galaxy/CONTRIBUTING.md

# Contributing

Galaxy welcomes new development!  This document briefly describes how to
contribute to the [core galaxy
repository](https://github.com/galaxyproject/galaxy).
For information on contributing more broadly to the Galaxy ecosystem and a
deeper discussion of some of these points - please see the
[Develop](https://galaxyproject.org/develop) section of the [Galaxy Community
Hub](https://galaxyproject.org) and the [Galaxy Code
Architecture](https://training.galaxyproject.org/training-material/topics/dev/tutorials/architecture/slides.html#1) slides that are part of the [Galaxy Training
Materials](https://training.galaxyproject.org/).

## 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](https://github.com/galaxyproject/galaxy/issues).
Browse through existing GitHub issues and if one seems related, comment on it.
For more direct communication, Galaxy developers are generally available via
[Gitter](https://gitter.im/galaxyproject/dev) and on the [development mailing
list](http://dev.list.galaxyproject.org).

If you're looking to help but aren't sure where to start, we also maintain a
[tag](https://github.com/galaxyproject/galaxy/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22)
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](https://github.com/galaxyproject/galaxy/issues/new).

## How to Contribute

All changes to the [core galaxy
repository](https://github.com/galaxyproject/galaxy) 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](https://swcarpentry.github.io/git-novice/) 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](https://github.com/) account. To increase
   the security of your account, we strongly recommend that you configure
   [two-factor authentication](https://docs.github.com/en/github/authenticating-to-github/securing-your-account-with-two-factor-authentication-2fa).
   Additionally, you may want to [sign your commits](https://docs.github.com/en/github/authenticating-to-github/managing-commit-signature-verification).

2. Fork the [galaxy repository](https://github.com/galaxyproject/galaxy) 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](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/syncing-a-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](doc/source/project/organization.rst#handling-pull-requests).

   * 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](SECURITY_POLICY.md) for information about
     responsibly disclosing security issues.

4. If your changes modify code please ensure the resulting files conform to
   the [style guidelines](#style-guidelines) below.

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

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](test/TESTING.md) 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](https://git-scm.com/book/en/v2/Distributed-Git-Contributing-to-a-Project#_commit_guidelines),
   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 external references
   (e.g. GitHub issue fixed) using full URLs, and errors or tracebacks the
   commit is supposed 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](https://help.github.com/en/github/using-git/pushing-commits-to-a-remote-repository).

8. Open a [pull
   request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-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 using e.g. Travis CI.

10. Your pull request will be handled according to [some
   rules](doc/source/project/organization.rst#handling-pull-requests).

## Style guidelines

### Python

- Galaxy follows [PEP-8](https://www.python.org/dev/peps/pep-0008/), 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 `setup.cfg`
  file.
- Python imports should be ordered following the
  [smarkets](https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py)
  style.
- Python [docstrings](http://www.python.org/dev/peps/pep-0257/) need to be in
  [reStructured Text (RST)](https://docutils.sourceforge.io/rst.html) format and
  compatible with [Sphinx](https://www.sphinx-doc.org).

## A Quick Note about Tools

For the most part, Galaxy tools should be published to a [Tool
Shed](https://galaxyproject.org/toolshed) and not in this repository directly.
More information about tool development can be found [on the community
hub](https://galaxyproject.org/develop).