We enthusiastically welcome contributions to BioSimulators-COPASI!
Before getting started, please contact the lead developers at info@biosimulators.org 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.
The repository follows standard Python conventions:
README.md
: Overview of the repositorybiosimulators_copasi/
: Python code for a BioSimulators-compliant command-line interface to COPASItests/
: unit tests for the command-line interfacesetup.py
: installation script for the command-line interfacesetup.cfg
: configuration for the installation of the command-line interfacerequirements.txt
: dependencies for the command-line interfacerequirements.optional.txt
: optional dependencies for the command-line interfaceMANIFEST.in
: a list of files to include in the package for the command-line interfaceLICENSE
: LicenseCONTRIBUTING.md
: Guide to contributing to BioSimulators-COPASI (this document)CODE_OF_CONDUCT.md
: Code of conduct for developers of BioSimulators-COPASI
BioSimulators-COPASI follows standard Python style conventions:
- Class names:
UpperCamelCase
- Function names:
lower_snake_case
- Variable names:
lower_snake_case
We strive to have complete test coverage for BioSimulators-COPASI.
The unit tests for BioSimulators-COPASI 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_copasi/htmlcov/index.html
with your browser.
pip install pytest pytest-cov coverage
python -m pytest tests --cov biosimulators_copasi
coverage html
BioSimulators-COPASI 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
Please use GitHub pull requests to submit changes. Each request should include a brief description of the new and/or modified features.
To release changes, contact the lead developers to request their release.
Below are instructions for releasing a new version:
- 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
- Commit the changes to this repository.
- Increment the
__version__
variable inbiosimulators_copasi/_version.py
. - Commit this change to
biosimulators_copasi/_version.py
. - Add a tag for the new version by running
git tag { version }
.version
should be equal to the value of the__version__
variable inbiosimulators_copasi/_version.py
. - Push these commits and the new tag to GitHub by running
git push && git push --tags
. - 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.
Please use GitHub issues to report any issues to the development community.
Please use GitHub issues to post questions or contact the lead developers at info@biosimulators.org.