Fix CI workflows: linting, changelog, and documentation - #489
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Fix CI workflows: linting, changelog, and documentation#489d-morrison with Copilot wants to merge 5 commits into
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Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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[WIP] Add interactive Shiny app for antigen-antibody kinetics visualization
Fix CI workflows: linting, changelog, and documentation
Jan 21, 2026
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Jan 21, 2026
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Self-review caught an imprecise claim in the NEWS entry. It said docs-check had been "red on every pull request", which a reader can check in about ten seconds and find false: 13 of the 30 open pull requests currently show a green docs-check. They are stale, not contradictory. Every green run predates roxygen2 8.1.0 (the most recent is 2026-07-28), and every run since the release has failed. Two further pull requests, #510 and #489, are red from 2026-06-15 and 2026-01-21 for older reasons unrelated to this one. Say "every run since" rather than "every pull request", and name the staleness so the green checks elsewhere do not read as counter-evidence. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Description
Resolves CI workflow failures for the decay-curve-2 branch by addressing linting violations, missing changelog entries, and incomplete pkgdown configuration.
Changes
Code style compliance
=→<-), brace placement, indentation, and spacing in 8 new R files.lintr.Rexclusions fort1.Randy1.R(internal functions with digit-letter naming pattern)Documentation
curve_app(), UI/server components) and decay curve functions (antibody_decay_curve(),pathogen_decay_curve(),t1f(),y1f(),plot_decay_curve())pkgdown/_pkgdown.ymlwith new reference sections: "Interactive visualization" and "Modeling and plotting decay curves"ggplotandUIto spelling dictionaryChecklist
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