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Contributing to imuGAP

Source: CONTRIBUTING.md

Thank you for your interest in contributing to imuGAP! 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 model workflow (imuGAP() -> Stan sampling -> post-processing). You can also open a blank issue if neither template fits.

Submitting Changes

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

Local Development Commands

# Full rebuild + install (required after editing any .stan file)
R CMD INSTALL --preclean .

# Regenerate documentation from roxygen comments
Rscript -e 'devtools::document()'

# Run the test suite
Rscript -e 'devtools::test()'

# Lint the package (config in .lintr)
Rscript -e 'lintr::lint_package()'

# Build and check
R CMD build . && R CMD check imuGAP_*.tar.gz

Style

  • R code is linted with lintr (configuration in .lintr). R/stanmodels.R and inst/analysis/ are excluded from linting because they are generated or standalone scripts, respectively.
  • Do not hand-edit generated files: R/stanmodels.R, src/stanExports_*.{cc,h}, configure, and configure.win are all produced by rstantools::rstan_config().
  • Stan model variants are composed via #include toggling in the top-level .stan files — prefer toggling includes over duplicating whole model files.

What Happens When You Open a PR

Every pull request triggers two GitHub Actions workflows:

Workflow What it does
R-CMD-check Runs R CMD check --as-cran on Ubuntu, macOS, and Windows across R release, oldrel, and devel (9 jobs total). R-devel jobs are allowed to fail without blocking the PR. Stan compilation artifacts are cached per OS and R version.
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.

Both 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.