https://www.vlaanderen.be/inbo/en

Why should you use checklist?

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  • QC/QA
    • R code in packages or projects
    • quarto / bookdown documents
  • strict rules
    • defined at the organisation level
  • automated workflows
    • CI/CD pipelines via GitHub Actions

What does checklist check?

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ER project project code\nstyle code style project--code\nstyle spelling spelling project--spelling citation citation project--citation license license project--license file name file name project--file name folder\nstructure folder structure project--folder\nstructure package package package--code\nstyle package--spelling package--citation package--license package--file name CRAN CRAN package--CRAN DESCRIPTION DESCRIPTION package--DESCRIPTION documentation documentation package--documentation version version package--version NEWS NEWS package--NEWS test\ncoverage test coverage package--test\ncoverage pkgdown pkgdown package--pkgdown

Basic usage

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Topic Package Project
Start from scratch create_package() create_project()
Apply to existing code setup_package() setup_project()
run checks check_package() check_project()

More details: vignette("getting_started", package = "checklist")

Content of a skeleton

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  • checklist.yml
  • RStudio project file
  • git repository
  • README.md, DESCRIPTION LICENSE.md
  • pkgdown styling
  • Actions workflow for checklist
  • Issues and PR templates
  • AI agents
  • Code of Conduct and Contributing guidelines

Warning

AI agents are experimental.

Two packages

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citeme

  • Citation metadata
  • Copyright and license information
  • Settings at the organisation level
  • Functions relevant for other packages requiring author information

checklist

  • Depends on citeme
  • Setup for projects and packages
  • Complete quality control workflows

Enforcing organisational requirements

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  1. Assumes code under version control (git)
  2. Determines the git organisation based on git remotes
    • https://<git provider>/<git organisation>/<repository>.git
  3. Store organisation requirements in your citeme repository
  4. No citeme repository? Repository rule set applies
  5. No repository rule set? Default rule set applies

Your organisation’s citeme repository

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  • organisation.yml
  • license texts
  • .lintr style file
  • pkgdown style files

local cache

organisation.yml

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a list of organisations

  • official name(s) and email
  • allowed licenses + link to license text
  • rules for rightsholders, funders and publishers
  • website, logo, ROR,
    zenodo community,
    ORCID required?

Tip

  • Create interactively with new_org_list()

citeme: potential useful for other packages

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interactive user input

  • add_individual(), select_individual()
  • ask and validate: email, language, ORCiD, ROR, url
  • with non-interactive default: menu_first() and ask_yes_no()
    • useful for unit testing

Validation

email, ORCiD, ROR, url, language

extend citeme repository

Checklist GitHub Actions

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  • automatically installed
  • runs check_package() or check_project() on every push to GitHub
  • on package
    • pushes test coverage to https://about.codecov.io
    • on main branch
      • updates GitHub Pages website with pkgdown site
      • creates release based on NEWS.md
      • publishes Zenodo archive with DOI

Questions?

Flanders, state of the art Instituut voor Natuur- en Bosonderzoek

https://www.vlaanderen.be/inbo/en