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Contributing to dar

Source: .github/CONTRIBUTING.md

This outlines how to propose a change to dar. For more detailed info about contributing to this, and other tidyverse packages, please see the development contributing guide.

Fixing typos

You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the source file. This generally means you’ll need to edit roxygen2 comments in an .R, not a .Rd file. You can find the .R file that generates the .Rd by reading the comment in the first line.

Bigger changes

If you want to make a bigger change, it’s a good idea to first file an issue and make sure someone from the team agrees that it’s needed. If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex (this will also help you write a unit test, if needed).

Pull request process

  • Fork the package and clone onto your computer. If you haven’t done this before, we recommend using usethis::create_from_github("MicrobialGenomics-IrsicaixaOrg/dar", fork = TRUE).

  • Install all development dependencies with devtools::install_dev_deps(), and then make sure the package passes R CMD check by running devtools::check(). If R CMD check doesn’t pass cleanly, it’s a good idea to ask for help before continuing.

  • Create a Git branch for your pull request (PR). We recommend using usethis::pr_init("brief-description-of-change").

  • Make your changes, commit to git, and then create a PR by running usethis::pr_push(), and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should contain Fixes #issue-number.

  • For user-facing changes, add a bullet to the top of NEWS.md (i.e. just below the first header). Follow the style described in https://style.tidyverse.org/news.html.

Code style

  • New code should follow the tidyverse style guide. You can use the styler package to apply these styles, but please don’t restyle code that has nothing to do with your PR.

  • We use roxygen2, with Markdown syntax, for documentation.

  • We use testthat for unit tests. Contributions with test cases included are easier to accept.

Package website

Every exported topic must be listed in _pkgdown.yml. Validate the reference index locally before opening a pull request:

Rscript --vanilla dev/check-pkgdown.R

This check validates the pkgdown configuration without publishing the website. GitHub Actions runs the same validation for pull requests and deploys the full site only from devel.

Bioconductor lifecycle

Released functions follow the three-cycle Bioconductor lifecycle: deprecated in one release, defunct in the next, and removed from R code and NAMESPACE in the following cycle while their migration alias remains documented. Every lifecycle change must name its target releases in NEWS and the statistical model vignette. BiocCheck warnings that point to intentional .Deprecated() or .Defunct() calls are reviewed against that schedule; other warnings must be fixed or justified in the pull request.

Code of Conduct

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