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Contributing

Galaxy welcomes new development! This document briefly describes how to contribute to the core galaxy repository. For general information on the Galaxy ecosystem, please see the Galaxy Community Hub. For a description of how the Galaxy code is structured, see the Galaxy Code Architecture slides that are part of the Galaxy Training Materials.

Before you Begin

If you have an idea for a feature to add or an approach for a bugfix, it is best to communicate with Galaxy developers early. The primary venue for this is the GitHub issue tracker. Browse through existing GitHub issues and if one seems related, comment on it. For more direct communication, Galaxy developers are generally available on the Galaxy Matrix space, in particular on the galaxyprojec/dev channel and in the various Working Group channels.

If you're looking to help but aren't sure where to start, we also maintain a tag on GitHub for smaller issues we believe would make the best entry points for new developers.

Reporting a new issue

If no existing Galaxy issue seems appropriate, a new issue can be opened using this form.

How to Contribute

All changes to the core galaxy repository should be made through pull requests (with just two exceptions outlined below).

If you are new to Git, the Software Carpentry's Version Control with Git tutorial is a good place to start. More learning resources are listed at https://help.github.com/en/github/getting-started-with-github/git-and-github-learning-resources

  1. Make sure you have a free GitHub account. To increase the security of your account, we strongly recommend that you configure two-factor authentication. Additionally, you may want to sign your commits.

  2. Fork the galaxy repository on GitHub to make your changes. To keep your copy up to date with respect to the main repository, you need to frequently sync your fork:

    $ git remote add upstream https://github.com/galaxyproject/galaxy
$ git fetch upstream
$ git checkout dev
$ git merge upstream/dev

  3. Choose the correct branch to develop your changes against.

    • The master branch is kept in sync with the latest tagged release, but should not be used as the base (i.e. target) branch of a pull request.

    • Additions of new features to the codebase should be based off the dev branch (git checkout -b feature_branch dev), with few exceptions.

    • Most bug fixes should target the oldest supported release exhibiting the issue (git checkout -b bugfix_branch release_XX.XX).

    • Serious security problems should not be fixed via pull request - please see the Galaxy security policies for information about responsibly disclosing security issues.

  4. If your changes modify code please ensure the resulting files conform to the style guidelines below.

    If you are working on the Galaxy user interface (i.e. JavaScript, styles, etc.), see more information in the client README.

  5. Galaxy contains hundreds of tests of different types and complexity and running each is difficult and probably not reasonable on your workstation. So please review the running tests documentation and run any that seem relevant.

    If possible, also try to add new tests for the features added or bugs fixed by your pull request.

    Developers reviewing your pull request will be happy to help you add or run the relevant tests as part of the pull request review process.

  6. Write a useful and properly formatted commit message. Follow these guidelines and template, in particular start your message with a short imperative sentence on a single line, possibly followed by a blank line and a more detailed explanation.

    In the detailed explanation it's good to include relevant references (e.g. any GitHub issue being fixed) using full URLs, and errors or tracebacks the commit is meant to fix. You can use the Markdown syntax for lists and code highlighting, wrapping the explanation text at 72 characters when possible.

    Example of a good commit message: https://github.com/galaxyproject/galaxy/commit/0429c4d515536f9cca6b70b2abeb019de807c955

  7. Commit and push your changes to your fork.

  8. Open a pull request with these changes. Your pull request message ideally should include:

    • Why you made the changes (e.g. references to GitHub issues being fixed).

    • A description of the implementation of the changes.

    • How to test the changes, if you haven't included specific tests already.

  9. The pull request should pass all the continuous integration tests which are automatically started by GitHub.

  10. Your pull request will be handled according to some rules.

  11. If, before your pull request is merged, conflicts arise between your branch and the target branch (because other commits were pushed to the target branch), you need to either:

    1. rebase your branch on top of the target branch, or
    2. merge the target branch into your branch.

    We recommend the first approach (i.e. rebasing) because it produces cleaner git histories, which are easier to bisect. If your branch is called feature_branch and your target branch is dev, you can rebase your branch with the following commands:

    $ git checkout feature_branch
$ git pull
$ git fetch upstream
$ git rebase upstream/dev

    Once you have resolved the conflicts in all commits of your branch, you can force-push the rebased branch to update the pull request:

    $ git push --force

Style guidelines

Python

  • Galaxy follows PEP-8, with particular emphasis on readability being the ultimate goal:
    • 4 spaces (not tabs!) per indentation level
    • divergences from PEP-8 are listed in the [flake8] section of the .flake8 file and in the [tool.ruff] section of the pyproject.toml file.
    • The Python code base is automatically formatted using isort (for imports) and black. To easily format your Python code before submitting your contribution, please either use make diff-format or run isort FILE; black FILE for each FILE you modify.
  • Python docstrings need to be in reStructured Text (RST) format and compatible with Sphinx.
  • String formatting should normally be done using formatted string literals (f-strings), except:
    • when the format string is kept in a separate variable, in which case the string format() method should be used;
    • when formatting a log message, in which case it's better to use a printf-style message format string and pass its arguments to the logging method separately. This is a bit more efficient than using f-strings and allows for better log aggregation. For more information, see this blog post.

Documentation

General documentation (e.g. admin, development, release notes) is found in the doc/source/ directory. The documentation source files need to be written in one of these markup languages:

A Quick Note about Tools

For the most part, Galaxy tools should be published to a Tool Shed and not in this repository directly. More information about tool development can be found on the community hub.