, and more. The README is the PyPI long-description, so it would ship looking authoritative but wrong. Replace both with one accurate, runnable quickstart taken from the test suite (setup_anndata -> TCRIModel -> train -> register_model -> mutual_information / clonotypic_entropy / phenotypic_entropy), and point to the Read the Docs site (real API reference + the D2 concepts page) rather than duplicating a hand-written API in the README. Docs build clean (0 warnings); the fabricated names are gone from the output. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
The README and
docs/usage/quickstart.mdboth documented an API that's wrong or nonexistent —global_joint_distribution,probability_ternary,polar_plot(deprecation path),register_model(..., "X_tcri_phenotypes")(real slot isX_tcri_probabilities),clonotypic_entropy(adata, cov, "phenotype")(no such positional),n_latent=10(real default 128), and more. Since the README is the PyPI long-description, this would ship to PyPI looking authoritative but broken.Replaced both with one accurate, runnable quickstart lifted from the test suite (ground truth):
setup_anndata→TCRIModel(adata)→train→register_model→mutual_information/clonotypic_entropy/phenotypic_entropy. The README now points to the Read the Docs site (the real API reference + the D2 concepts page) instead of duplicating a hand-written API.Verification
tests/test_metricsand the function defs).python -m sphinx -b html docs <out>→ build succeeded, 0 warnings; the fabricated names are gone from the builtquickstart.html.Closes the README API-cleanup item flagged before the PyPI release.
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