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Contributing to clustifyr

Source: .github/CONTRIBUTING.md

Thank you for using and helping to improve clustifyr and its data hub clustifyrdatahub. Any discussion of bugs, fixes, and feature enhancements is greatly appreciated.

Fixing typos

You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the source file. This generally means you’ll need to edit roxygen2 comments in an .R, not a .Rd file. You can find the .R file that generates the .Rd by reading the comment in the first line.

Bigger changes

If you want to make a bigger change, it’s a good idea to first file an issue and make sure someone from the team agrees that it’s needed. If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex (this will also help you write a unit test, if needed).

Pull request process

  • Fork the package and clone onto your computer. If you haven’t done this before, we recommend using usethis::create_from_github("rnabioco/clustifyr", fork = TRUE).

  • Install all development dependences with devtools::install_dev_deps(), and then make sure the package passes R CMD check by running devtools::check(). If R CMD check doesn’t pass cleanly, it’s a good idea to ask for help before continuing.

  • Create a Git branch for your pull request (PR). We recommend using usethis::pr_init("brief-description-of-change").

  • Make your changes, commit to git, and then create a PR by running usethis::pr_push(), and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should contain Fixes #issue-number.

  • For user-facing changes, add a bullet to the top of NEWS.md (i.e. just below the first header). Follow the style described in https://style.tidyverse.org/news.html.

*. Increase the version numbers in the README.md and DESCRIPTION to the new version that this Pull Request would represent. Please follow Bioconductor versioning schemes.

*. Please request code review for Pull Requests. Once you have the sign-off of two other developers, you may then merge the updated code.

Code style

  • New code should follow the Bioconductor style guide. You can use the styler package to apply these styles, but please don’t restyle code that has nothing to do with your PR.

  • We use roxygen2, with Markdown syntax, for documentation.

  • We use testthat for unit tests. Contributions with test cases included are easier to accept.

Code of Conduct

Please note that the clustifyr project is released with a Contributor Code of Conduct. By contributing to this project you agree to abide by its terms.