SBML → Chaste

chaste_codegen_sbml converts SBML models to C++ Chaste code. It relies on libSBML for parsing SBML.

Installation

Installation via pipx is recommended

pipx install git+https://github.com/Chaste/chaste-codegen-sbml@develop

Alternatively, install via pip

# Create and activate a virtual environment (optional)
python -m venv sbml-venv
source sbml-venv/bin/activate

# Install
pip install git+https://github.com/Chaste/chaste-codegen-sbml@develop

Usage

chaste_codegen_sbml [-h]

Development

Getting the code

# Clone the repository
git clone https://github.com/Chaste/chaste-codegen-sbml
cd chaste-codegen-sbml

# Create and activate a virtual environment
python -m venv venv
source venv/bin/activate

# Install in editable mode along with dev dependencies
pip install -e ."[dev]"

Running tests

python -m pytest