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.
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).
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).
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
To facilitate style checking, we make use of
pre-commit to automatically
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
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
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
doc8) before the commit happens. To install
$ pip install pre-commit # Activate pre-commit for biopython $ cd biopython-repository $ pre-commit install
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).
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
(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