run¶

Running the simulation experiments of a model and collecting their figures.

This is the helpers.run_experiments and the run_simulation_experiments of simulations.py which every model of pkdb_models had as a copy: the experiments run with the simulator settings of the model, the figures are drawn with its figure settings, the HTML report is written, and run_simulation_experiments copies the figures into _figures.

Every experiment runs, also after another one failed: sbmlsim logs a failure with its traceback and records it. Once the report (and the collected figures) are written, a run with a failure raises ExperimentRunError, whose failures name every failed experiment and figure.

create_simulator ¶

create_simulator(settings)

Get the simulator of sbmlsim with the settings of a model.

Parameters:

Name	Type	Description	Default
`settings`	`SimulatorSettings`	the tolerances and the processes of the simulations.	required

Returns:

Type	Description
`Simulator`	The simulator.

run_experiments ¶

run_experiments(
    model,
    experiment_classes,
    output_dir,
    *,
    save_results=None,
    show_report=False,
    figure_formats=None,
    simulator=None,
)

Run simulation experiments of a model and create their report.

sbmlsim does not configure logging, so the messages of the package are shown on the rich console explicitly.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model whose experiments run.	required
`experiment_classes`	`type[SimulationExperiment] \| Sequence[type[SimulationExperiment]]`	the experiment class or classes to run.	required
`output_dir`	`str \| Path`	directory of the results; a relative directory is below the simulation results of the model (`model.simulation_dir`).	required
`save_results`	`bool \| None`	store the results of the simulations, `model.save_results` by default.	`None`
`show_report`	`bool`	open the report in a web browser.	`False`
`figure_formats`	`Sequence[str] \| None`	the formats of the figures, those of the model by default; an empty sequence falls back to the formats of the model as well.	`None`
`simulator`	`SimulatorSettings \| None`	the settings of the simulator, those of the model by default, e.g. with more processes.	`None`

Returns:

Type	Description
`Path`	The directory the results were written to.

Raises:

Type	Description
`TypeError`	if `figure_formats` is a single string.
`ExperimentRunError`	after the report is written, if an experiment or a figure failed; its `failures` name them, the log of the run has the tracebacks.

run_simulation_experiments ¶

run_simulation_experiments(
    model,
    experiment_classes,
    output_dir,
    *,
    show_report=False,
    figure_formats=None,
    simulator=None,
)

Run simulation experiments and collect their figures.

The static figures of all experiments (COLLECTED_FORMATS) are copied into _figures of the output directory, also those of a run with failures.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model whose experiments run.	required
`experiment_classes`	`Sequence[type[SimulationExperiment]]`	the experiments to run.	required
`output_dir`	`str \| Path`	directory of the results, see `run_experiments`.	required
`show_report`	`bool`	open the report in a web browser.	`False`
`figure_formats`	`Sequence[str] \| None`	the formats of the figures, those of the model by default.	`None`
`simulator`	`SimulatorSettings \| None`	the settings of the simulator, those of the model by default.	`None`

Returns:

Type	Description
`Path`	The directory of the collected figures.

Raises:

Type	Description
`ExperimentRunError`	after the figures are collected, if an experiment or a figure failed.