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Remove generated documentation files from repository - #37
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The pkgdown workflow only triggered on push to main/master, but this repo's development branch is devel, so the site was never rebuilt and GitHub Pages was serving nothing. Point the workflow at devel and stop committing the built docs/ site into that branch since the workflow now publishes it to the gh-pages branch instead.
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Pull request overview
This PR removes pkgdown-generated site artifacts from the docs/ tree so that documentation is produced by CI (or locally) rather than stored in version control. It also adjusts the pkgdown GitHub Actions workflow triggers to run only for the devel branch.
Changes:
- Removed generated pkgdown HTML pages under
docs/(reference pages, articles, and site pages). - Removed generated pkgdown assets/config in
docs/(CSS/JS/SVG/YAML). - Updated
.github/workflows/pkgdown.yamlto trigger ondevelinstead ofmain/master.
Reviewed changes
Copilot reviewed 29 out of 69 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| docs/reference/index.html | Removed generated pkgdown reference index page. |
| docs/reference/hpaXmlTissueExprSum.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaXmlTissueExpr.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaXmlProtClass.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaXmlGet.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaXmlAntibody.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaXml.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaVisTissue.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaVisSubcell.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaVisPatho.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaVis.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaExport.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpaDownload.html | Removed generated pkgdown reference topic page. |
| docs/reference/hpa_histology_data.html | Removed generated pkgdown dataset documentation page. |
| docs/reference/hpa_downloaded_histology_v18.html | Removed generated pkgdown dataset documentation page. |
| docs/pkgdown.yml | Removed generated pkgdown build metadata file. |
| docs/pkgdown.js | Removed generated pkgdown site JavaScript. |
| docs/pkgdown.css | Removed generated pkgdown site CSS. |
| docs/link.svg | Removed generated pkgdown asset. |
| docs/index.html | Removed generated pkgdown site homepage. |
| docs/docsearch.js | Removed generated pkgdown search JavaScript. |
| docs/authors.html | Removed generated pkgdown authors/citation page. |
| docs/articles/z_HPAanalyze_paper_figures_files/elevate-section-attrs-2.0/elevate-section-attrs.js | Removed generated vignette dependency asset. |
| docs/articles/index.html | Removed generated pkgdown articles index page. |
| docs/articles/f_HPAanalyze_case_images.html | Removed generated pkgdown article page. |
| docs/articles/f_HPAanalyze_case_images_files/elevate-section-attrs-2.0/elevate-section-attrs.js | Removed generated vignette dependency asset. |
| docs/articles/e_HPAanalyze_case_json.html | Removed generated pkgdown article page. |
| docs/articles/e_HPAanalyze_case_json_files/elevate-section-attrs-2.0/elevate-section-attrs.js | Removed generated vignette dependency asset. |
| docs/articles/d_HPAanalyze_case_offline_xml.html | Removed generated pkgdown article page. |
| docs/articles/d_HPAanalyze_case_offline_xml_files/elevate-section-attrs-2.0/elevate-section-attrs.js | Removed generated vignette dependency asset. |
| docs/articles/c_HPAanalyze_case_query_files/elevate-section-attrs-2.0/elevate-section-attrs.js | Removed generated vignette dependency asset. |
| docs/articles/b_HPAanalyze_indepth_files/elevate-section-attrs-2.0/elevate-section-attrs.js | Removed generated vignette dependency asset. |
| docs/articles/a_HPAanalyze_quick_start_files/elevate-section-attrs-2.0/elevate-section-attrs.js | Removed generated vignette dependency asset. |
| docs/404.html | Removed generated pkgdown 404 page. |
| docs/_config.yml | Removed generated Jekyll config used by site output. |
| .github/workflows/pkgdown.yaml | Updated workflow triggers to run only on devel for push/PR events. |
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This PR removes all generated pkgdown documentation files from the
docs/directory that are automatically created during the documentation build process.Summary
The
docs/directory contained generated HTML files, CSS, JavaScript, and other assets that are produced by pkgdown when building the package documentation. These files should not be committed to version control as they are:Changes Made
docs/articles/anddocs/reference/pkgdown.css,pkgdown.js,docsearch.css,docsearch.js, etc.)pkgdown.yml,_config.yml).github/workflows/pkgdown.yamlto only trigger on thedevelbranch instead ofmainandmasterNotes
The source documentation (R roxygen comments, vignettes, and articles) remain in the repository. The
docs/directory should be regenerated locally or by CI/CD as needed usingpkgdown::build_site().https://claude.ai/code/session_015TQGZgokVqe94wb1AYKRMi