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Complete Doxygen API overview, styling, and publishing - #256
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The Doxygen API had no introductory page, project styling, or automated publishing. This adds a library overview with links to the main class families, coordinate and energy conventions, and integration guidance, together with an IntaRNA header, footer, and responsive stylesheet.
Addresses the remaining checklist in #22 (the issue is already closed).
The new Documentation workflow builds the existing Jekyll user guide and the API together, preserving the homepage and adding the reference at
/api/. Pull requests produce a review artifact; only the upstreammasterbranch can deploy. A standalone HTML build needs only Doxygen and Graphviz. The existing Autotools target shares the same inputs and now rebuilds when headers or documentation assets change. All new documentation sources/helpers are included in source distributions.Validation
GitHub Actions documentation build: passed on the final PR head, including Jekyll, Doxygen, link/assets checks, and artifact upload. Deployment was correctly skipped for the PR.
Doxygen 1.9.8 / Graphviz HTML build and
python3 doc/check-api.py doxygen-doc/html: passed; 58 entry-page links/assets checked, including class/member anchors.Autotools bootstrap, configure with
--disable-doxygen-pdf, andmake doxygen-doc: passed; checked that header and overview changes trigger regeneration.make dist, followed by standalone generation from the extracted, unconfigured archive into a path containing spaces: passed.Headless Chromium: verified branding, desktop/mobile layout, and search navigation to
RnaSequence; no JavaScript errors or landing-page horizontal overflow.actionlint .github/workflows/documentation.yml, Bash syntax validation, andgit diff --check: passed.The 58 Doxygen configuration/header warnings match
masterexactly; no warnings originate in the new overview. No C++ prediction code changed, so the C++ test suite was not rerun locally.Publishing activation after merge
The repository currently uses branch-based Pages publishing. A repository administrator must change Settings → Pages → Build and deployment → Source to GitHub Actions, then run Documentation on
master(or push another commit). Live Pages settings have not been changed by this PR. Both the user guide and API are included in the deployment artifact.