petab.yaml¶
Code regarding the PEtab YAML config files
Functions
add_constructor |
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add_implicit_resolver |
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add_multi_constructor |
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add_multi_representer |
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add_path_resolver |
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add_representer |
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compose |
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compose_all |
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dump |
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dump_all |
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emit |
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full_load |
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full_load_all |
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load |
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load_all |
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load_warning |
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parse |
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safe_dump |
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safe_dump_all |
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safe_load |
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safe_load_all |
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scan |
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serialize |
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serialize_all |
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unsafe_load |
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unsafe_load_all |
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warnings |
Python part of the warnings subsystem. |
Classes
YAMLObject |
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YAMLObjectMetaclass |
Exceptions
YAMLLoadWarning |
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petab.yaml.
assert_single_condition_and_sbml_file
(problem_config: Dict[KT, VT]) → None¶ 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.
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petab.yaml.
create_problem_yaml
(sbml_files: Union[str, List[str]], condition_files: Union[str, List[str]], measurement_files: Union[str, List[str]], parameter_file: str, observable_files: Union[str, List[str]], yaml_file: str, visualization_files: Union[str, List[str], None] = None) → None¶ 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 lsit of such
- yaml_file – Path to which YAML file should be written
- visualization_files – Optional Path to visualization file or list of
- such –
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petab.yaml.
is_composite_problem
(yaml_config: Union[Dict[KT, VT], str]) → bool¶ Does this YAML file comprise multiple models?
Parameters: yaml_config – PEtab configuration as dictionary or YAML file name
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petab.yaml.
load_yaml
(yaml_config: Union[Dict[KT, VT], str]) → Dict[KT, VT]¶ 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.
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petab.yaml.
validate
(yaml_config: Union[Dict[KT, VT], str], path_prefix: Optional[str] = None)¶ 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.
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petab.yaml.
validate_yaml_semantics
(yaml_config: Union[Dict[KT, VT], str], path_prefix: Optional[str] = None)¶ 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
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petab.yaml.
validate_yaml_syntax
(yaml_config: Union[Dict[KT, VT], str], schema: Union[None, Dict[KT, VT], str] = None)¶ 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
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petab.yaml.
write_yaml
(yaml_config: Dict[str, Any], filename: str) → None¶ Write PEtab YAML file
Parameters: - yaml_config – Data to write
- filename – File to create