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Contributing to MolEvolvR

Source: .github/CONTRIBUTING.md

This outlines how to propose a change to MolEvolvR. For a detailed discussion on contributing to this and other tidyverse packages, please see the development contributing guide and our code review principles.

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 our guide on 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.

  • Install and load the usethis package with:

    install.packages("usethis")

library("usethis")

  • Clone and fork the MolEvolvR package using:

    usethis::create_from_github("JRaviLab/MolEvolvR", fork = TRUE)

  • Install BiocManager from Bioconductor:

    if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.19")

  • Install other development dependencies and then ensure that the package passes R CMD check using devtools:

    install.packages("devtools")

library("devtools")

devtools::install_dev_deps()

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.

Code style

  • New code should follow the tidyverse 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.

  • Lint Your Code: Ensure your code adheres to our style guidelines by using lintr:

    install.packages("lintr")

library("lintr")

lintr::lint("path/to/your/file.R")

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