Contributing to imuRUN

Thank you for your interest in contributing to imuRUN! This document explains how to report issues, propose changes, and what to expect from the CI pipeline when you open a pull request.

Code of Conduct

All contributors are expected to be respectful and professional in all interactions — issues, pull requests, code reviews, and discussions. Constructive feedback is welcome; personal attacks and dismissive language are not.

Reporting Bugs

Use the bug report template when opening a new issue. It asks for a description, a minimal reprex, your sessionInfo() output, and your operating system.

Suggesting Features

Use the feature request template. Describe the use case and, if possible, how the feature fits into the existing CLI workflow (read inputs -> validate -> run an imuGAP fit). You can also open a blank issue if neither template fits.

Submitting Changes

Fork & branch. Create a feature branch off main (e.g. fix/missing-input-message or feature/xlsx-input).
Make your changes. Follow the style conventions below.
Test locally. Run R CMD check and the test suite before pushing (see the commands below).
Open a pull request against main with a clear description of what changed and why.

Development Workflow & `just` Recipes

imuRUN is pure R — it has no compiled code and no Stan toolchain. It imports imuGAP, which installs as an ordinary CRAN dependency.

We use just to automate development tasks:

Recipe	Description	Equivalent Base Command
`just`	Run full validation pipeline: clean, format, lint, docs, test	(compound command)
`just format`	Format R code using `air`	`air format .`
`just lint`	Lint R code using `air` and `lintr`	`air format . --check && Rscript -e "lintr::lint_package()"`
`just docs`	Regenerate roxygen documentation (`man/*.Rd`)	`Rscript -e "roxygen2::roxygenize()"`
`just install`	Install package into local R library	`R CMD INSTALL .`
`just test`	Run complete unit test suite via `testthat` / `devtools`	`Rscript -e "devtools::test()"`
`just test-fast`	Run tests, stopping on first failure	`Rscript -e "devtools::test(stop_on_failure = TRUE)"`
`just coverage`	Measure test coverage via `covr`	`Rscript -e "covr::package_coverage()"`
`just spell`	Check spelling across docs and vignettes via `spelling`	`Rscript -e "spelling::spell_check_package()"`
`just render`	Render all vignettes to HTML and PDF	`Rscript -e "rmarkdown::render(...)"`
`just site` / `just site-quick`	Fast build of `pkgdown` documentation site (no package reinstall)	`Rscript -e "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"`
`just site-full`	Full build of `pkgdown` site with package reinstallation	(compound: install + site)
`just site-preview [port=8000]`	Build and preview pkgdown documentation site on localhost	`Rscript -e "httpuv::runStaticServer(dir = 'docs', port = 8000)"`
`just data`	Regenerate bundled template, example workbooks, and test fixtures	`Rscript data-raw/make_workbooks.R`
`just build`	Build package `.tar.gz` archive	`R CMD build .`
`just check`	Check package archive	`R CMD check imuRUN_*.tar.gz --no-manual --no-tests`
`just check-cran`	Check package archive using strict CRAN settings	`R CMD check imuRUN_*.tar.gz --as-cran`
`just clean`	Clean up build artifacts and temporary files	`rm -f .tar.gz && rm -rf .Rcheck/`

Style

R code is linted with lintr (configuration in .lintr). Object names use snake_case; the bundled CLI script in inst/scripts/ is excluded from linting because it is a standalone script.
Formatting is handled by air (configuration in air.toml). Run air format . before committing.
Do not hand-edit generated files: documentation under man/ is produced by roxygen2 from the roxygen comments in R/.

What Happens When You Open a PR

Every pull request triggers four GitHub Actions workflows:

Workflow	What it does
R-CMD-check	Runs `R CMD check --as-cran` on Ubuntu (release, oldrel, devel) and Windows (release) — 4 jobs. The matrix is intentionally leaner than imuGAP’s because imuRUN is pure R (no compiled code). R-devel is allowed to fail without blocking the PR.
lint	Runs `lintr::lint_package()` and fails the build on any lint.
test-coverage	Runs the test suite under `covr` and uploads coverage to Codecov.
pkgdown	Builds the documentation site. On PRs this is a build-only check (no deployment); the site is deployed to GitHub Pages on pushes to `main`, published releases, and manual workflow dispatches.

All workflows should pass before a PR is merged.

Questions?

If something is unclear, open an issue or comment on an existing one — we are happy to help.