Skip to contents

Contributing to RGraphSpace

Source: .github/CONTRIBUTING.md

This outlines how to propose a change to RGraphSpace.

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). See how to create a great issue for more advice.

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("sysbiolab/RGraphSpace", fork = TRUE).

  • Install all development dependencies 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.

Code style

  • Because RGraphSpace integrates different systems, we use more than one style. The main GraphSpace methods are S4 generics and follow S4 class style. Whenever possible, S3 accessors follow the tidyverse style guide; accessors also use the gs_* prefix to reduce the risk of name conflicts with other packages, particularly the graph-analysis packages commonly used alongside RGraphSpace. Functions that build on ggplot2 geoms follow the ggplot2 style. Graph attributes use camelCase to coexist with ggplot2 aesthetics, serving as a functional boundary between two different aesthetic interfaces (see Why camelCase attribute names?).

  • 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 RGraphSpace project is released with a Contributor Code of Conduct. By contributing to this project you agree to abide by its terms.