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Code generation for cardiac Chaste

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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.


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]
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


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


For guidelines on contributing to chaste_codegen, please see

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