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Pull request overview
This PR introduces an automated Bookdown build/publish workflow and a script-to-Rmd conversion utility to generate workshop chapters from the Botany2026 R scripts, along with comment/header formatting updates across those scripts.
Changes:
- Added
convert_to_rmd.Rto convert workshop.Rscripts into Bookdown chapter.Rmdfiles. - Added Bookdown scaffolding (
book/index.Rmd,book/_bookdown.yml) and a GitHub Actions workflow to build/publish the rendered book. - Standardized/cleaned top-of-file headers and section markers across several Botany2026 scripts.
Reviewed changes
Copilot reviewed 12 out of 12 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| Botany2026/scripts/tools/convert_to_rmd.R | New converter script intended to generate chapter Rmds from workshop scripts. |
| .github/workflows/build-book.yml | New CI workflow to convert scripts, build Bookdown, and publish to a bookdown branch. |
| book/index.Rmd | New Bookdown index/front-matter for the workshop book. |
| book/_bookdown.yml | Bookdown configuration listing chapter file patterns. |
| Botany2026/scripts/00_Setup.R | Header/section marker cleanup for setup/install script. |
| Botany2026/scripts/01_Data_Downloads.R | Header/section marker cleanup for download script. |
| Botany2026/scripts/02_Data_Cleaning.R | Header/section marker cleanup for cleaning script. |
| Botany2026/scripts/03_Data_Exploration.R | Header/section marker cleanup; introduces some malformed section headers. |
| Botany2026/scripts/04_AccessibleArea_VariableSelection.R | Header/section marker cleanup for climate processing/variable selection. |
| Botany2026/scripts/05_Ecological_Niche_Modeling.R | Header/section marker cleanup for ENM modeling script. |
| Botany2026/scripts/06_Null_ENMs.R | Header/section marker cleanup for null model script. |
| Botany2026/scripts/07_ENM_Processing.R | Header/section marker cleanup for ENM processing script. |
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added 3 commits
July 2, 2026 12:09
added 3 commits
July 2, 2026 13:08
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Using the pull request to work through additions - do not merge.