Development

System setup for development purposes

• Make sure the Mathematica unit testing framework MUnit` is on your Mathematica Path.

Version control

• Fork the repository if you would like to contribute but don't have write access. After implementing and testing your contributions you can send a pull request.
• Before committing any changes, clean up output and cache information from all Mathematica notebooks (using the notebook in the Housekeeping directory).
• Run all unit tests before committing, under no circumstances, commit anything that breaks established tests.

Unit testing

• The unit tests can be executed with the Wolfram Workbench (if available). A standalone MathematicaScript test runner is also provided.

Coding guidlines

• Try to avoid platform specific code. This is especially import for wrapping command-line utilities.

Design principles

• Data types, e.g., metabolite, reaction etc., should overload ToString to provide unique string representations for them. This is necessary for model export purposes and to make composite data types (like enzyme, which can contain metabolites bound as activators or inhibitors) safe against ReplaceAll.