testing¶

The tests of a model as functions: the registry, the experiments, the fits.

A repository of models calls them from its own tests, so that a model which is exported into a repository of its own keeps them (check_model checks that the model object belongs to its package):

# not executed
@pytest.mark.parametrize("model", MODELS)
def test_experiments_registered(model: PKPDModel) -> None:
    testing.check_registry(model)

The known exceptions of the tests (experiments which are not registered on purpose, modules which do not import, the reason to run the experiments one at a time, the checks of the battery which fail) are the checks of the model object, each with its reason.

The functions raise AssertionError with a message which names every problem, also for experiments which fail to initialize or to run.

experiment_modules ¶

experiment_modules(model)

Import the modules below experiments of a model.

The modules in model.checks.not_importable are skipped.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required

Returns:

Type	Description
`list[ModuleType]`	The imported modules and the traceback of every module which does not
`dict[str, str]`	import, by its name relative to the package of the model.

defined_experiments ¶

defined_experiments(modules)

Get the experiments defined in modules, without the base experiments.

A base experiment is a class from which another of the found classes derives.

registered_experiments ¶

registered_experiments(model)

Get the experiments of the group all of the registry of a model.

check_registry ¶

check_registry(model)

Check that every experiment a model defines is in its registry.

Every module below experiments imports, every experiment is registered in all once, and the known exceptions of model.checks are still exceptions (a listed class is defined and not registered, a listed module exists).

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required

Raises:

Type	Description
`AssertionError`	naming every problem.

check_model ¶

check_model(model)

Check that a model object belongs to its package and its references hold.

A slip in package or path of a model resolves the references of another model, or names the paths wrongly, without an error otherwise. The name is the last component of the package (or the component ends with _<name>), the builds (model_path, female_model_path), the factory directory and archive_path lie below path, the data paths exist, and every parameter of an adopted fit has its value and a distribution in the model (pkpdsim.uncertainty.check_fit_parameters).

Raises:

Type	Description
`AssertionError`	naming every problem.

initialize_experiments ¶

initialize_experiments(model)

Initialize the registered experiments with their data, figures, mappings.

Every experiment is initialized, also after one which cannot be.

Returns:

Type	Description
`dict[str, SimulationExperiment]`	The experiments by name.

Raises:

Type	Description
`AssertionError`	naming every experiment which cannot be initialized with its error; the tracebacks are in the log of sbmlsim.

run_all_experiments ¶

run_all_experiments(model, output_dir)

Run the registered experiments, as run_simulation does.

Every experiment runs, also after one which failed.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required
`output_dir`	`Path`	the directory of the results. With `model.checks.one_at_a_time` every experiment runs on its own, into a directory named after it: the memory of a run of all experiments of a large model exceeds that of a runner of a continuous integration.	required

Raises:

Type	Description
`AssertionError`	naming every failed experiment and figure, and every run which wrote no report.

check_battery ¶

check_battery(model, *, rebuild=True, cross_simulator=True)

Run the battery of the checks of the builds of a model.

A failed check is a problem unless the model knows it (CheckSettings.battery); a known failure whose check passes or is not applicable no longer applies and is a problem as well.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required
`rebuild`	`bool`	rebuild the model with its factory.	`True`
`cross_simulator`	`bool`	compare the builds with AMICI when it is installed, see `pkpdsim.credibility.battery.run_battery`.	`True`

Returns:

Type	Description
`Battery`	The battery.

Raises:

Type	Description
`AssertionError`	naming every problem.

start_fits ¶

start_fits(model, output_dir, max_nfev=2)

Start a fit of every fit definition: one start with a few evaluations.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required
`output_dir`	`Path`	the directory of the results of the fits.	required
`max_nfev`	`int`	evaluations of the cost per start.	`2`

Returns:

Type	Description
`dict[str, dict[str, FitRun]]`	The runs of every fit definition.

Raises:

Type	Description
`AssertionError`	if a fit definition did not run.