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Contributing to plyxp

Source: CONTRIBUTING.md

Thank you for your interest in improving plyxp. Contributions of all kinds are welcome, including bug reports, documentation fixes, and new features.

Reporting issues and asking questions

Please use the GitHub issue tracker for bug reports and feature requests. For usage questions, please open a discussion. When reporting a bug, include:

  • a minimal reproducible example (the reprex package is helpful), ideally using a small SummarizedExperiment;
  • the output of sessionInfo();
  • what you expected to happen and what happened instead.

Usage questions may also be asked on the Bioconductor support site using the plyxp tag.

Development setup

plyxp follows Bioconductor’s release model. New work targets the devel branch, which corresponds to Bioconductor devel.

# install development dependencies
install.packages(c("devtools", "BiocManager"))
BiocManager::install(version = "devel")

# from the root of your clone
devtools::install_dev_deps()
devtools::load_all()

Running tests and checks

Tests use testthat and live in tests/testthat/.

devtools::test()      # run the test suite
devtools::document()  # regenerate documentation after editing roxygen comments
devtools::check()     # full R CMD check
BiocCheck::BiocCheck(".")  # Bioconductor-specific checks

Continuous integration (.github/workflows/check-bioc.yml) runs these checks on every push and pull request.

Submitting changes

  1. Fork the repository and create a feature branch from devel.
  2. Make your change, adding tests for new behavior or fixed bugs.
  3. Document user-facing changes with roxygen and add an entry to NEWS.
  4. Bump the patch version in DESCRIPTION (e.g., 1.7.4 to 1.7.5), as required by Bioconductor for changes to be propagated.
  5. Ensure devtools::test() and devtools::check() pass.
  6. Open a pull request against devel describing the motivation for the change and linking any related issues.

For larger changes, please open an issue first to discuss the design.

Code of conduct

Please be respectful and constructive. This project follows the Bioconductor Code of Conduct.