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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,160 @@ | ||
| import argparse | ||
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| import petab | ||
| from amici.petab_import import import_model | ||
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|
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| def _parse_cli_args(): | ||
| """ | ||
| Parse command line arguments | ||
| :return: | ||
| Parsed CLI arguments from :mod:`argparse`. | ||
| """ | ||
| parser = argparse.ArgumentParser( | ||
| description="Import PEtab-format model into AMICI." | ||
| ) | ||
|
|
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| # General options: | ||
| parser.add_argument( | ||
| "-v", | ||
| "--verbose", | ||
| dest="verbose", | ||
| action="store_true", | ||
| help="More verbose output", | ||
| ) | ||
| parser.add_argument( | ||
| "-o", | ||
| "--output-dir", | ||
| dest="model_output_dir", | ||
| help="Name of the model directory to create", | ||
| ) | ||
| parser.add_argument( | ||
| "--no-compile", | ||
| action="store_false", | ||
| dest="compile", | ||
| help="Only generate model code, do not compile", | ||
| ) | ||
| parser.add_argument( | ||
| "--no-validate", | ||
| action="store_false", | ||
| dest="validate", | ||
| help="Skip validation of PEtab files", | ||
| ) | ||
| parser.add_argument( | ||
| "--flatten", | ||
| dest="flatten", | ||
| default=False, | ||
| action="store_true", | ||
| help="Flatten measurement specific overrides of " | ||
| "observable and noise parameters", | ||
| ) | ||
| parser.add_argument( | ||
| "--no-sensitivities", | ||
| dest="generate_sensitivity_code", | ||
| default=True, | ||
| action="store_false", | ||
| help="Skip generation of sensitivity code", | ||
| ) | ||
|
|
||
| # Call with set of files | ||
| parser.add_argument( | ||
| "-s", "--sbml", dest="sbml_file_name", help="SBML model filename" | ||
| ) | ||
| parser.add_argument( | ||
| "-m", | ||
| "--measurements", | ||
| dest="measurement_file_name", | ||
| help="Measurement table", | ||
| ) | ||
| parser.add_argument( | ||
| "-c", | ||
| "--conditions", | ||
| dest="condition_file_name", | ||
| help="Conditions table", | ||
| ) | ||
| parser.add_argument( | ||
| "-p", | ||
| "--parameters", | ||
| dest="parameter_file_name", | ||
| help="Parameter table", | ||
| ) | ||
| parser.add_argument( | ||
| "-b", | ||
| "--observables", | ||
| dest="observable_file_name", | ||
| help="Observable table", | ||
| ) | ||
|
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| parser.add_argument( | ||
| "-y", | ||
| "--yaml", | ||
| dest="yaml_file_name", | ||
| help="PEtab YAML problem filename", | ||
| ) | ||
|
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| parser.add_argument( | ||
| "-n", | ||
| "--model-name", | ||
| dest="model_name", | ||
| help="Name of the python module generated for the " "model", | ||
| ) | ||
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| args = parser.parse_args() | ||
|
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| if not args.yaml_file_name and not all( | ||
| ( | ||
| args.sbml_file_name, | ||
| args.condition_file_name, | ||
| args.observable_file_name, | ||
| ) | ||
| ): | ||
| parser.error( | ||
| "When not specifying a model name or YAML file, then " | ||
| "SBML, condition and observable file must be specified" | ||
| ) | ||
|
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| return args | ||
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| def _main(): | ||
| """ | ||
| Command line interface to import a model in the PEtab | ||
| (https://github.com/PEtab-dev/PEtab/) format into AMICI. | ||
| """ | ||
| args = _parse_cli_args() | ||
|
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| if args.yaml_file_name: | ||
| pp = petab.Problem.from_yaml(args.yaml_file_name) | ||
| else: | ||
| 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, | ||
| observable_files=args.observable_file_name, | ||
| ) | ||
|
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| # Check for valid PEtab before potentially modifying it | ||
| if args.validate: | ||
| petab.lint_problem(pp) | ||
|
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| if args.flatten: | ||
| petab.flatten_timepoint_specific_output_overrides(pp) | ||
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| import_model( | ||
| model_name=args.model_name, | ||
| sbml_model=pp.sbml_model, | ||
| condition_table=pp.condition_df, | ||
| observable_table=pp.observable_df, | ||
| measurement_table=pp.measurement_df, | ||
| model_output_dir=args.model_output_dir, | ||
| compile=args.compile, | ||
| generate_sensitivity_code=args.generate_sensitivity_code, | ||
| verbose=args.verbose, | ||
| validate=False, | ||
| ) | ||
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| if __name__ == "__main__": | ||
| _main() |
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