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Contributing to Biopython

We welcome pull requests to fix bugs or add new features. Please read http://biopython.org/wiki/Contributing for a general overview about contributing - this file is primarily concerned with the practicalities.

Licensing

Biopython is moving towards dual licensing the code. In your git commit and/or pull request, please explicitly state that you agree to your contributions being dual licensed under both our original "Biopython License Agreement" and the more widely used "3-Clause BSD License" (see our LICENSE file for more details).

Git Usage

We have a git introduction online at http://biopython.org/wiki/GitUsage

If you are planning to make a pull request, start by creating a new branch with a short but descriptive name (rather than using your master branch).

Coding Conventions

Biopython tries to follow the coding conventions laid out in PEP8 and PEP257, with the notable exception of existing module names which are not lower case.

For docstrings (Python's in-code documentation), in addition to PEP257 we are using reStructuredText (RST) markup language which allows basic formatting like italics and bold once rendered into HTML webpages for our online API documentation. We also use reStructuredText for files like README.rst.

To facilitate style checking, we make use of pre-commit to automatically run various flake8 plugins as well as black on the Python code, and restructuredtext-lint (also known as rst-lint) to check the RST files too. We also use continuous integration on GitHub to run these checks, but we strongly suggest you install and run pre-commit in your local machine (see below).

Testing

Any new feature or functionality will not be accepted without tests. Likewise for any bug fix, we encourage including an additional test. See the testing chapter in the Biopython Tutorial for more information on our test framework: http://biopython.org/DIST/docs/tutorial/Tutorial.html

Local Development

As mentioned above, to simplify your contributions, we provide a pre-commit configuration. Pre-commit is a Python package which automatically hooks into git. When you run "git commit" within the biopython repository, it will automatically run various fast checks (including black, flake8, rst-lint and doc8) before the commit happens. To install this, run:

$ pip install pre-commit

# Activate pre-commit for biopython
$ cd biopython-repository
$ pre-commit install

Local Testing

Please always run the style checks (see above) and the full test suite on your local computer before submitting a pull request, e.g.:

$ git commit Bio/XXX.py Tests/test_XXX.py  -m "Fixed bug 123"
$ python setup.py build
$ python setup.py test

If you have multiple versions of Python installed, ideally test them all (the Python tool tox can be helpful here).

Continuous Integration

Once you submit your pull request on GitHub, several automated tests should be run via continuous integration services, and their results reported on the pull request. These will run most of the Biopython tests (although not with all the optional dependencies included), plus also style checks using pre-commit (also used for git pre-commit checks, see above).

The continuous integration checks must pass before your pull request will be merged.

The continuous integration tests collect test coverage information via CodeCov: https://codecov.io/github/biopython/biopython/

Ideally the CodeCov checks will also pass, but we currently do not insist on this when reviewing pull requests.

Contributing to the Biopython Tutorial

For instructions, see the Biopython Tutorial README