cellml¶

Reading, writing and validating CellML models with libcellml.

The functions wrap the libcellml Parser, Printer, Validator and Analyser. Issues are returned instead of printed, so a caller decides what to do with them; errors filters the issues of level ERROR.

CellMLValidationError ¶

Bases: ValueError

A CellML model has issues of level ERROR.

format_issue ¶

format_issue(issue)

Format an issue as [LEVEL] description.

Parameters:

Name	Type	Description	Default
`issue`	`Issue`	issue of a libcellml logger.	required

Returns:

Type	Description
`str`	The one line description of the issue.

format_issues ¶

format_issues(issues)

Format issues as one line per issue.

Parameters:

Name	Type	Description	Default
`issues`	`list[Issue]`	issues of a libcellml logger.	required

Returns:

Type	Description
`str`	The formatted issues joined by newlines.

errors ¶

errors(issues)

The issues of level ERROR.

Parameters:

Name	Type	Description	Default
`issues`	`list[Issue]`	issues of a libcellml logger.	required

Returns:

Type	Description
`list[Issue]`	The subset of issues with level `ERROR`.

model_to_string ¶

model_to_string(model)

Serialize a model to CellML 2.0.

Parameters:

Name	Type	Description	Default
`model`	`Model`	CellML model.	required

Returns:

Type	Description
`str`	The CellML xml.

write_model ¶

write_model(model, cellml_path)

Write a model as CellML file.

Parameters:

Name	Type	Description	Default
`model`	`Model`	CellML model.	required
`cellml_path`	`Path`	path of the file, overwritten if it exists.	required

read_model ¶

read_model(cellml_path)

Read a CellML file.

Parameters:

Name	Type	Description	Default
`cellml_path`	`Path`	path of the CellML file.	required

Returns:

Type	Description
`Model`	The parsed model.

Raises:

Type	Description
`CellMLValidationError`	if the parser reports errors.

validate_model ¶

validate_model(model)

Validate and analyse a model.

The validator checks the model against the CellML specification, the analyser checks that the equations define every variable exactly once.

Parameters:

Name	Type	Description	Default
`model`	`Model`	CellML model.	required

Returns:

Type	Description
`list[Issue]`	The issues of the validator followed by the issues of the analyser,
`list[Issue]`	empty for a valid model.