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 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.
Look through the GitHub issues for bugs. Anything tagged with “bug” is open to whoever wants to implement it.
Look through the GitHub issues for features. Anything tagged with “feature” is open to whoever wants to implement it.
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.
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.
Ready to contribute? Here’s how to set up snp-pipeline for local development.
Fork the snp-pipeline repo on GitHub.
Clone your fork locally:
$ git clone email@example.com:your_name_here/snp-pipeline.git
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 $ cd snppipeline/ $ python setup.py develop $ pip install sphinx_rtd_theme # the documentation uses the ReadTheDocs theme
Run the unit tests on the supplied data set to verify your installation is working:
$ python setup.py test
Create a branch for local development:
$ git checkout -b name-of-your-bugfix-or-feature
Now you can make your changes locally.
When you’re done making changes, check that your changes pass the tests, including testing other Python versions:
$ python setup.py test $ tox - or - $ . run_tests.sh -c # source this script to test other python versions without using tox
To get tox, just pip install it into your virtualenv.
Run the regression tests:
To get shunit2, install from https://code.google.com/p/shunit2/
Update the documentation and review the changes locally with sphinx:
$ cd docs $ sphinx-build -b html . ./_build $ xdg-open _build/index.html
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
Submit a pull request through the GitHub website.
Pull Request Guidelines¶
Before you submit a pull request, check that it meets these guidelines:
- The pull request should include tests.
- 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.
- The pull request should work for Python 2.6, 2.7, 3.3, 3.4, and 3.5, and for PyPI.
To run a subset of tests:
$ python -m unittest test.test_snppipeline $ python -m unittest test.test_utils