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hubDevs

The goal of hubDevs is to provide utilities for creating and standardising Hubverse packages

Installation

You can install the development version of hubDevs from GitHub with:

# install.packages("remotes")
remotes::install_github("Infectious-Disease-Modeling-Hubs/hubDevs")

Initialise a hubverse package

Create a hubverse package skeleton

First create a package skeleton.

library(hubDevs)

temp_dir <- tempdir()
path <- fs::path(temp_dir, "testPkg")
create_hubdev_pkg(path)
#> ✔ Creating '/var/folders/p2/ywqk6z3n5nq3csvhfnvwfpzh0000gp/T/RtmpIUZtzk/testPkg/'
#> ✔ Setting active project to '/private/var/folders/p2/ywqk6z3n5nq3csvhfnvwfpzh0000gp/T/RtmpIUZtzk/testPkg'
#> ✔ Creating 'R/'
#> ✔ Writing 'DESCRIPTION'
#> Package: testPkg
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.0.0.9000
#> Authors@R (parsed):
#>     * Anna Krystalli <annakrystalli@googlemail.com> [aut, cre] (<https://orcid.org/0000-0002-2378-4915>)
#> Description: What the package does (one paragraph).
#> License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#>     license
#> Encoding: UTF-8
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.2.3
#> ✔ Writing 'NAMESPACE'
#> ✔ Writing 'testPkg.Rproj'
#> ✔ Adding '^testPkg\\.Rproj$' to '.Rbuildignore'
#> ✔ Adding '.Rproj.user' to '.gitignore'
#> ✔ Adding '^\\.Rproj\\.user$' to '.Rbuildignore'
#> ✔ Setting active project to '<no active project>'
#> ✔ Setting active project to '/private/var/folders/p2/ywqk6z3n5nq3csvhfnvwfpzh0000gp/T/RtmpIUZtzk/testPkg'
#> ✔ Adding '.DS_Store', '.Rhistory', '.Rdata', '.httr-oauth', and '.secrets' to '.gitignore' and '.Rbuildignore'
#> 
#> ✔ Adding 'testthat' to Suggests field in DESCRIPTION
#> ✔ Adding '3' to Config/testthat/edition
#> ✔ Creating 'tests/testthat/'
#> ✔ Writing 'tests/testthat.R'
#> • Call `use_test()` to initialize a basic test file and open it for editing.
#> ✔ Adding 'MIT + file LICENSE' to License
#> ✔ Writing 'LICENSE'
#> ✔ Writing 'LICENSE.md'
#> ✔ Adding '^LICENSE\\.md$' to '.Rbuildignore'
#> ✔ Writing 'README.Rmd'
#> ✔ Adding '^README\\.Rmd$' to '.Rbuildignore'
#> ✔ Adding Lifecycle: experimental badge to 'README.Rmd'
#> • Re-knit 'README.Rmd' with `devtools::build_readme()`
#> ✔ Adding CRAN status badge to 'README.Rmd'
#> • Re-knit 'README.Rmd' with `devtools::build_readme()`
#> ℹ Installing testPkg in temporary library
#> ℹ Building
#>   '/private/var/folders/p2/ywqk6z3n5nq3csvhfnvwfpzh0000gp/T/RtmpIUZtzk/testPkg/README.Rmd'
#> ✔ Creating '.github/'
#> ✔ Adding '^\\.github$' to '.Rbuildignore'
#> ✔ Adding '*.html' to '.github/.gitignore'
#> ✔ Writing '.github/CODE_OF_CONDUCT.md'
#> ✔ Writing '.github/CONTRIBUTING.md'
#> ✔ Initialising Git repo
#> ✔ Adding '.quarto' to '.gitignore'
#> ✔ Writing '.git/hooks/pre-commit'
#> ✔ Setting active project to '<no active project>'

This creates all basic infrastructure including a hubverse template README, logo, community documents, MIT LICENSE and initiates the package as a git repository.

#> /var/folders/p2/ywqk6z3n5nq3csvhfnvwfpzh0000gp/T/RtmpIUZtzk/testPkg
#> ├── .Rbuildignore
#> ├── .git
#> │   ├── HEAD
#> │   ├── config
#> │   ├── description
#> │   ├── hooks
#> │   │   ├── README.sample
#> │   │   └── pre-commit
#> │   ├── info
#> │   │   └── exclude
#> │   ├── objects
#> │   │   ├── info
#> │   │   └── pack
#> │   └── refs
#> │       ├── heads
#> │       └── tags
#> ├── .github
#> │   ├── .gitignore
#> │   ├── CODE_OF_CONDUCT.md
#> │   └── CONTRIBUTING.md
#> ├── .gitignore
#> ├── DESCRIPTION
#> ├── LICENSE
#> ├── LICENSE.md
#> ├── NAMESPACE
#> ├── R
#> ├── README.Rmd
#> ├── README.md
#> ├── man
#> │   └── figures
#> │       └── logo.png
#> ├── testPkg.Rproj
#> └── tests
#>     ├── testthat
#>     └── testthat.R

Set up package on GitHub

Once the new package is launched, you can set it up on GitHub with:

Note: Your GitHub token must have rights to create a repository in the hubverse organisation for this to succeed.

The function runs a number of internal utilities for setting up a hubverse package on GitHub:

  • Creates a repo in the hubverse GitHub organisation
  • Adds details of the repository to the DESCRIPTION file
  • Initialises pkgdown documentation including configuring site to use the hubStyle pkgdown template.
  • Creates GitHub Action workflows for:
    • standard R CMD CHECK
    • test coverage
    • linting with lintr
    • building pkgdown documentation and deploying production docs to GitHub Pages and PR previews to a Netlify site

Individual Utilities

The high level functions above are wrappers for a number of individual utilities that can be run separately.

Add community documents

To add a Code of Conduct and Contributing guide to your package, run:

This runs use_hubdev_coc() and use_hubdev_contributing() and creates a CODE_OF_CONDUCT.md and CONTRIBUTING.md in the .github/ directory.

Configure pkgdown site to use hubverse defaults

To configure your package site to pkgdown with the hubStyle template, and deploy using the hubverse’s pkgdown deployment GitHub action run:

The function performs a number of actions to configure a hubverse package’s pkgdown site to use the hubStyle template for docs styling.

  • Runs use_pkgdown() to initialise pkgdown documentation.
  • Runs use_github_pages() to initialise GitHub Pages for the package.
  • Adds a GitHub Action workflow for building pkgdown documentation and deploying to GitHub Pages (productions) and Netlify (PR previews) using use_hubdev_pkgdown_action().
  • Adds the hubStyle repository to the DESCRIPTION’s Config/Needs/website property using add_website_needs().
  • Creates a favicon for the package using the hubStyle logo.
  • Overwrites standard _pkgdown.yml file with customised configuration to use the hubverse hubStyle package for docs styling.

Code of Conduct

Please note that the hubDevs package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Contributing

Interested in contributing back to the open-source Hubverse project? Learn more about how to get involved in the Hubverse Community or how to contribute to the hubDevs package.