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Contributing to Signac development

The goal of this guide is to help you get up and contributing to Signac as quickly as possible. The guide is divided into two main pieces:

  1. Filing a bug report or feature request in an issue.
  2. Suggesting a change via a pull request.

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

Issues

GitHub issues are intended for filing bug reports, feature requests, or requests for changes to the documentation. For general discussion of analysis steps, opening a discussion topic on the Signac discussion forum is preferred.

When filing a bug report, it is extremely useful if you can include a minimal reproducible example so that we can quickly verify the problem, and then figure out how to fix it. There are three things you need to include to make your example reproducible: packages, data, code.

  1. Include the output of sessionInfo() in your issue. This lets us see what packages you have loaded and their version number

  2. The easiest way to include data is to use the small example dataset included in Signac (atac_small). Sometimes bugs are more complex and can't be reproduced using the small example data. In these cases, try to use one of the datasets used in the Signac vignettes. These are all publicly available data, and instructions on how to download these datasets are available on the vignette pages.

  3. Spend some time ensuring that your code is easy for others to read:

    • do your best to remove everything that is not related to the problem.
      The shorter your code is, the easier it is to understand.

    • make sure you've used spaces and your variable names are concise, but informative

    • use comments to indicate where your problem lies

    • properly format the code in your issue. Information about formatting is available here

Before posting your issue, make sure to start a new R session and run your reproducible example, and verify that it reproduces your issue.

Pull requests

To contribute a change to Signac, you follow these steps:

  1. Fork the Signac repository
  2. Clone your forked version of the repository
  3. Run git checkout develop to change to the develop branch
  4. Create a new branch for your changes (git checkout -b <new branch name>)
  5. Add your changes to the branch (git commit <files to commit>)
  6. Push your branch to github (git push)
  7. Open a pull request (PR) in the Signac repository

If you get stuck at any point, please reach out for help by opening a discussion topic on the Signac GitHub page.

If you're not familiar with git or GitHub, you can find some useful information here.

When reviewing your PR, we will check for the following things:

  1. Motivation. Your pull request should clearly and concisely motivate the need for change. You need to describe the problem and show how your pull request solves it. If the PR fixes a bug or implements a feature request that was reported in an issue, you should reference that issue in your PR.

  2. Only related changes. Before you submit your pull request, please check to make sure that you haven't accidentally included any unrelated changes. These make it harder to see exactly what's changed, and to evaluate any unexpected side effects.

  3. If you're adding new parameters or a new function or updating function documentation, you'll also need to update the documentation pages by running roxygen. Make sure to re-run devtools::document() on the code before submitting.

  4. We encourage you to add a testthat unit test if including new functionality.

This can seem like a lot of work but don't worry if your pull request isn't perfect. We are very happy to receive contributions and will help to update your PR to make it acceptable to merge into the Signac package. If you can't include all the things listed above, please still submit your PR and we can work together on improving it.

Finally, remember that Signac is being used by many people, and so we try not to add changes that will alter the existing functionality unless absolutely necessary, as that may break someone's code. Cases where existing functionality will be changed will be reserved for major version releases.