Contributing to NACHO

Thanks for thinking about contributing to NACHO. This page explains how to propose a change.

Where to start

• Questions go in Discussions, Q&A.
• Ideas for new features go in Discussions, Ideas.
• Confirmed bugs go through the bug report form, with a minimal reprex.

Before you start a substantial pull request, please open an issue or a discussion first, so we can agree it’s worth doing.

Fixing typos

You can fix small typos in the documentation straight from the GitHub web interface, as long as you edit the source file.

• Edit the roxygen comment in the .R file under R/.
• Don’t edit the .Rd files under man/, because they are generated.
• Edit README.Rmd, not README.md, and render it with devtools::build_readme().

Pull request process

• Create a Git branch for each pull request. Name it with a conventional commit type, for example fix/plexset-detection.

• Format R code with Air (air format .), and please don’t reformat code your change doesn’t touch.

• Check the code with lintr (lintr::lint_package()) and fix what it reports in the lines you change.

• Document functions with roxygen2 using Markdown, then run devtools::document().

• Add or update tests with testthat (edition 3). Pull requests with tests are much easier to review.

• Run devtools::check() before you open the pull request.

• GitHub Actions runs R CMD check on macOS, Windows and Ubuntu for every pull request that isn’t a draft.

• For user-facing changes, add an entry to NEWS.md under # NACHO (development version). Entries sit under a section such as ## Fixes, grouped by the file they change, with one prefix: sentence. item each:

  - In `R/geometric_housekeeping.R`,
    - fix: replace background-corrected housekeeping counts below 1 with 1. ([#53](https://github.com/mcanouil/NACHO/issues/53))

Code of Conduct

NACHO is released with a Contributor Code of Conduct. By contributing, you agree to follow it.