Contributing

Contributions to SODAR are welcome and they are greatly appreciated! Every little bit helps, and credit will always be given. You can contribute in many ways detailed in the following subsection.

Note

Please ensure your feedback and contributions are directed at the correct repository. The SODAR repository contains the functionalities for sample sheets, landing zones, ontology access and iRODS operations. For more details, see SODAR App Development.

Other applications, project management functionalities and the general UI can be found in SODAR Core.

Warning

SODAR repositories and their issue trackers are publicly viewable. Please ensure you do not include any sensitive information such as patient or donor IDs (even pseudonymous ones) in your feedback or contributions. This includes e.g. issue descriptions, screenshots, logs for bug reports and documentation.

Types of Contributions

Report Bugs

Report bugs through the SODAR issue tracker in GitHub.

When reporting a bug, please follow the provided template. Make sure to include the following information:

  • Your operating system name and version.

  • Any details about your local setup that might be helpful in troubleshooting.

  • Detailed steps to reproduce the bug.

Make sure your report does not contain any sensitive information regarding e.g. patients and donors.

Fix Bugs

Look through the issue tracker for bugs. Anything tagged with bug and help wanted is open to whoever wants to implement it.

Implement Features

Look through the issue tracker for features. Anything tagged with feature and help wanted is open to whoever wants to implement it.

Write Documentation

SODAR can always use more documentation, whether as part of the SODAR Manual, in docstrings, or even on the web in blog posts, articles, and such.

For contributing to the SODAR Manual official documentation, see Documentation Guidelines.

For editing docstrings, see Code Conventions.

Submit Feedback

The best way to send feedback is to file an issue in the issue tracker.

If you are proposing a feature:

  • Follow the provided template.

  • Explain in detail how it would work.

  • Keep the scope as narrow as possible, to make it easier to implement.

  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started

Ready to contribute code to SODAR? Here are the steps to get started.

  1. Fork the sodar-server repo on GitHub.

  2. Clone your fork locally.

    $ git clone git@github.com:your_name_here/sodar-server.git

  3. Set up SODAR for development. For instructions see Installation for Development.

  4. Create a branch for local development. Make sure to base it on the dev branch. You can now make your changes locally.

    $ git checkout -b 123-branch-name dev

  5. When you’re done making changes, make sure to apply proper formatting using Black and the settings specified in the accompanying black.sh script. Next, check that your changes pass flake8. Finally, run the tests. It is recommended to use the Makefile to ensure the correct Django configuration for testing is selected.

    $ ./black.sh
$ flake8 .
$ make test
$ make test_samplesheets_vue

  6. Once the tests and flake8 pass, commit your changes and push your branch to GitHub.

    $ git add .
$ git commit -m "add/update/fix issue-description-here (#issue-id)"
$ git push origin 123-branch-name

  7. Submit a pull request through the GitHub website.

For specific requirements and recommendations regarding work branches, commits and pull requests, see SODAR Development Guidelines.

For guidelines regarding the code itself, see Code Conventions.