We enthusiastically welcome contributions to BioSimulators-iBioSim!
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.
The repository follows standard Python conventions:
README.md
: Overview of the repositorybiosimulators_ibiosim/
: Python code for a BioSimulators-compliant command-line interface to iBioSimtests/
: 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-iBioSim (this document)CODE_OF_CONDUCT.md
: Code of conduct for developers of BioSimulators-iBioSim
BioSimulators-iBioSim 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-iBioSim.
The unit tests for BioSimulators-iBioSim 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_ibiosim/htmlcov/index.html
with your browser.
pip install pytest pytest-cov coverage
python -m pytest tests --cov biosimulators_ibiosim
coverage html
BioSimulators-iBioSim is documented using reStructuredText and the napoleon Sphinx plugin.
Please use GitHub pull requests to submit changes. Each request should include a brief description of the new and/or modified features.
Contact the BioSimulators Team to request release and deployment of new changes.
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 [email protected].