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Contributing to BioSimulators-COBRApy

We enthusiastically welcome contributions to BioSimulators-COBRApy!

Coordinating contributions

Before getting started, please contact the lead developers at [email protected] to coordinate your planned contributions with other ongoing efforts. Please also use GitHub issues to announce your plans to the community so that other developers can provide input into your plans and coordinate their own work.

Repository organization

The repository follows standard Python conventions:

  • README.md: Overview of the repository
  • biosimulators_cobrapy/: Python code for a BioSimulators-compliant command-line interface to COBRApy
  • tests/: unit tests for the command-line interface
  • setup.py: installation script for the command-line interface
  • setup.cfg: configuration for the installation of the command-line interface
  • requirements.txt: dependencies for the command-line interface
  • requirements.optional.txt: optional dependencies for the command-line interface
  • MANIFEST.in: a list of files to include in the package for the command-line interface
  • LICENSE: License
  • CONTRIBUTING.md: Guide to contributing to BioSimulators-COBRApy (this document)
  • CODE_OF_CONDUCT.md: Code of conduct for developers of BioSimulators-COBRApy

Coding convention

BioSimulators-COBRApy follows standard Python style conventions:

  • Class names: UpperCamelCase
  • Function names: lower_snake_case
  • Variable names: lower_snake_case

Testing and continuous integration

We strive to have complete test coverage for BioSimulators-COBRApy.

The unit tests for BioSimulators-COBRApy are located in the tests directory. The tests can be executed by running the following command:

pip install pytest
python -m pytest tests

The tests are also automatically evaluated upon each push to GitHub.

The coverage of the tests can be evaluated by running the following commands and then opening /path/to/biosimulators_cobrapy/htmlcov/index.html with your browser.

pip install pytest pytest-cov coverage
python -m pytest tests --cov biosimulators_cobrapy
coverage html

Documentation convention

BioSimulators-COBRApy is documented using reStructuredText and the napoleon Sphinx plugin. The documentation can be compiled by running the following commands:

python -m pip install -r docs-src/requirements.txt
sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
sphinx-build docs-src docs

Submitting changes

Please use GitHub pull requests to submit changes. Each request should include a brief description of the new and/or modified features.

Releasing new versions

To release changes, contact the lead developers to request their release.

Below are instructions for releasing a new version:

  1. Make the required changes to the repository.
  • To update the version of the underyling simulator, update its version numbers in the following files:
    • requirements.txt
    • Dockerfile
    • biosimulators.json
  1. Commit the changes to this repository.
  2. Increment the __version__ variable in biosimulators_cobrapy/_version.py.
  3. Commit this change to biosimulators_cobrapy/_version.py.
  4. Add a tag for the new version by running git tag { version }. version should be equal to the value of the __version__ variable in biosimulators_cobrapy/_version.py.
  5. Push these commits and the new tag to GitHub by running git push && git push --tags.
  6. This push will trigger a GitHub action which will execute the following tasks:
    • Create a GitHub release for the version.
    • Push the release to PyPI.
    • Compile the documentation and push the compiled documentation to the repository so that the new documentation is viewable at github.io.

Reporting issues

Please use GitHub issues to report any issues to the development community.

Getting help

Please use GitHub issues to post questions or contact the lead developers at [email protected].