packagetemplate 2.0.0

Automated checks

Infrastructure and internal changes

• GitHub Actions workflows now include the necessary permissions field to run in a secure environment with minimal permissions granted by default to the GITHUB_TOKEN secret (#114, @Bisaloo).

• testthat tests now run in parallel (#93, @Bisaloo). Number of cores on GitHub Actions workflows is 2 by default and number of cores on local computers can be set as documented in the dedicated vignette.

• GitHub Actions workflows are now run in more contexts:

  • In merge queues (#94, @Bisaloo, based on a report from @jamesmbaazam in #72).
  • On all branches for pull requests (#64 & #66, @Bisaloo, based on a report from @Karim-Mane). This makes packagetemplate more suitable for git flows with several long-lived branches, such as a develop branch alongside the main branch.

• pkgdown website is now rendered with clean: true on releases, so that each release starts with a clean slate and does not accidentally still include removed vignettes (#58, @Bisaloo, based on a report from @TimTaylor).

• GitHub Actions workflows pushing updates to files (at this time: render_readme.yml & update-citation-cff.yaml) no longer run on git tags or releases (#92 and #109, @Bisaloo, based on a report from @joshwlambert and early feedback from @sbfnk).

• GitHub Actions workflows pushing updates to files (at this time: render_readme.yml & update-citation-cff.yaml) no longer fail because they try to push to an outdated branch when they run at the same time. This is achieved by running git pull --rebase before attempting to push (#92 by @Bisaloo, thanks to a report from @joshwlambert).

• READMEs that reference external files (images, bibliography, etc.) are now rendered without errors by the automated render-readme GitHub Actions workflow (#57, @Bisaloo).

New checks

• Internal links are not checked on pkgdown website before deploying in our pkgdown.yaml GitHub Actions workflow (#117, @Bisaloo, based on a report from @pratikunterwegs in #102.). This prevents stale links to deleted vignettes to go unnoticed.

• Spellchecking via the spelling package is now part of the standard continuous integration of Epiverse-TRACE packages (#56, @Bisaloo, #105, @bahadzie, based on reports from @pratikunterwegs and @jamesmbaazam).

• testthat warnings and R CMD check warnings & notes now result in failure in our continuous integration (#96, @Bisaloo). This will help correcting early some minor issues that were until now going undetected for a while.

• the template includes a new testthat help helper-state.R to ensure global state is not modified (or restored correctly) by the package (#90, @Bisaloo, and improved in #111 based on feedback from the epinowcast community, and in particular @medewitt and @pearsonca).

• partial matching of arguments, dollars and attributes now generate warnings as part of our testing & continuous integration process but setting special arguments in testthat runs (#61, @Bisaloo, based on a report from @TimTaylor and a tip from @gaborcsardi).

• Two new linters are enabled by default:

  • undesirable_function_linter(), which signals potential bugs such as leftover debugging calls, error-prone or slow functions (#87, @Bisaloo).
  • additional custom linters via the etdev package (#85, @Bisaloo)

• packagetemplate now includes an extra workflow dependency-change.yaml to analyze the impact of dependency changes in terms of total (direct & indirect) dependencies and system dependencies (#107, @Bisaloo, with feedback from @joshwlambert and @pratikunterwegs).

False positives

• Some auto-generated files are excluded from linting:

  • R/RcppExports.R (#95, @Bisaloo, based on a report from @pratikunterwegs).
  • R/stanmodels.R (#106, @Bisaloo)

• Some lintr are disabled globally:

  • lintr::indentation_linter() because as of lintr 3.1.0, it generates too many false-positive and conflicts with styler (#75, @Bisaloo).
  • library_call_linter(), to offer more flexibility in vignettes, tests, or development scripts (#88, @Bisaloo)

• Additionally, missing_package_linter() and namespace_linter() are now disabled in the data-raw/ folder to avoid pushing extra package inclusion as dependencies in DESCRIPTION (#81, @Bisaloo). It is indeed generally not advisable to add development dependencies to DESCRIPTION.

Release process

• Three new good practice reminders have been added to the release checklist:

  • Ensure every contributor in acknowledged in some way, as documented in our blueprints (@Bisaloo, #115).
  • Review the WORDLIST to ensure misspelled words were not added by accident (#68, @Bisaloo).
  • Go through # nolint comments in the code to check if these comments are still necessary. (#84, @Bisaloo).

• This template now includes explicitly a NEWS.md file. This is meant to encourage the documentation of changes as early as possible in the development process, rather than waiting until usethis::use_release_issue() points it out (#82, @Bisaloo, based on discussions with @ntorresd).

Documentation & community

• The svg template for package logos (by @dgmascarina) is now included in man/figures/logo.svg (standard location and name for R package logo) (#71, @Bisaloo).

• packagetemplate includes a new GitHub Actions workflow update-citation-cff.yaml to create and keep in sync a file CITATION.cff which contains information on how to cite the package in a standard, language-agnostic way that is nicely integrated with GitHub (#31, @Bisaloo).

Vignettes

• A template is now provided for the design vignette that all Epiverse-TRACE packages should contain (#97 and #99, @joshwlambert and @pratikunterwegs).

GitHub community infrastructure

• bibtex (.bib) files are now excluded from repository statistics via a custom linguist override. This helps making sure our repositories are correctly identified as R projects, rather than TeX (#76 @Bisaloo, based on discussions with @jamesmbaazam, @pratikunterwegs, @sbfnk & @TimTaylor).

• Pull request and issue templates have been transferred out of this repository and now live as community defaults under epiverse-trace/.github (#74, @Bisaloo). Developers are still encouraged to write specific templates better tailored to each individual package.

• GitHub Actions workflows now include some instructions indicating how to reproduce their results locally for easier debugging (#70, @Bisaloo).

Meta changes

packagetemplate itself is now more thoroughly tested to limit the risk that a broken package is shipped to users:

• R CMD check (#100, @Bisaloo).
• lintr (#69, @Bisaloo)
• pkgdown