R/use_bioc_github_action.R
use_bioc_github_action.Rd
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,
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)
)
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.
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.
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.
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.
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"
.
A logical(1)
specifying whether to run RUnit
unit tests.
Check http://bioconductor.org/developers/how-to/unitTesting-guidelines/
for more information about RUnit
.
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.
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.
This function adds and/or replaces the
.github/workflows/check-bioc.yml
file in your R package.
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.
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)