Code generation for cardiac Chaste

The chaste_codegen module takes CellML models as input, via cellmlmanip to read and manipulate them, then uses templating to generate C++ code.

The jinja2 templating engine is used.

Installing

We recommend installing chaste_codegen in a virtual environment (using virtualenv or conda)

Users install chaste_codegen using pip.

pip install chaste_codegen

Using chaste_codegen

After installation, chaste_codegen can be called using the chaste_codegen command:

usage: chaste_codegen [-h] [--version] [--normal] [--cvode]
                      [--cvode-data-clamp] [--backward-euler] [--rush-larsen]
                      [--grl1] [--grl2] [--rush-larsen-labview]
                      [--rush-larsen-c] [-j] [-o OUTFILE]
                      [--output-dir OUTPUT_DIR] [--show-outputs] [-c CLS_NAME]
                      [-q] [--skip-ingularity-fixes] [-y] [--opt] [-m]
                      [--lookup-table <metadata tag> min max step]
                      [--use-model-factory]
                      cellml_file
chaste_codegen: error: the following arguments are required: cellml_file

For more information about the available options call chaste_codegen -h or see the CodeGenerationFromCellML guide

Release notes

For release notes see RELEASE.md

Documentation

API documentation explaining how to use cellmlmanip can be found on readthedocs

Contributing

For guidelines on contributing to chaste_codegen, please see CONTRIBUTING.md.