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Contributing

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

Report bugs using the issue tracker

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.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues and projects for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.

Write Documentation

cobrapy could always use more documentation, whether as part of the official cobrapy docs, in docstrings, or even on the web in blog posts, articles, and such - all contributions are welcome!

Submit Feedback

The best way to send feedback is to file an issue.

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.
  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

If you like cobrapy please remember to 'star' our github page (click on the star at top right corner), that way we also have an idea of who is using cobrapy!

Get Started!

Want to contribute a new feature or improvement? Consider starting by raising an issue and assign it to yourself to describe what you want to achieve. This way, we reduce the risk of duplicated efforts and you may also get suggestions on how to best proceed, e.g. there may be half-finished work in some branch that you could start with.

Here's how to set up cobrapy for local development to contribute smaller features or changes that you can implement yourself.

  1. Fork the cobrapy repository on GitHub.

  2. Clone your fork locally:

    $ git clone [email protected]:your_name_here/cobrapy.git

  3. Install libglpk using your package manager. For macOS:

    $ brew install homebrew/science/glpk

    For Debian-based Linux systems (including Ubuntu and Mint):

    $ sudo apt-get install libglpk-dev

  4. If virtualenvwrapper is not installed, follow the directions to install virtualenvwrapper.

  5. Install your local copy of cobrapy into a virtualenv with virtualenvwrapper:

    $ cd cobrapy
$ mkvirtualenv cobrapy

    Use the --python option to select a specific version of Python for the virtualenv. Note on macOS, matplotlib requires Python be installed as a framework but virtualenv creates a non-framework build of Python. See the matplotlib FAQ for details on a workaround.

  6. Install the required packages for development in the virtualenv using pip install:

    (cobrapy)$ pip install --upgrade pip
(cobrapy)$ pip install -r develop-requirements.txt

  7. Setup cobrapy for development:

    (cobrapy)$ python setup.py develop

  8. Create a branch for local development (see below for details on the branching model):

    (cobrapy)$ git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  9. When you are done making changes, check that your changes pass pep8 and the tests with tox for the supported Python versions:

    (cobrapy)$ tox -e py27
(cobrapy)$ tox -e py34
(cobrapy)$ tox -e py35

  10. Commit your changes and push your branch to GitHub:

    (cobrapy)$ git add .
(cobrapy)$ git commit -m "Your detailed description of your changes."
(cobrapy)$ git push origin name-of-your-bugfix-or-feature

  11. Submit a pull request through the GitHub website.

For larger features that you want to work on collaboratively with other cobrapy team members, you may consider to first request to join the cobrapy developers team to get write access to the repository so that you can create a branch in the main repository (or simply ask the maintainer to create a branch for you). Once you have a new branch you can push your changes directly to the main repository and when finished, submit a pull request from that branch to devel.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. The pull request should include tests in the cobra/test directory. Except in rare circumstances, code coverage must not decrease (as reported by codecov which runs automatically when you submit your pull request)
  2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring and consider creating a notebook that demonstrates the usage in documentation_builder (documentation is written as jupyter notebooks in the documentation_builder directory, which are then converted to rst by the autodoc.sh script.)
  3. The pull request should work for Python 2.7, 3.4 and 3.5. Check https://travis-ci.org/biosustain/cobrapy/pull_requests and make sure that the tests pass for all supported Python versions.
  4. Assign a reviewer to your pull request. If in doubt, assign Henning Redestig. Your pull request must be approved by at least one reviewer before it can be merged.

Unit tests and benchmarks

cobrapy uses pytest for its unit-tests and new features should in general always come with new tests that make sure that the code runs as intended. Since COBRA rapidly can become quite resource intensive fundamental methods such as model manipulation, adding and removing reactions, metabolites etc also must work efficiently. We use pytest-benchmark to compare different implementations to make sure that new code do not come with unacceptable increased computation time. If you add benchmarked tests, make sure to also include a test with and without the benchmark as we do not want to slow down continuous integration by running benchmarks, for examples, see e.g. test_add_metabolite in test_model.py. test_add_metabolite is the main test, test_add_metabolite_benchmark takes the special benchmark fixture that enables profiling the important code snippet but is skipped when running:

(cobrapy)$ pytest --benchmark-skip

When the test function itself is small and can safely be assumed to not take many resources, we can directly profile the test as in test_subtract_metabolite_benchmark which calls benchmark(self.test_subtract_metabolite, model).

To run all tests and benchmarks do:

(cobrapy)$ pytest

and to compare two implementations you may keep them in two branches e.g. old and new and then do:

(cobrapy)$ git checkout old
(cobrapy)$ pytest --benchmark-save
(cobrapy)$ git checkout new
(cobrapy)$ pytest --benchmark-compare

Branching model

devel
Is the branch all pull-requests should be based on.
master
Is only touched by maintainers and is the branch with only tested, reviewed code that is released or ready for the next release.
{fix, bugfix, doc, feature}/descriptive-name
Is the recommended naming scheme for smaller improvements, bugfixes, documentation improvement and new features respectively.

Please use concise descriptive commit messages and consider using git pull --rebase when you update your own fork to avoid merge commits.

  1. Tests are in the cobra/test directory. They are automatically run through continuous integration services on both python 2 and python 3 when pull requests are made.
  2. Please write tests for new functions. Writing documentation as well would also be very helpful.
  3. Ensure code will work with both python 2 and python 3. For example, instead of my_dict.iteritems() use six.iteritems(my_dict)

Thank you very much for contributing to cobrapy!