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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

Report Bugs

Report bugs at https://github.com/CFSAN-Biostatistics/snp-pipeline/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" is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with "feature" is open to whoever wants to implement it.

Write Documentation

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

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/CFSAN-Biostatistics/snp-pipeline/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.

Get Started!

Ready to contribute? Here's how to set up snp-pipeline for local development.

  1. Fork the snp-pipeline repo on GitHub.

  2. Clone your fork locally:

    $ git clone [email protected]:your_name_here/snp-pipeline.git

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

    $ mkvirtualenv snppipeline
$ toggleglobalsitepackages        # to access Biopython from the global site-packages
$ cd snppipeline/
$ python setup.py develop
$ pip install sphinx_rtd_theme    # the documentation uses the ReadTheDocs theme

  4. Run the pipeline on the supplied data set:

    The unit tests will not run successfully until after you prepare the reference and samples for the supplied Lambda Virus data set. See the :ref:`usage-label` section.

  5. Create a branch for local development:

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

    Now you can make your changes locally.

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

    $ flake8 snppipeline test
$ python setup.py test
$ tox

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

  7. Update the documentation and review the changes locally with sphinx:

    $ cd docs
$ sphinx-build -b html . ./_build
$ firefox ./_build/index.html

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

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

  9. Submit a pull request through the GitHub website.

Pull Request Guidelines

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

  1. The pull request should include tests.
  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 README.rst.
  3. The pull request should work for Python 2.6, 2.7, and 3.3, and for PyPI.

Tips

To run a subset of tests:

$ python -m unittest test.test_snppipeline
$ python -m unittest test.test_utils