Spring cleaning @ cynkra dev day 🧼 #174

Mise en Place

• Ask maintainer to set up access rights
  💡

  (if acceptable -- for smoother workflow; and necessary for a few items) For repositories under a personal account refer to https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-user-account-settings/permission-levels-for-a-personal-account-repository#collaborator-access-for-a-repository-owned-by-a-personal-account and for repositories under an organization account refer to https://docs.github.com/en/organizations/managing-user-access-to-your-organizations-repositories/managing-repository-roles/repository-roles-for-an-organization (Write Access)
• pak::pak("r-lib/usethis")
  💡

  Install the development version of usethis which has the Air setup function.
• pak::pak("cynkra/cynkradown")
  💡

  Install our pkgdown template that has a function to set up its usage.

Quick Wins

• pr_init("upkeep-2025-06")
  💡

  Create a branch for this spring cleaning work
• usethis::use_readme_rmd()
  💡

  If you didn't use a Rmd README, switch to one and port the content from README.md. If you did, please make sure it has the <!-- badges: start --> and <!-- badges: end --> comments.
• usethis::use_roxygen_md()
  💡

  Activate the usage of Markdown in roxygen2 comments https://roxygen2.r-lib.org/articles/rd-formatting.html
• usethis::use_github_links()
  💡

  Register the GitHub links in DESCRIPTION
• usethis::use_pkgdown_github_pages()
  💡

  Implement the GitHub setup needed to automatically publish your pkgdown site to GitHub pages
• usethis::use_tidy_github_labels()
  💡

  Create "tidy" issue labels https://usethis.r-lib.org/reference/use_github_labels.html#tidyverse-label-usage You might need to update the labelling of open issues.
• urlchecker::url_check()
  💡

  Check whether URLs are valid. Use https://urlchecker.r-lib.org/reference/url_update.html for automatic fixing of some broken URLs.
• usethis::use_package_doc()
  💡

  Create a package level manual page. Also use it to store imports useful for the whole page.
• usethis::use_testthat(3)
  💡

  Activate testthat's third edition. https://testthat.r-lib.org/articles/third-edition.html
• Remove check environments section from cran-comments.md
  💡

  In case you had submitted your package to CRAN
• Handle and close any still-open master --> main PRs
  💡

  https://www.tidyverse.org/blog/2021/10/renaming-default-branch/
• usethis::git_default_branch_rename()
  💡

  https://www.tidyverse.org/blog/2021/10/renaming-default-branch/
• Update lifecycle badges with more accessible SVGs: usethis::use_lifecycle()
  💡

  If you already use lifecycle for communicating changes in your package.
• Use pak::pak("tidyverse/hms") in README
  💡

  Better way to install packages than devtools these days.
• Use R-universe installation instructions
  💡

  For instance install.packages('blockr.ui', repos = c('https://cynkra.r-universe.dev', 'https://cloud.r-project.org'))
• usethis::use_mit_license() : if there are external contributors, see deep dives
  💡

  https://www.tidyverse.org/blog/2021/12/relicensing-packages/
• usethis::use_tidy_description()
  💡

  Clean up the formatting of DESCRIPTION
• usethis::use_github_action("check-standard")
  💡

  GHA workflow for R CMD check, will also add a badge.
• usethis::use_github_action("test-coverage")
  💡

  GHA workflow for test coverage uploaded on codecov.io, will also add a badge.
• Delete any outdated CI configuration file
  💡

  Travis, Appveyor, old GitHub Actions workflows. Also check README badges!
• usethis::use_air()
  💡

  You can also reformat files with Air
• devtools::build_readme()
  💡

  Build the README.Rmd with a temporary installation of the package

cynkra Quick Wins

• cynkratemplate::use_cynkra_pkgdown()
  💡

  Register the use of our awesome pkgdown template.
• cynkrathis::register_cynkra() if cynkra is not in authors yet
• cynkrathis:: add_cynkra_ror() if cynkra was already in authors
  💡

  https://ropensci.org/blog/2025/05/09/ror/

Deep Dives

• Before usethis::use_mit_license(), ask external contributors if it's ok
• Align the names of R/ files and test/ files
  💡

  https://www.tidyverse.org/blog/2022/02/upkeep-testthat-3/#corresponding-files-in-r-and-teststestthat
• Use lifecycle instead of artisanal deprecation messages
  💡

  https://lifecycle.r-lib.org/articles/communicate.html
• Use cli for messages
  💡

  https://blog.r-hub.io/2023/11/30/cliff-notes-about-cli/
• Add alt-text to pictures, plots, etc; see posit.co/blog/knitr-fig-alt for examples
• Place all @import and @importFrom in the pkg doc file
  💡

  Follow a nice newish convention to find them when you look for them.
• If checks show notes for global variables, use .data and .env in tidyverse style functions, then if globals remain, use roxyglobals::use_roxyglobals()
  💡

  https://dplyr.tidyverse.org/articles/programming.html, https://tidyr.tidyverse.org/articles/programming.html, https://github.com/anthonynorth/roxyglobals

Wrap Up

• desc::add_me()
  💡

  Register yourself as ctb in DESCRIPTION
• Ask maintainer to review PR + merge + and cleanup access rights of relevant