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If you use the templateR R package template, or any of the
rworkflows suite tools,
please cite:
Brian M. Schilder, Alan E. Murphy, & Nathan G. Skene (2023) The rworkflows suite: automated continuous integration for quality checking, documentation website creation, and containerised deployment of R packages, Research Square; https://doi.org/10.21203/rs.3.rs-2399015/v1
templateR is a template designed to make developing new R packages
easy by providing:
- DESCRIPTION, vignettes/, tests/, R/, man/, inst/: Basic skeleton for the package itself.
- README.Rmd: Auto-populates based on the DESCRIPTION file (that can be knit to create README.md). Also contains badges that automatically update themselves.
- inst/hex/hexSticker.Rmd: Template for creating hex stickers.
- .github/workflows/*.yml: GitHub
Actions
workflow files that will automatically trigger code checks and pushing
images to DockerHub every time you
make a push to your GitHub repo (from
r_workflows). - inst/CITATIONS : Allows users of your package to call
citation("<packageName>"). Also used to auto-populate the README.Rmd.
To get started, simply click on the green Use this template button
at the top right of the templateR repo.
Before pushing changes to your new R package, you will need to add two GitHub Secrets:
PAT_GITHUB: Speeds up installations and gives access to private repos on GitHub Actions. You can generate your very own Personal Authentication Token using these instructions.CODECOV_TOKEN: Allows code coverage results to be displayed via therworkflows::use_badges()at the top of the README.Rmd. This Codecov token is repository-specific and can be found here.DOCKER_TOKEN: Allows GitHub Actions to push to the neurogenomicslab DockerHub account. Ask a fellow Neurogenomics Lab member for this token.
The GitHub Actions workflows included in this template will automatically create a documentation website for your package via GitHub Pages. This requires several initial setup steps (you only need to do these once per repo):
- After check-bioc-docker.yml has successfully run on Ubuntu for the first, a new branch will appear in your repo called “gh-pages”.
- In the Settings tab of your repo, go to Pages on the left.
Then under Source select
"branch: gh-pages"and"root"from the respective dropdown menus. Finally, click the Save button.
Note: If you don’t have admin access to your repo, you will need to ask someone who does to change this for you.
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If you use templateR, please cite:
author1, author2, author3 (publicationYear) articleTitle, journalName; volumeNumber, linkToPublication
if(!require("remotes")) install.packages("remotes")
remotes::install_github("neurogenomics/templateR")
library(templateR)UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
GitHub
DockerHub