fit.petab_v2.extension¶

The sbmlsim extension of a PEtab v2 problem.

PEtab v2 problems carry extensions, i.e., a block in the YAML of the problem which a tool reads if it knows it and ignores if it does not. The sbmlsim extension holds what the tables of PEtab do not express, see sbmlsim.fit.petab_v2.gaps: the units, the settings of the fit, what a fit does with a mapping and the structure of the timecourses.

The extension is required, because the settings it carries are the objective of the fit: a tool which does not know it has to reject the problem rather than fit the same data with another objective without saying so. A round trip through sbmlsim keeps the fit it started from, and to_petab(..., required_extension=False) writes a problem which other tools read and fit with the objective PEtab defines.

SbmlsimExtension ¶

Bases: ExtensionConfig

What PEtab v2 does not express about an sbmlsim fit.

PEtab says that an extension which changes the mathematical interpretation of a problem must be required, and that a tool must reject a problem which requires an extension it does not know but may ignore one which is not required (PEtab v2, extensions). The settings this extension carries, i.e. the residual, the loss function and the weighting, are the objective sbmlsim optimizes, so a problem which is read without them is fitted with a different objective on the same data. It is therefore required, and a tool which does not know sbmlsim has to say so instead of fitting the problem differently without telling anyone.

to_petab(..., required_extension=False) writes it as not required, which is what a problem meant for other tools wants: they read the tables and optimize the objective PEtab defines.

Attributes:

Name	Type	Description
`version`	`str`	version of the extension.
`required`	`bool`	whether a tool needs the extension to interpret the problem, `True` because the settings it carries are the objective of the fit.
`opid`	`str \| None`	id of the optimization problem.
`settings`	`dict[str, Any]`	the `FitSettings` of the fit as a dictionary.
`parameters`	`dict[str, dict[str, Any]]`	unit and start value per fit parameter.
`observables`	`dict[str, dict[str, Any]]`	the fit mapping behind every observable, i.e. its kind, the weight of the curve, the units of the data, the experiment and the task it belongs to and the metadata of the curve.
`experiments`	`dict[str, dict[str, Any]]`	the structure of the `TimecourseSim` behind every PEtab experiment, i.e. the timecourses with their steps and what is discarded, and the fit mapping collection it belongs to.
`collections`	`dict[str, dict[str, Any]]`	the `FitMappingCollection` objects of the fit, i.e. the id of the collection, the simulation experiment class its mappings come from and what the fit does with them.
`models`	`dict[str, dict[str, Any]]`	the settings of the integrator per model.
`gaps`	`list[dict[str, Any]]`	what this export lost, see `sbmlsim.fit.petab_v2.gaps`.

extension_of ¶

extension_of(config)

Get the sbmlsim extension of a PEtab problem configuration.

Parameters:

Name	Type	Description	Default
`config`	`Any`	`ProblemConfig` of a PEtab v2 problem, `None` if the problem was not read from a YAML file.	required

Returns:

Type	Description
`SbmlsimExtension \| None`	The extension, or `None` if the problem does not carry one.