petab.yaml
Code regarding the PEtab YAML config files
Functions
Check that there is only a single condition file and a single SBML file specified. |
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Create and write default YAML file for a single PEtab problem |
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Does this YAML file comprise multiple models? |
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Load YAML |
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Validate syntax and semantics of PEtab config YAML |
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Validate PEtab YAML file semantics |
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Validate PEtab YAML file syntax |
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Write PEtab YAML file |
- petab.yaml.assert_single_condition_and_sbml_file(problem_config: Dict) None [source]
Check that there is only a single condition file and a single SBML file specified.
- Parameters
problem_config – Dictionary as defined in the YAML schema inside the problems list.
- Raises
NotImplementedError – If multiple condition or SBML files specified.
- petab.yaml.create_problem_yaml(sbml_files: Union[str, Path, List[Union[str, Path]]], condition_files: Union[str, Path, List[Union[str, Path]]], measurement_files: Union[str, Path, List[Union[str, Path]]], parameter_file: Union[str, Path], observable_files: Union[str, Path, List[Union[str, Path]]], yaml_file: Union[str, Path], visualization_files: Optional[Union[str, Path, List[Union[str, Path]]]] = None, relative_paths: bool = True) None [source]
Create and write default YAML file for a single PEtab problem
- Parameters
sbml_files – Path of SBML model file or list of such
condition_files – Path of condition file or list of such
measurement_files – Path of measurement file or list of such
parameter_file – Path of parameter file
observable_files – Path of observable file or list of such
yaml_file – Path to which YAML file should be written
visualization_files – Optional Path to visualization file or list of such
relative_paths – whether all paths in the YAML file should be relative to the location of the YAML file. If
False
, then paths are left unchanged.
- petab.yaml.is_composite_problem(yaml_config: Union[Dict, str, Path]) bool [source]
Does this YAML file comprise multiple models?
- Parameters
yaml_config – PEtab configuration as dictionary or YAML file name
- petab.yaml.load_yaml(yaml_config: Union[Dict, Path, str]) Dict [source]
Load YAML
Convenience function to allow for providing YAML inputs as filename, URL or as dictionary.
- Parameters
yaml_config – PEtab YAML config as filename or dict or URL.
- Returns
The unmodified dictionary if
yaml_config
was dictionary. Otherwise the parsed the YAML file.
- petab.yaml.validate(yaml_config: Union[Dict, str, Path], path_prefix: Union[None, str, Path] = None)[source]
Validate syntax and semantics of PEtab config YAML
- Parameters
yaml_config – PEtab YAML config as filename or dict.
path_prefix – Base location for relative paths. Defaults to location of YAML file if a filename was provided for
yaml_config
or the current working directory.
- petab.yaml.validate_yaml_semantics(yaml_config: Union[Dict, str, Path], path_prefix: Union[None, str, Path] = None)[source]
Validate PEtab YAML file semantics
Check for existence of files. Assumes valid syntax.
Version number and contents of referenced files are not yet checked.
- Parameters
yaml_config – PEtab YAML config as filename or dict.
path_prefix – Base location for relative paths. Defaults to location of YAML file if a filename was provided for
yaml_config
or the current working directory.
- Raises
AssertionError – in case of problems
- petab.yaml.validate_yaml_syntax(yaml_config: Union[Dict, str, Path], schema: Union[None, Dict, str] = None)[source]
Validate PEtab YAML file syntax
- Parameters
yaml_config – PEtab YAML file to validate, as file name or dictionary
schema – Custom schema for validation
- Raises
see jsonschema.validate –