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().

Development setup

NACHO uses rig to manage the package library of the project. Install rig, then run this command in the root of the repository:

rig proj sync

The command installs the dependencies from rproj.toml and NACHO itself into .rvenv/. The .Renviron file of the repository tells R to use this library. The command does not install development tools such as devtools and lintr. Install them in the tools library of rig, which rig adds to every project (see rig proj --help). If you do not use rig, R shows ! Project is not synced. Run: rig proj sync when it starts in the repository, and uses your usual library.

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.