petab.yaml

Code regarding the PEtab YAML config files

petab.yaml._Path

alias of pathlib.Path

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, 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: Optional[Union[str, List[str]]] = 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 lsit 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

  • the location of the YAML file. If False (to) –

  • paths are left (then) –

  • unchanged. –

petab.yaml.get_handle(path_or_buf: Union[PathLike[str], str, IO[pandas._typing.T], io.RawIOBase, io.BufferedIOBase, io.TextIOBase, _io.TextIOWrapper, mmap.mmap], mode: str, encoding: Optional[str] = None, compression: Optional[Union[str, Dict[str, Any]]] = None, memory_map: bool = False, is_text: bool = True, errors: Optional[str] = None, storage_options: Optional[Dict[str, Any]] = None) → pandas.io.common.IOHandles[source]

Get file handle for given path/buffer and mode.

Parameters

  • path_or_buf (str or file handle) – File path or object.

  • mode (str) – Mode to open path_or_buf with.

  • encoding (str or None) – Encoding to use.

  • compression (str or dict, default None) –

    If string, specifies compression mode. If dict, value at key ‘method’ specifies compression mode. Compression mode must be one of {‘infer’, ‘gzip’, ‘bz2’, ‘zip’, ‘xz’, None}. If compression mode is ‘infer’ and filepath_or_buffer is path-like, then detect compression from the following extensions: ‘.gz’, ‘.bz2’, ‘.zip’, or ‘.xz’ (otherwise no compression). If dict and compression mode is one of {‘zip’, ‘gzip’, ‘bz2’}, or inferred as one of the above, other entries passed as additional compression options.

    Changed in version 1.0.0: May now be a dict with key ‘method’ as compression mode and other keys as compression options if compression mode is ‘zip’.

    Changed in version 1.1.0: Passing compression options as keys in dict is now supported for compression modes ‘gzip’ and ‘bz2’ as well as ‘zip’.

  • memory_map (boolean, default False) – See parsers._parser_params for more information.

  • is_text (boolean, default True) – Whether the type of the content passed to the file/buffer is string or bytes. This is not the same as “b” not in mode. If a string content is passed to a binary file/buffer, a wrapper is inserted.

  • errors (str, default 'strict') – Specifies how encoding and decoding errors are to be handled. See the errors argument for open() for a full list of options.

  • storage_options (StorageOptions = None) – Passed to _get_filepath_or_buffer

  • versionchanged: (.) – 1.2.0:

  • the dataclass IOHandles (Returns) –

petab.yaml.is_composite_problem(yaml_config: Union[Dict, str]) → 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, 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_prefix: Optional[str] = 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_prefix: Optional[str] = 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], 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 –

petab.yaml.write_yaml(yaml_config: Dict[str, Any], filename: str) → None[source]

Write PEtab YAML file

Parameters

  • yaml_config – Data to write

  • filename – File to create