Mid year cleanup

[pratikunterwegs]

This issue tracks tasks for a mid-year package cleanup.

Supercharge your pkgdown website

• Verify that website URL is listed in _pkgdown.yml
• Verify pkgdown site is using epiversetheme
• Check for manual specification of Bootstrap version (currently 5)
• Add logo to epiverse-trace/hex-stickers
• Use svg version of logo
• Verify logo is properly detected by pkgdown & r-universe (path and name need to be exactly man/figures/logo.png or man/figures/logo.svg)
• Add a pkgdown reference index: https://pkgdown.r-lib.org/reference/build_reference.html#reference-index.
  Use selectors (e.g., starts_with() or contains()) to select functions rather than an explicit list. This serves the double purpose of checking that functions follow a coherent naming scheme.
• Verify intro vignette appears under 'Get started'
• Verify vignettes are ordered correctly (if applicable)
  - [ ] Verify all images include helpful alt-text

Developer tools

• Update lintr, roxygen, usethis, testthat, devtools to the latest version on your local computer: pak::pak(c("lintr", "devtools"), dependencies = TRUE)
• Copy from packagetemplate:
  - .lintr config file see Temporarily disable backport linter #184
  • GitHub Actions worfklows
  • tools/ folder
  • tests/spelling.R
  • tests/testthat/helper-state.R
  • tests/testthat/setup-options.R
• Run spelling::spell_check_package()

Misc good practice

• Change files ending in .r to .R in R/ and/or tests/testthat/"
• Review usage of # nolint comments. New versions of lintr may have squashed previous bugs
• Update year in license file

Documentation

• Use roxygen2 markdown syntax (usethis::use_roxygen_md())
• Add a related project section at the end of the README
• Check that all URLs are working, up-to-date, and leading directly to the expected page: urlchecker::url_check()
• Add package-level documentation page: usethis::use_package_doc()
• Move package-level imports to the package-level documentation
• Verify that all @import and @importFrom import functions that are actually used in the relevant function
• Identify potential for reuse in documentation
• Run devtools::document()

DESCRIPTION

• Verify if any package in Remotes is still necessary
• Check that package Description is still in line with the current scope
• Make sure links to GitHub repository and issue tracker are listed: usethis::use_github_links()
• Re-order and standardize DESCRIPTION with desc::desc_normalize()
• Submit a PR adding yourself as author to packagetemplate

Final R CMD check

• Run devtools::check() locally to catch NOTEs and WARNINGs that can still easily slip through continuous integration
• devtools::check(remote = TRUE, manual = TRUE)
• devtools::check_win_devel(): cannot complete due to curl issues

GitHub

• Check if issues are still relevant. If not, please close them, ideally with a link to the commit fixing them or a comment explaining why they no longer apply.
• Check if discussions you started are still ongoing. If not, please close the thread.