This function is very similar to usethis::use_github_action() except that it uses a template from biocthis. It creates a Bioconductor-friendly GitHub action workflow for your package. You can also use this GitHub Actions workflow by executing usethis::use_github_action().

use_bioc_github_action(
  biocdocker,
  pkgdown = getOption("biocthis.pkgdown", FALSE),
  testthat = getOption("biocthis.testthat", FALSE),
  covr = testthat,
  RUnit = getOption("biocthis.RUnit", FALSE),
  pkgdown_covr_branch = getOption("biocthis.pkgdown_covr_branch", "master"),
  docker = getOption("biocthis.docker", FALSE)
)

Arguments

biocdocker

A character(1) specifying the Bioconductor docker version you want to use. Valid names are "devel" or in the "RELEASE_X_Y" format such as "RELEASE_3_11". Check http://bioconductor.org/help/docker/ for more information on the Bioconductor docker images. If you don't specify this, it will be determined automatically using your current Bioconductor version. The R version will be set to match the Bioconductor version.

pkgdown

A logical(1) specifying whether to run pkgdown. Check https://cran.r-project.org/web/packages/pkgdown/index.html for more information on pkgdown which is useful for creating documentation websites. If TRUE, then pkgdown will only run on the Linux (Bioconductor docker) test.

testthat

A logical(1) specifying whether to run testthat. Check https://cran.r-project.org/web/packages/testthat/index.html for more information about testthat which is useful for unit tests. The testing chapter at https://r-pkgs.org/tests.html is also very useful.

covr

A logical(1) specifying whether to run covr. Check https://cran.r-project.org/web/packages/covr/index.html for more information about covr, which is useful for displaying for assessing your test coverage. If TRUE, then covr will only run on the Linux (Bioconductor docker) test.

RUnit

A logical(1) specifying whether to run RUnit unit tests. Check http://bioconductor.org/developers/how-to/unitTesting-guidelines/ for more information about RUnit.

pkgdown_covr_branch

A character(1) specifying the name of the GitHub branch that will be used creating the pkgdown website and running covr.

docker

A logical(1) specifying whether to build a docker image with the resulting package.

Value

This function adds and/or replaces the .github/workflows/check-bioc.yml file in your R package.

Details

For the full history on how this GitHub Actions workflow came to be, check the "biocthis developer notes" vignette https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html.

Examples


if (FALSE) {
## Run this function in your package
biocthis::use_bioc_github_action()
}

## I have the following options on my ~/.Rprofile set
## Check
## <https://github.com/lcolladotor/biocthis/issues/9#issuecomment-702401032>
## for more information.
options("biocthis.pkgdown" = TRUE)
options("biocthis.testthat" = TRUE)