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Contributing to spatialdataR

Source: .github/CONTRIBUTING.md

This document gives some information on how you can contribute to spatialdataR.

Reporting bugs & requesting new feature

Our team has a wide variety of expertise but Spatial Biology is a vast field and it is possible that we are not supporting your specific use case simply because we don’t know about it.

Just hearing from you, how you use spatialdataR, and how it could be improved, is a very valuable contribution.

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 the tidyverse guide on how to create a great issue for more advice.

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 to make sure someone from the team agrees that it’s needed, and to discuss how it interacts with other pending changes.

As a rule of thumb, please start with a brainstorming issue if you are considering the following:

  • breaking changes
  • addition of a new dependency

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("HelenaLC/spatialdataR", fork = TRUE).

  • Install all development dependencies with pak::local_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 and check that the package passes R CMD check by running devtools::check() again. Commit the changes to git, and then create a PR by running usethis::pr_push(), and follow 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.

  • Summarize key changes in NEWS.md (i.e. just below the first header). See existing entries for inspiration on length, depth, and style.

Code style

  • We follow the Bioconductor coding style guide. In particular, it differs from other popular style guide on the following points:

    • Indents are 4 spaces
    • Function and variable names use camelCase

  • 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 spatialdataR follows the Bioconductor Code of Conduct. By contributing to this project you agree to abide by its terms.