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TODO.md

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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 r-lib/usethis#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 r-lib/pkgdown#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:
  • 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 r-lib/pkgdown#2376)
  • Replace GITHUB_PAT in .Renviron with gitcreds
  • Review use of usethis functions, including pull request helpers
  • Replace dev = TRUE logic after renv 1.1.6+ is released; see renv #1695, #2190
  • Update tests with new testthat features (testthat::auto_test_package(), testthat::describe(), Reporters, testthat::local_mocked_bindings())
  • 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.

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