use_bioc_github_action: Create a biocthis-style GitHub Actions workflow

In lcolladotor/biocthis: Automate package and project setup for Bioconductor packages

Create a biocthis-style GitHub Actions workflow

Description

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().

Usage

use_bioc_github_action(
  biocdocker = "release",
  pkgdown = getOption("biocthis.pkgdown", FALSE),
  testthat = getOption("biocthis.testthat", FALSE),
  covr = testthat,
  covr_coverage_type = getOption("biocthis.covr_coverage_type", "all"),
  RUnit = getOption("biocthis.RUnit", FALSE),
  pkgdown_covr_branch = getOption("biocthis.pkgdown_covr_branch", "devel"),
  docker = getOption("biocthis.docker", FALSE)
)

Arguments

biocdocker	A character(1) specifying the Bioconductor docker version you want to use. Valid names are "release", "devel" or in the "RELEASE_X_Y" format such as "RELEASE_3_11". "release" is a special case where the latest bioc-release version will be automatically detected. Check http://bioconductor.org/help/docker/ for more information on the Bioconductor docker images.
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.
covr_coverage_type	A character(1) specifying the code used to calculate the covr coverage. Option are package "tests", "vignettes", "examples", "all", or "none". The default is "all".
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. Since biocthis version 1.9.3 this changed from "master" to "devel" by default to match https://twitter.com/Bioconductor/status/1631234299423850497.
docker	A logical(1) specifying whether to build a docker image with the resulting package. This will also create a Dockerfile. You can alternatively try using this excellent template: https://github.com/seandavi/BuildABiocWorkshop.

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.

Value

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

Examples

## Not run: 
## Run this function in your package
biocthis::use_bioc_github_action()

## End(Not run)

## 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)

lcolladotor/biocthis documentation built on March 29, 2025, 4:22 a.m.