Releases · epiverse-trace/packagetemplate

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to files (at this time: render_readme.yml & update-citation-cff.yaml) no longer fail because they try to push to an outdated branch when they run at the same time.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).