The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
If you use rworkflows
, please cite:
Schilder, B.M., Murphy, A.E. & Skene, N.G. rworkflows: automating reproducible practices for the R community. Nat Commun 15, 149 (2024). https://doi.org/10.1038/s41467-023-44484-5
rworkflows
is a suite of tools to make it easy for R developers to implement reproducible best practices on GitHub.
It includes three main components:
1. templateR
template: a CRAN
/Bioc
-compatible R package template that automatically generates essential documentation using package metadata.
2. rworkflows
R package: a lightweight CRAN
package to automatically set up short, customisable workflows that trigger the rworkflows
action.
3. rworkflows
action: an open-source action available on the GitHub Actions Marketplace.
rworkflows
action stepsGitHub Actions are a powerful way to automatically launch workflows every time you push changes to a GitHub repository. This is a form of Continuous Integration/Deployment (CI/CD), which helps ensure that your code is always working as expected (without having to manually check each time).
Here, we have designed a robust, reusable, and flexible action specifically for the development of R packages. We also provide an R function to automatically generate a workflow file that calls the rworkflows
composite action:
Currently, rworkflows
action can perform the following tasks (with options to enable/disable/modify each step):
conda
environment.rworkflows::use_badges()
.Importantly, this workflow is designed to work with any R package out-of-the-box. This means you won’t have to manually edit any yaml files, just run the rworkflows::use_workflow()
function and you’re ready to go within seconds!
Note:
rworkflows
uses, was inspired by, and benefits from the work of many other projects, especially:
biocthis
,usethis
,actions/
,r-lib/actions
,bioc-actions
,JamesIves/github-pages-deploy-action
,docker/build-push-action
,bioconductor_docker
. For more details on how these projects relate torworkflows
, please see below.
Install and create the workflow in your R package’s project folder.
## in R
#### Install rworkflows R package ####
### For the stable CRAN release
if(!require("rworkflows")) install.packages("rworkflows")
### Or, for the latest development version
# if(!require("rworkflows")) remotes::install_github("neurogenomics/rworkflows")
### Create workflow file
path <- rworkflows::use_workflow()
Push to GitHub, and let everything else run automatically! You can check the status of your workflow by clicking on the Actions tab in your GitHub repo.
Note: If you want to skip running GitHub Actions on a particular push, simply add “[skip ci]” somewhere in the commit message, e.g.: git commit -m "Update README [skip ci]"
Introductory vignette for using rworkflows
.
Copy-and-paste instructions for creating a Docker or Singularity container with the rworkflows
R package pre-installed.
Interactive graph showing all the GitHub repos that currently use the rworkflows
action.
Talk on the background, motivation, and utility of rworkflows
.
Step-by-step tutorial showing how to use rworkflows
in an R package.
To use certain features of rworkflows
, you may need to set up one or more GitHub Secrets:
PAT_GITHUB
[Optional]: Can grant access to private repos on GitHub Actions. You can generate your very own Personal Authentication Token with usethis::create_github_token()
. See the GitHub docs for details.DOCKER_TOKEN
[Optional]: Allows GitHub Actions to push to a DockerHub account.rworkflows
builds upon the work of many others, especially the following:
biocthis
This workflow is largely inspired by the workflow generated by the use_bioc_github_action()
function within the biothis
package, developed by @lcolladotor.
rworkflows
r: "latest"
) and the name of your R package, as opposed to static names that are likely to become outdated (e.g. r: "4.0.1"
).README.Rmd
before rebuilding the documentation website.usethis
biocthis
was in turn inspired by usethis
.
actions/
A general set of GitHub Actions maintained by the core GitHub team.
r-lib/actions
A set of GitHub Actions for R development maintained by the Rstudio/Posit team.
bioc-actions
Bioconductor-oriented GitHub Actions created by @grimbough.
JamesIves/github-pages-deploy-action
Builds and deploys the GitHub Pages documentation website in the rworkflows
GHA workflows.
docker/build-push-action
A set of GitHub Actions for building/pushing Docker containers.
bioconductor_docker
Uses the official bioconductor/bioconductor_docker
Docker container.
NOTE: Whenever a new version of Bioconductor is released, the bioconductor/bioconductor_docker
container will often lag behind the actual Bioconductor releases for up to several days, due to the time it takes to update the container. This means that sometimes “devel” in Bioconductor/bioconductor_docker
is actually referring to the current “release” version of Bioconductor (i.e. the previous Bioc version’s “devel”). For further details, see this Issue, and the Bioconductor release schedule.
scFlow
This Dockerfile was partly adapted from the scFlow Dockerfile. Unlike other Dockerfiles, this one does not require any manual editing when applying to different R packages. This means that users who are unfamiliar with Docker do not have to troubleshoot making this file correctly. It also means that it will continue to work even if your R package dependencies change.
act
A very useful command line tool for testing GitHub Actions locally.
actions/runner-images
Runner images for each OS provided by GitHub.
actions/setup-miniconda
GitHub Action to setup Miniconda and conda environments.
## R version 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.2.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.4 jsonlite_1.8.8 renv_1.0.3
## [4] dplyr_1.1.4 compiler_4.3.1 BiocManager_1.30.22
## [7] tidyselect_1.2.0 rvcheck_0.2.1 scales_1.3.0
## [10] yaml_2.3.8 fastmap_1.1.1 here_1.0.1
## [13] ggplot2_3.4.4 R6_2.5.1 generics_0.1.3
## [16] knitr_1.45 yulab.utils_0.1.2 tibble_3.2.1
## [19] desc_1.4.3 dlstats_0.1.7 rprojroot_2.0.4
## [22] munsell_0.5.0 pillar_1.9.0 RColorBrewer_1.1-3
## [25] rlang_1.1.2 utf8_1.2.4 cachem_1.0.8
## [28] badger_0.2.3 xfun_0.41 fs_1.6.3
## [31] memoise_2.0.1.9000 cli_3.6.2 magrittr_2.0.3
## [34] rworkflows_1.0.1 digest_0.6.33 grid_4.3.1
## [37] rstudioapi_0.15.0 lifecycle_1.0.4 vctrs_0.6.5
## [40] data.table_1.14.10 evaluate_0.23 glue_1.6.2
## [43] fansi_1.0.6 colorspace_2.1-0 rmarkdown_2.25
## [46] tools_4.3.1 pkgconfig_2.0.3 htmltools_0.5.7
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.