TODO

Content

• Add README.Rmd
• Update DESCRIPTION and use description data in README.Rmd
• Add ORCID
• Update my ORCID details

Package

• Write a utility function to sort .Rbuildignore
• Implement pkgdown
• Add links / update Rd formatting for all function documentation.
• Add dummy imports to silence R CMD check note per tidyverse
• Migrate build_analysis_site() to rdev
• Switch from development version of styler (1.3.2.9000) when a new release becomes available
• Validate that lint_all works as expected within ci
• Add ‘create package’ workflow example to README, remove TODO section “Analysis package creation process”
• Move _pkgdown.yml to repository root to make projects discoverable by the pgkdown GitHub query
• Update README.Rmd template to dynamically generate list of notebooks in analysis
• Automate release process
• Automate creation of feature branches, including ‘Bump version’ using desc::desc_bump_version("dev")
• Add check to stage_release() to look for missing topics in _pkgdown.yml reference section
• Update use_rdev_package()
• Handle .Rmd files that already have an html_document section
• Move rmd_metadata() from README-analysis.Rmd to rdev package
• Add tests per comments in R/ after reading package book, documentation
• Update Roxygen comments after reading package book, documentation, review and merge duplicate Roxygen docs
• Write a manual regression test script (notes with R commands) as a vignette to validate ‘Creating Packages’ and ‘GitHub Releases’
• Add messages, warnings to build_analysis_site() to report on progress
• Add function to spell check notebooks
• Automate branch protection
• Address issue https://github.com/r-lib/usethis/issues/1568, which has been closed
• Add dplyr when running use_analysis_package()
• 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).”
• Support creating repos in organizations
• Consider incorporating the GitHub description into DESCRIPTION
• Create a wrapper for spelling that includes notebooks in package spell checking, WORDLIST
• Add a spell_check_test_notebooks() function for CI spellchecks on notebooks
• Convert manual tests (Setup.Rmd) into an R Script that can be run from within the package created with create_github_repo()
• Add a function to add missing (notebook) dependencies to DESCRIPTION, see renv::dependencies() and desc::desc_get_deps()
• Add check_renv() to ci() and stop if renv::status() is not up to date
• 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)
• Move scripts from tools to inst/bin or similar, per Stack Overflow and R Packages
• 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.
• Add trailing slash to GitHub Pages URL
• Update lint_all() to lint all types, including .Rpres
• 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)
• Remove pkgdown/extra.css if https://github.com/r-lib/pkgdown/issues/2377 is accepted
• Establish default knitr options, including knitr::opts_chunk$set(fig.align = "center"), add to analysis template, also review settings for Advanced R
• Consider using RStudio Extensions:
  • Use Project Templates like vertical?
  • Add CSS to R Markdown Template instead of assets/extra.css?
• Move shift-heading-level-by: 1 from _quarto.yml to analysis/_metadata.yml, so TODO.md renders properly
• 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.

GitHub

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