petab.v2.lint

Validation of PEtab problems

Module Attributes

default_validation_tasks

Validation tasks that should be run on any PEtab problem

Functions

`get_placeholders`(problem[, observable, noise])	Get all placeholder parameters from observable table observableFormulas and noiseFormulas.
`get_required_parameters_for_parameter_table`(problem)	Get the set of parameters that need to go into the parameter table
`get_valid_parameters_for_parameter_table`(problem)	Get the set of parameters which may be present inside the parameter table
`lint_problem`(problem)	Validate a PEtab problem.

Classes

`CheckAllParametersPresentInParameterTable`()	Ensure all required parameters are contained in the parameter table with no additional ones.
`CheckExperimentConditionsExist`()	A task to validate that all conditions in the experiment table exist in the condition table.
`CheckExperimentTable`()	A task to validate the experiment table of a PEtab problem.
`CheckInitialChangeSymbols`()	Check that changes of any first period of any experiment only refers to allowed symbols.
`CheckMeasuredExperimentsDefined`()	A task to check that all experiments referenced by measurements are defined.
`CheckMeasuredObservablesDefined`()	A task to check that all observables referenced by the measurements are defined.
`CheckMeasurementModelId`()	Validate model IDs of measurements.
`CheckModel`()	A task to validate the model of a PEtab problem.
`CheckObservablesDoNotShadowModelEntities`()	A task to check that observable IDs do not shadow model entities.
`CheckOverridesMatchPlaceholders`()	A task to check that the number of observable/noise parameters in the measurements matches the number of placeholders in the observables.
`CheckPosLogMeasurements`()	Check that measurements for observables with log-transformation are positive.
`CheckPriorDistribution`()	A task to validate the prior distribution of a PEtab problem.
`CheckProblemConfig`()	A task to validate the configuration of a PEtab problem.
`CheckUndefinedExperiments`()	A task to check for experiments that are used in the measurement table but not defined in the experiment table.
`CheckUniquePrimaryKeys`()	Check that all primary keys are unique.
`CheckUnusedConditions`()	A task to check for conditions that are not used in the experiment table.
`CheckUnusedExperiments`()	A task to check for experiments that are not used in the measurement table.
`CheckValidConditionTargets`()	Check that all condition table targets are valid.
`CheckValidParameterInConditionOrParameterTable`()	A task to check that all required and only allowed model parameters are present in the condition or parameter table.
`ValidationError`(message[, task])	A validation result with level ERROR.
`ValidationIssue`(level, message[, task])	The result of a validation task.
`ValidationIssueSeverity`(*values)	The severity of a validation issue.
`ValidationResultList`([iterable])	A list of validation results.
`ValidationTask`()	A task to validate a PEtab problem.
`ValidationWarning`(message[, task])	A validation result with level WARNING.

class petab.v2.lint.CheckAllParametersPresentInParameterTable[source]

Bases: ValidationTask

Ensure all required parameters are contained in the parameter table with no additional ones.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckExperimentConditionsExist[source]

Bases: ValidationTask

A task to validate that all conditions in the experiment table exist in the condition table.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckExperimentTable[source]

Bases: ValidationTask

A task to validate the experiment table of a PEtab problem.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckInitialChangeSymbols[source]

Bases: ValidationTask

Check that changes of any first period of any experiment only refers to allowed symbols.

The only allowed symbols are those that are present in the parameter table.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckMeasuredExperimentsDefined[source]

Bases: ValidationTask

A task to check that all experiments referenced by measurements are defined.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckMeasuredObservablesDefined[source]

Bases: ValidationTask

A task to check that all observables referenced by the measurements are defined.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckMeasurementModelId[source]

Bases: ValidationTask

Validate model IDs of measurements.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckModel[source]

Bases: ValidationTask

A task to validate the model of a PEtab problem.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckObservablesDoNotShadowModelEntities[source]

Bases: ValidationTask

A task to check that observable IDs do not shadow model entities.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckOverridesMatchPlaceholders[source]

Bases: ValidationTask

A task to check that the number of observable/noise parameters in the measurements matches the number of placeholders in the observables.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckPosLogMeasurements[source]

Bases: ValidationTask

Check that measurements for observables with log-transformation are positive.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckPriorDistribution[source]

Bases: ValidationTask

A task to validate the prior distribution of a PEtab problem.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckProblemConfig[source]

Bases: ValidationTask

A task to validate the configuration of a PEtab problem.

This corresponds to checking the problem YAML file semantics.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckUndefinedExperiments[source]

Bases: ValidationTask

A task to check for experiments that are used in the measurement table but not defined in the experiment table.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckUniquePrimaryKeys[source]

Bases: ValidationTask

Check that all primary keys are unique.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckUnusedConditions[source]

Bases: ValidationTask

A task to check for conditions that are not used in the experiment table.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckUnusedExperiments[source]

Bases: ValidationTask

A task to check for experiments that are not used in the measurement table.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckValidConditionTargets[source]

Bases: ValidationTask

Check that all condition table targets are valid.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.CheckValidParameterInConditionOrParameterTable[source]

Bases: ValidationTask

A task to check that all required and only allowed model parameters are present in the condition or parameter table.

run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

class petab.v2.lint.ValidationError(message: str, task: str | None = None)[source]

Bases: ValidationIssue

A validation result with level ERROR.

level: ValidationIssueSeverity = 30

class petab.v2.lint.ValidationIssue(level: ValidationIssueSeverity, message: str, task: str | None = None)[source]

Bases: object

The result of a validation task.

level

The level of the validation event.

Type:: petab.v2.lint.ValidationIssueSeverity

message

The message of the validation event.

Type:: str

level: ValidationIssueSeverity

message: str

task: str | None = None

class petab.v2.lint.ValidationIssueSeverity(*values)[source]

Bases: IntEnum

The severity of a validation issue.

CRITICAL = 40

ERROR = 30

INFO = 10

WARNING = 20

class petab.v2.lint.ValidationResultList(iterable=(), /)[source]

Bases: list[ValidationIssue]

A list of validation results.

Contains all issues found during the validation of a PEtab problem.

has_errors() → bool[source]: Check if there are any errors in the validation results.

log(*, logger: Logger = <Logger petab.v2.lint (WARNING)>, min_level: ValidationIssueSeverity = ValidationIssueSeverity.INFO, max_level: ValidationIssueSeverity = ValidationIssueSeverity.CRITICAL)[source]

Log the validation results.

Parameters:

logger – The logger to use for logging. Defaults to the module logger.
min_level – The minimum severity level to log.
max_level – The maximum severity level to log.

class petab.v2.lint.ValidationTask[source]

Bases: ABC

A task to validate a PEtab problem.

abstractmethod run(problem: Problem) → ValidationIssue | None[source]

Run the validation task.

Parameters:: problem – PEtab problem to check.
Returns:: Validation results or None

petab.v2.lint.default_validation_tasks = [<petab.v2.lint.CheckProblemConfig object>, <petab.v2.lint.CheckModel object>, <petab.v2.lint.CheckUniquePrimaryKeys object>, <petab.v2.lint.CheckMeasurementModelId object>, <petab.v2.lint.CheckMeasuredObservablesDefined object>, <petab.v2.lint.CheckPosLogMeasurements object>, <petab.v2.lint.CheckOverridesMatchPlaceholders object>, <petab.v2.lint.CheckValidConditionTargets object>, <petab.v2.lint.CheckExperimentTable object>, <petab.v2.lint.CheckExperimentConditionsExist object>, <petab.v2.lint.CheckUndefinedExperiments object>, <petab.v2.lint.CheckObservablesDoNotShadowModelEntities object>, <petab.v2.lint.CheckAllParametersPresentInParameterTable object>, <petab.v2.lint.CheckValidParameterInConditionOrParameterTable object>, <petab.v2.lint.CheckUnusedExperiments object>, <petab.v2.lint.CheckUnusedConditions object>, <petab.v2.lint.CheckPriorDistribution object>, <petab.v2.lint.CheckInitialChangeSymbols object>]: Validation tasks that should be run on any PEtab problem

petab.v2.lint.lint_problem(problem: Problem | str | Path) → ValidationResultList[source]

Validate a PEtab problem.

Parameters:: problem – PEtab problem to check. Instance of Problem or path to a PEtab problem YAML file.
Returns:: A list of validation results. Empty if no issues were found.