How to use the petab.Problem.from_files function in petab

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github ICB-DCM / AMICI / python / bin / amici_import_petab.py View on Github external
def main():
    args = parse_cli_args()

    # First check for valid PEtab
    pp = petab.Problem.from_files(
        sbml_file=args.sbml_file_name,
        condition_file=args.condition_file_name,
        measurement_file=args.measurement_file_name,
        parameter_file=args.parameter_file_name)
    petab.lint_problem(pp)

    import_model(model_name=args.model_name,
                 sbml_file=args.sbml_file_name,
                 condition_file=args.condition_file_name,
                 measurement_file=args.measurement_file_name,
                 model_output_dir=args.model_output_dir,
                 compile=args.compile,
                 verbose=True)
github ICB-DCM / AMICI / python / amici / petab_import.py View on Github external
def main():
    """
    Command line interface to import a model in the PEtab
    (https://github.com/ICB-DCM/PEtab/) format into sAMICI
    """
    args = parse_cli_args()

    # First check for valid PEtab
    pp = petab.Problem.from_files(
        sbml_file=args.sbml_file_name,
        condition_file=args.condition_file_name,
        measurement_file=args.measurement_file_name,
        parameter_file=args.parameter_file_name)
    petab.lint_problem(pp)

    import_model(model_name=args.model_name,
                 sbml_file=args.sbml_file_name,
                 condition_file=args.condition_file_name,
                 measurement_file=args.measurement_file_name,
                 model_output_dir=args.model_output_dir,
                 compile=args.compile,
                 verbose=True)