cobra.io.yaml#

Provide functions for I/O in YAML format.

Attributes#

`YAML_SPEC`
`yaml`

Classes#

CobraYAML

Define custom subclass for YAML I/O.

Functions#

`to_yaml`(→ str)	Return the model as a YAML string.
`from_yaml`(→ cobra.Model)	Load a cobra model from a YAML string.
`save_yaml_model`(→ None)	Write the cobra model to a file in YAML format.
`load_yaml_model`(→ cobra.Model)	Load a cobra model from a file in YAML format.

Module Contents#

cobra.io.yaml.YAML_SPEC = '1.2'#

class cobra.io.yaml.CobraYAML(*, typ: List[Text] | Text | None = None, pure: Any = False, output: Any = None, plug_ins: Any = None)[source]#

Bases: ruamel.yaml.main.YAML

Define custom subclass for YAML I/O.

dump(data: Dict, stream: io.TextIOBase | None = None, **kwargs: Any) → str[source]#

Dump YAML data.

Parameters:

data (dict) – A dictionary representing the cobra model and its components.
stream (TextIOBase, optional) – A text stream object inheriting from io.TextIOBase. If None, ruamel.yaml.compat.StringIO is used (default None).
**kwargs (Any) – Keyword arguments passed on to ruamel.yaml.main.YAML.dump.

Returns:

YAML string representation of data.

Return type:

str

cobra.io.yaml.yaml#

cobra.io.yaml.to_yaml(model: cobra.Model, sort: bool = False, **kwargs: Any) → str[source]#

Return the model as a YAML string.

Parameters:

model (cobra.Model) – The cobra model to represent.
sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False).
**kwargs (Any) – Keyword arguments passed on to CobraYAML.dump.

Returns:

YAML string representation of the cobra model.

Return type:

str

See also

save_yaml_model: Write directly to a file.
ruamel.yaml.dump: Base function.

cobra.io.yaml.from_yaml(document: str) → cobra.Model[source]#

Load a cobra model from a YAML string.

Parameters:: document (str) – The YAML string representation of a cobra model.
Returns:: The cobra model as interpreted from the YAML document.
Return type:: cobra.Model

See also

load_yaml_model: Load directly from a file.

cobra.io.yaml.save_yaml_model(model: cobra.Model, filename: str, sort: bool = False, **kwargs: Any) → None[source]#

Write the cobra model to a file in YAML format.

Parameters:

model (cobra.Model) – The cobra model to represent.
filename (str or file-like) – File path or descriptor that the YAML representation should be written to.
sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False).
**kwargs (Any) – Keyword arguments passed to CobraYAML.dump.

See also

to_yaml: Return a string representation.
ruamel.yaml.dump: Base function.

cobra.io.yaml.load_yaml_model(filename: str | pathlib.Path) → cobra.Model[source]#

Load a cobra model from a file in YAML format.

Parameters:: filename (str or file-like) – File path or descriptor that contains the YAML document describing the cobra model.
Returns:: The cobra model as represented in the YAML document.
Return type:: cobra.Model

See also

from_yaml: Load from a string.