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Contributing to rTASSEL

Source: .github/CONTRIBUTING.md

Thank you for taking time to contribute!

Since rTASSEL is an open source project and is maintained by a small team, we encourage interested members of the research community to seek out issues and propose changes where needed. In this document, we detail outlines to how you may contribute to the rTASSEL project.

Minor changes

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. Since we use roxygen2 for document generation, please alter only typos found in .R files and not .Rd files. roxygen2 comments can be identified within .R files with the #' header.

Bigger changes and bug reporting

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).

Submitting a pull request

  • Fork the rTASSEL package from GitHub and clone onto your computer. If you are not familiar with git actions, the usethis package provides a series of git-based methods to help you out. For forking, you can use:

    usethis::create_from_github("maize-genetics/rTASSEL", fork = TRUE)

  • From this fork, make sure you have all dependencies installed for rTASSEL. This can be accomplished using devtools::install_dev_deps().

  • Once all dependencies are installed, run an R CMD check using either RStudio’s integrated check features under the “Build” tab, or by running devtools::check() in the console.

  • If build check does not fail, create a Git branch for your pull request (PR). The usethis package has a method for this that you may wish to use:

    usethis::pr_init("brief-description-of-change")

  • Make your changes, commit to git, and then create a PR by running usethis::pr_push() or other git-related commands/software, and following the prompts in your browser. Please provide a descriptive PR. Your PR should have the following:

    • Descriptive title (briefly document the change)
    • What number does this PR fix? Please provide this in the body of the PR with the language Fixes #<issue number>.

  • If accepted, this will be documented in the NEWS material (NEWS.md) with the next version update and acknowledgement of the user.

Code style

  • We try to follow the guidelines proposed by Bioconductor in terms of code style. When styling code, please only style your own code and not restyle code that falls out of your PR scope.

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

Unit testing

  • Please test your code! Like all good scientific projects, rigorous testing is a must. We use testthat for unit tests. Contributions with test cases included are easier to accept and will have higher priority for integration.

Code of Conduct

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