fit.petab_v2.export¶

Write an sbmlsim optimization problem as a PEtab v2 problem.

The export walks an initialized OptimizationProblem, i.e., a problem whose fit mappings are resolved, and builds the tables of PEtab v2 from it:

every model of the fit is a model of the problem, written as the model the problem was defined with when the fit simulates a derived one (compiled networks, formula observables, see sbmlsim.model.provenance),
the fit mappings which share a model and a simulation are one experiment, its periods are the timecourses of the TimecourseSim and their changes are the conditions,
every fit mapping is one observable, named after the mapping; mappings which observe one thing in several experiments are one observable, its reference data are the measurements of that observable,
every fit parameter is a parameter which is estimated.

What the tables do not hold goes into the sbmlsim extension of the problem, see sbmlsim.fit.petab_v2.extension, and what is lost is reported by sbmlsim.fit.petab_v2.gaps.

PetabExporter ¶

PetabExporter(
    problem,
    settings=None,
    kinds=None,
    required_extension=True,
    parameter_set=None,
)

Write an optimization problem as a PEtab v2 problem.

A problem with hybridizations is written with its networks as PEtab SciML, see sbmlsim.fit.petab_v2.sciml_export, which needs the extra sciml.

Initialize the export of a problem.

Parameters:

Name	Type	Description	Default
`problem`	`OptimizationProblem`	problem to export, it is initialized if it is not.	required
`settings`	`FitSettings \| None`	settings of the fit, required if the problem is not initialized.	`None`
`kinds`	`set[MappingKind] \| None`	kinds of fit mappings to write, everything the problem resolved by default, i.e. the training data, the validation data and the outliers, so that a round trip keeps the fit. The data the model does not describe is not part of the problem. Which of them a fit uses is in the extension: a tool which reads the problem without it would fit everything it finds.	`None`
`required_extension`	`bool`	mark the `sbmlsim` extension as required, which it is: the settings it carries are the objective of the fit, so a tool which does not know it has to reject the problem instead of fitting the same data differently. `False` writes a problem which other tools fit with the objective PEtab defines, see `sbmlsim.fit.petab_v2.extension.SbmlsimExtension`.	`True`
`parameter_set`	`ParameterSet \| None`	values of the parameters of the fit to write, e.g. the result of a fit, which must have every parameter of the problem. They are the nominal values of the parameter table, the start values of the `sbmlsim` block and the values of the arrays of the networks, i.e. the exported problem starts from the set: a problem which is read has one start value per parameter and the arrays of a network cannot carry a second one, so a set which was written next to the start values would read back as the elements of the set and the parameters of the start. The problem is not changed. An element of a network which the problem freezes keeps its value.	`None`

Raises:

Type	Description
`ValueError`	if the problem is not initialized and no settings are given, or if the parameter set has a value for an element of a network which is no parameter of the fit.
`KeyError`	if the parameter set lacks a parameter of the problem.

check ¶

check()

Check that the problem can be written.

Raises:

Type	Description
`ValueError`	for a gap which has no representation in PEtab v2, i.e. a structural model change, an observable which is a python function or a mapping over something else than time; or for a selector without its own id, see `_check_unnamed_versions`.

to_problem ¶

to_problem()

Build the PEtab v2 problem.

Returns:

Type	Description
`Problem`	The problem with its models, conditions, experiments, observables,
`Problem`	measurements and parameters, and the `sbmlsim` extension.

Raises:

Type	Description
`ValueError`	if the problem uses features PEtab v2 cannot express.

petab_id ¶

petab_id(*parts)

Get a PEtab identifier from the parts of an sbmlsim key.

Parameters:

Name	Type	Description	Default
`parts`	`str`	parts of the identifier, joined with `__`.	`()`

Returns:

Type	Description
`str`	An identifier of letters, digits and underscores which does not start
`str`	with a digit.

period_condition_id ¶

period_condition_id(experiment_id, k)

Get the id of the condition of a period of an experiment.

Parameters:

Name	Type	Description	Default
`experiment_id`	`str`	id of the experiment.	required
`k`	`int`	index of the period, i.e. of the timecourse of the simulation.	required

Returns:

Type	Description
`str`	The id, e.g. `e1__tc0`, which the arrays of the inputs of the
`str`	networks are keyed by for the first period.

to_petab ¶

to_petab(
    problem,
    output_dir,
    settings=None,
    kinds=None,
    required_extension=True,
    parameter_set=None,
)

Write an optimization problem as a PEtab v2 problem.

Parameters:

Name	Type	Description	Default
`problem`	`OptimizationProblem`	problem to write, it is initialized if it is not.	required
`output_dir`	`Path`	directory the problem is written to, created if it does not exist.	required
`settings`	`FitSettings \| None`	settings of the fit, required if the problem is not initialized.	`None`
`kinds`	`set[MappingKind] \| None`	kinds of fit mappings to write, everything the problem resolved by default, i.e. the training data, the validation data and the outliers.	`None`
`required_extension`	`bool`	mark the `sbmlsim` extension as required, which it is: the settings it carries are the objective of the fit. `False` writes a problem other tools fit with the objective of PEtab.	`True`
`parameter_set`	`ParameterSet \| None`	values of the parameters of the fit to write, e.g. the result of a fit: the exported problem starts from them, see `PetabExporter`. The start values of the problem are written if there is none.	`None`

Returns:

Type	Description
`Path`	Path of the YAML file of the problem.

Raises:

Type	Description
`ValueError`	if the problem uses features PEtab v2 cannot express, or if the parameter set has a value for an element of a network which is no parameter of the fit.
`KeyError`	if the parameter set lacks a parameter of the problem.