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 use the continuous integration service TravisCI to enforce some of these checks, so if you are making a contribution it is best to check this locally.
We use the tool flake8 for code style checks, together with various plugins which can be installed as follows:
$ pip install flake8 flake8-docstrings flake8-blind-except flake8-rst-docstringsUnless you are using Python 2.7, please also install the bugbear plugin:
$ pip install flake8-bugbear
You can then run flake8 directly as follows:
$ flake8 Bio/
$ flake8 BioSQL/
$ flake8 Tests/
$ flake8 Scripts/
$ flake8 Doc/examples/Each of these folders has its own flake8 settings file, but in the long term we would like all the code to follow the same strict settings.
You can run the reStructuredText checks with the restructuredtext-lint tool (also known as rst-lint):
$ pip install restructuredtext_lint
$ rst-lint --level warning *.rstMore simply, we currently suggest you install the git pre-commit hook described here which will check our basic coding conventions as you work: biopython#493
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
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"
$ python3.5 setup.py build
$ python3.5 setup.py testIf 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 the pydocstyle plugin (flake8-docstrings), and reStructuredText using rst-lint. 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.