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.
To facilitate style checking, we make use of pre-commit to automatically
run various flake8 plugins as well as black. We use the continuous
integration service TravisCI to run these checks, but we strongly suggest you
install and run pre-commit in your local machine (see below).
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. You can run the
reStructuredText checks with the restructuredtext-lint tool (also known as
rst-lint):
$ pip install restructuredtext_lint $ rst-lint --level warning *.rst
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 flake8 and black) before the commit happens. In order to install it, run:
$ 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, and their results reported on the pull request.
We use TravisCI to run most of the Biopython tests (although currently only
under Linux, and not with all the optional dependencies included), plus also
check Python coding style using the flake8 tool with lots of plugins, and
reStructuredText files using rst-lint and doc8.
https://travis-ci.org/biopython/biopython/branches
We use AppVeyor to run most of the tests under Windows (although currently without any optional dependencies). https://ci.appveyor.com/project/biopython/biopython/history
The TravisCI and AppVeyor checks must pass before your pull request will be merged.
Some of the TravisCI and AppVeyor runs 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.
For instructions, see the Biopython Tutorial README