verify.definitions¶

The fit definitions and the run settings of a project, verify fits, definitions, settings.

fits ¶

fits(args)

Run a minimal fit (one start, a few evaluations) of every fit definition.

Returns:

Type	Description
`int`	1 if a fit failed, else 0.

Raises:

Type	Description
`UsageError`	for a project without fits or an unknown subset.

definitions ¶

definitions(args)

Write the fit definitions of a project as json.

The settings, the parameters and the mappings of the collections of every fit definition, so that the definitions of two checkouts are compared with diff. The checkout directory (--root, else the root of the project) is replaced by <root>.

Raises:

Type	Description
`UsageError`	for a project without fits.

capture_settings ¶

capture_settings(project, experiment, root, run=None)

Capture the settings a run of an experiment hands to sbmlsim.

The run is intercepted where it reaches sbmlsim: the arguments of the simulator (Simulator), of the runner (without the simulator) and of the run (without the output path; with the figure settings of the run), bound to the signatures, so positional and keyword calls agree, and every matplotlib rcParams entry which differs from the value before the run, at the time of the run. calls counts the intercepted calls. The simulator is the one created before the runner: the designs of an experiment (sbmlsim.simulation.sampling.parameters_of, local) create simulators of their own while the runner initializes it, which are neither recorded nor counted. Nothing is simulated and no report is written.

Parameters:

Name	Type	Description	Default
`project`	`Project`	the project, whose `run_experiments` is intercepted.	required
`experiment`	`type[SimulationExperiment]`	the experiment class the run gets.	required
`root`	`Path`	the checkout; it is replaced by `<root>` in the paths.	required
`run`	`Callable[[type[SimulationExperiment], Path], object] \| None`	the run to intercept, called with the experiment and an output directory; `project.run_experiments` with its settings without.	`None`

Returns:

Type	Description
`dict[str, Any]`	The settings as json values.

Raises:

Type	Description
`RuntimeError`	if the run does not reach the simulator, the runner and the run of the experiments of sbmlsim.

settings ¶

settings(args)

Write the settings of a run of the experiments of a project as json.

Raises:

Type	Description
`UsageError`	for a project without experiments, an unknown experiment or a run which does not reach sbmlsim.