Report redesign + --always-top-n/--class search options + MkDocs docs site#12
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Report:
- carousel per cluster solution with dropdown (All by default) and X-of-N nav
- paginated, searchable Top-N results table; left TOC with scroll-spy
- per-section/plot info popovers; PCC colourbar; network group legend
- canonical allele names matching the reference logo titles; favicon
- citation + repository links; graceful missing-logo placeholders
Search:
- --always-top-n: return each cluster's top-N regardless of threshold
(below-threshold hits are flagged in the report); opt-in, off by default
- --class {I,II,all}: restrict the reference by MHC class
- document the Pearson-correlation method and formula in engine docstrings
Tests updated for canonical display names and the new search behaviours.
- mkdocs.yml: Material theme + mkdocstrings (API auto-generated from docstrings) - home / usage / API-reference pages; standalone report linked as example-report.html - 'docs' optional-dependency group; GitHub Pages deploy workflow (Actions) - replace the root report demo (docs/index.html) with the docs site
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Summary
Report (standalone HTML):
Search:
--always-top-n: return each cluster's top-N regardless of threshold (sub-threshold hits flagged "below cutoff"); opt-in, off by default--class {I,II,all}: restrict the reference by MHC classDocs:
Tests: 226 passing.
Manual step after merge
Set repo Settings -> Pages -> Source to "GitHub Actions" so the docs workflow deploys the new site.