sbmlsim.experiment.runner

Runner for SimulationExperiments.

The ExperimentRunner is used to execute simulation experiments. This includes - loading of datasets - loading of models - running tasks (simulation on models) - creating outputs

Module Contents

Classes

ExperimentRunner

Class for running simulation experiments.

Functions

run_experiments(experiments, output_path[, base_path, ...])

Run simulation experiments.

Attributes

logger

sbmlsim.experiment.runner.logger

class sbmlsim.experiment.runner.ExperimentRunner(experiment_classes, base_path, data_path, simulator=None, ureg=None, **kwargs)

Bases: object

Class for running simulation experiments.

Parameters:

• experiment_classes (Union[Type[sbmlsim.experiment.SimulationExperiment], List[Type[sbmlsim.experiment.SimulationExperiment]]]) –

• base_path (pathlib.Path) –

• data_path (pathlib.Path) –

• simulator (Union[sbmlsim.simulator.SimulatorSerialRR, sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR]) –

• ureg (sbmlsim.units.UnitRegistry) –

set_simulator(simulator)

Set simulator on the runner and experiments.

Parameters:

simulator (sbmlsim.simulator.SimulatorSerialRR) –

Return type:

None

initialize(experiment_classes, **kwargs)

Initialize ExperimentRunner.

Initialization is required in addition to construction to allow serialization of information for parallelization.

Parameters:

experiment_classes (Union[List[Type[sbmlsim.experiment.SimulationExperiment]], Tuple[Type[sbmlsim.experiment.SimulationExperiment]], Set[Type[sbmlsim.experiment.SimulationExperiment]]]) –

run_experiments(output_path, show_figures=False, save_results=False, figure_formats=None, reduced_selections=True)

Run the experiments.

Parameters:

• output_path (pathlib.Path) –

• show_figures (bool) –

• save_results (bool) –

• figure_formats (List[str]) –

• reduced_selections (bool) –

Return type:

List[sbmlsim.experiment.ExperimentResult]

sbmlsim.experiment.runner.run_experiments(experiments, output_path, base_path=None, data_path=None, parallel=True)

Run simulation experiments.

Parameters:

• experiments (Union[Type[sbmlsim.experiment.SimulationExperiment], List[Type[sbmlsim.experiment.SimulationExperiment]]]) –

• output_path (pathlib.Path) –

• base_path (pathlib.Path) –

• data_path (Union[List[pathlib.Path], Tuple[pathlib.Path], Optional[pathlib.Path]]) –

• parallel (bool) –

Return type:

pathlib.Path