.github/CONTRIBUTING.md

In wolski/prolfqua: Proteomics Label Free Quantification

Contributing to the prolfqua package

Code of conduct

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

How you can contribute

There are several ways you can contribute to this project. If you want to know more about why and how to contribute to open source projects like this one, see this Open Source Guide.

Share the work

Think prolfqua is useful? Let others discover it, by telling them in person, via Twitter or a blog post.

Using prolfqua for a paper you are writing? Retrieve all citation information by running citation("prolfqua") in the R console.

Ask a question

Using prolfqua and got stuck? Browse the documentation to see if you can find a solution. Still stuck? Post your question as an issue on GitHub.

Want to ask a question in private? Contact the package maintainer by mail.

Propose an idea

Have an idea for a new prolfqua feature? Take a look at the documentation and issue list to see if it isn't included or suggested yet. If not, suggest your idea as an issue on GitHub. While we can't promise to implement your idea, it helps to:

• Explain in detail how it would work.
• Keep the scope as narrow as possible.

See below if you want to contribute code for your idea as well.

Get support for your metabolic cart

Do you want your metabolic cart to be supported by the prolfqua package? Consider sending me example raw data files via mail.

Report a bug

Using prolfqua and discovered a bug? That's annoying! Don't let others have the same experience and report it as an issue on GitHub so we can fix it. A good bug report makes it easier for us to do so, so please include:

• Any details about your local setup that might be helpful in troubleshooting.
• Detailed steps to reproduce the bug.

Improve the documentation

Noticed a typo on the website? Think a function could use a better example? Good documentation makes all the difference, so your help to improve it is very welcome!

The website

This website is generated with pkgdown. That means we don't have to write any html: content is pulled together from documentation in the code, vignettes, Markdown files, the package DESCRIPTION and _pkgdown.yml settings. If you know your way around pkgdown, you can propose a file change to improve documentation. If not, report an issue and we can point you in the right direction.

Function documentation

Functions are described as comments near their code and translated to documentation using roxygen2. If you want to improve a function description:

1. Go to R/ directory in the code repository.
2. Look for the file with the name of the function.
3. Propose a file change to update the function documentation in the roxygen comments (starting with #').

Contribute code

Care to fix bugs or implement new functionality for prolfqua? Awesome! Have a look at the issue list and leave a comment on the things you want to work on. See also the development guidelines below.

Development guidelines

We try to follow the GitHub flow for development.

1. Fork this repo and clone it to your computer. To learn more about this process, see this guide.
2. If you have forked and cloned the project before and it has been a while since you worked on it, pull changes from the original repo to your clone by using git pull upstream master.
3. Open the RStudio project file (.Rproj).
4. Make your changes:
   • Write your code.
   • Test your code (bonus points for adding unit tests).
   • Document your code (see function documentation above).
   • Check your code with devtools::check() and aim for 0 errors and warnings.
5. Commit and push your changes.
6. Submit a pull request.

wolski/prolfqua documentation built on Oct. 31, 2024, 9:22 a.m.