Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit
helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

• Web development with the Dash for the OpenOmics dashboard webserver.
• Documentation standards for the OpenOmics Python API.
• Organize the library of genomics, functional ontologies, interactions, and sequence databases for variety of
  biological studies.
• Implement general purpose utilities for importing various fasta, gtf and sequencing files.

Report Bugs

Report bugs at openomics/issues.

If you are reporting a bug, please include:

• Your operating system name and version.
• Any details about your local setup that might be helpful in troubleshooting.
• Detailed steps to reproduce the bug.

Fix Bugs

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

Implement Features

Look through the GitHub issues for features. Anything tagged with "enhancement"
and "help wanted" is open to whoever wants to implement it.

Write Documentation

OpenOmics could always use more documentation, whether as part of the
official OpenOmics docs, in docstrings within the API, or even on the web in blog posts,
articles, and such.

If you'd like to help write RTD documentations, note:
- Documentation pages are written in markdown using myst-parser
- The Sphinx theme used is furo
- The autodoc package used is sphinx-automodapi

Submit Feedback

The best way to send feedback is to file an issue at openomics/issues.

If you are proposing a feature:

• 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? Here's how to set up openomics for local development.

1. Fork the openomics repo on GitHub.
2. Clone your fork locally and work on the develop branch:

$ git clone git@github.com:your_name_here/openomics.git
$ git checkout develop

1. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:

$ mkvirtualenv openomics
$ cd openomics/
$ python setup.py develop

1. Create a branch for local development:

$ git checkout -b name-of-your-bugfix-or-feature

Now you can make your changes locally.

1. When you're done making changes, check that your changes pass flake8 and the
   tests, including testing other Python versions with tox:

$ flake8 openomics tests
$ python setup.py test or py.test $ tox

To get flake8 and tox, just pip install them into your virtualenv.

1. Commit your changes and push your branch to GitHub:

$ git add .
$ git commit -m "Your detailed description of your changes."
$ git push develop name-of-your-bugfix-or-feature

1. Submit a pull request through the GitHub website to the develop branch. Once major features are tested, we can create
   another pull-request to the master branch.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

1. The pull request should include tests. Run tests by with pytest ./ and make sure tests are 100% passing.
2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a
   docstring, and add the feature to the list
   in docs/history.md.
3. The pull request should work for Python 3.6 or higher, and for PyPi. Check
   Github Actions Tests
   and make sure that the tests pass for all supported Python versions and operating systems.

Tips

To run the automated tests locally, run this at the root directory:

pytest ./

To run a subset of tests:

    $ py.test tests.test_openomics

To run tests targeting various operating systems and Python versions, make a pull-request to the master branch which
will run as Github Actions Tests.

Deploying

A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in
HISTORY.rst). Then run:

$ bumpversion patch # possible: major / minor / patch
$ git push --tags

Github Actions will then deploy to PyPI if tests pass.

Code of Conduct

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