TODO.md
In jabenninghoff/rdev: R Development Tools

TODO

[x] Add README.Rmd
[x] Update DESCRIPTION and use description data in README.Rmd
[x] Add ORCID
[ ] Update my ORCID details

[x] Write a utility function to sort .Rbuildignore
[x] Implement pkgdown
[x] Add links / update Rd formatting for all function documentation.
[x] Add dummy imports to silence R CMD check note per tidyverse
[x] Migrate build_analysis_site() to rdev
[x] Switch from development version of styler (1.3.2.9000) when a new release becomes available
[x] ~~Validate that lint_all works as expected within ci~~
[x] Add 'create package' workflow example to README, remove TODO section "Analysis package creation process"
[x] Move _pkgdown.yml to repository root to make projects discoverable by the pgkdown GitHub query
[x] Update README.Rmd template to dynamically generate list of notebooks in analysis
[x] Automate release process
[x] Automate creation of feature branches, including 'Bump version' using desc::desc_bump_version("dev")
[x] Add check to stage_release() to look for missing topics in _pkgdown.yml reference section
[x] Update use_rdev_package()
[x] Handle .Rmd files that already have an html_document section
[x] Move rmd_metadata() from README-analysis.Rmd to rdev package
[x] Add tests per comments in R/ after reading package book, documentation
[x] Update Roxygen comments after reading package book, documentation, review and merge duplicate Roxygen docs
[x] Write a manual regression test script (notes with R commands) ~~as a vignette~~ to validate 'Creating Packages' ~~and 'GitHub Releases'~~
[x] Add messages, warnings to build_analysis_site() to report on progress
[x] Add function to spell check notebooks
[x] Automate branch protection
[x] Address issue https://github.com/r-lib/usethis/issues/1568, which has been closed
[x] Add dplyr when running use_analysis_package()
[x] ~~Consider switching getOption("pkgType") from source to both per R options~~ per the R macOS FAQ, "Only the CRAN build is guaranteed to be compatible with the package binaries on CRAN (or Bioconductor)."
[x] Support creating repos in organizations
[x] ~~Consider incorporating the GitHub description into DESCRIPTION~~
[x] Create a wrapper for spelling that includes notebooks in package spell checking, WORDLIST
[x] Add a spell_check_test_notebooks() function for CI spellchecks on notebooks
[x] Convert manual tests (Setup.Rmd) into an R Script that can be run from within the package created with create_github_repo()
[x] Add a function to add missing (notebook) dependencies to DESCRIPTION, see renv::dependencies() and desc::desc_get_deps()
[x] Add check_renv() to ci() and stop if renv::status() is not up to date
[x] Replace proof-docs with urlchecker, support checking GitHub Pages docs directory using url_db_from_HTML_files ~~(ask if a PR for this would be accepted)~~
[x] Move scripts from tools to inst/bin or similar, per Stack Overflow and R Packages
[x] Switch from development versions of styler (1.3.2.9000) and lintr (2.0.1.9000) when a new release becomes available - both were needed to address bugs in the current release versions, 1.3.2 and 2.0.1.
[x] Add trailing slash to GitHub Pages URL
[x] Update lint_all() to lint all types, including .Rpres
[x] ~~Add custom CSS files to _site.yml and analysis notebook templates to control font size, as described in this article, or possibly using bs_theme(), since pkgdown customizes the default using build_bslib()~~ (issue exists in unsupported Safari 14 but not Safari 15)
[x] ~~Remove pkgdown/extra.css if https://github.com/r-lib/pkgdown/issues/2377 is accepted~~
[x] ~~Establish default knitr options, including knitr::opts_chunk$set(fig.align = "center"), add to analysis template, also review settings for Advanced R~~
[x] ~~Consider using RStudio Extensions:~~
[x] ~~Use Project Templates like vertical?~~
[x] ~~Add CSS to R Markdown Template instead of assets/extra.css?~~
[x] Move shift-heading-level-by: 1 from _quarto.yml to analysis/_metadata.yml, so TODO.md renders properly
[x] Remove preset: bootstrap workaround when pkgdown 2.0.8+ is released (per https://github.com/r-lib/pkgdown/issues/2376)
[ ] Replace dev = TRUE logic if https://github.com/rstudio/renv/issues/1695 is accepted
[ ] Update errors and messages after reading Advanced R Conditions and re-reading the Tidyverse Style Guide
[ ] Reduce the number of Imports, per R CMD check:

> devtools::check()

...

> checking package dependencies ... NOTE
  Imports includes 30 non-default packages.
  Importing from so many packages makes the package vulnerable to any of
  them becoming unavailable.  Move as many as possible to Suggests and
  use conditionally.

[x] Set up GitHub Actions
[x] Use standard R CMD check
[x] Use lintr
[x] Faster CI checks
[x] ~~Switch to full R CMD check ?~~
[x] Update GitHub Actions from r-lib examples
[x] Run test coverage
[x] ~~Skip CI checks for changes in only the docs/ directory~~
[x] ~~Add GitHub Action for html/link checking using something like htmlproofer~~
[x] ~~Autobuild docs/ like pkgdown ?~~