amici

AMICI

The AMICI Python module provides functionality for importing SBML or PySB models and turning them into C++ Python extensions.

var amici_path

absolute root path of the amici repository or Python package

var amiciSwigPath

absolute path of the amici swig directory

var amiciSrcPath

absolute path of the amici source directory

var amiciModulePath

absolute root path of the amici module

var hdf5_enabled

boolean indicating if amici was compiled with hdf5 support

var has_clibs

boolean indicating if this is the full package with swig interface or the raw package without

Classes

ModelModule(*args, **kwargs)	Enable Python static type checking for AMICI-generated model modules
add_path(path)	Context manager for temporarily changing PYTHONPATH

Functions Summary

ExpData(*args)	Convenience wrapper for amici.amici.ExpData constructors
get_model_settings(model)	Get model settings that are set independently of the compiled model.
import_model_module(module_name[, module_path])	Import Python module of an AMICI model
readSolverSettingsFromHDF5(file, solver[, ...])	Convenience wrapper for amici.readSolverSettingsFromHDF5()
runAmiciSimulation(model, solver[, edata])	Convenience wrapper around amici.amici.runAmiciSimulation()
runAmiciSimulations(model, solver, edata_list)	Convenience wrapper for loops of amici.runAmiciSimulation
set_model_settings(model, settings)	Set model settings.
writeSolverSettingsToHDF5(solver, file[, ...])	Convenience wrapper for amici.amici.writeSolverSettingsToHDF5()

Functions

amici.ExpData(*args)

Convenience wrapper for amici.amici.ExpData constructors

Parameters

args – arguments

Return type

amici.amici.ExpData

Returns

ExpData Instance

amici.get_model_settings(model)

Get model settings that are set independently of the compiled model.

Parameters

model (typing.Union[amici.amici.Model, amici.amici.ModelPtr]) – The AMICI model instance.

Return type

typing.Dict[str, typing.Any]

Returns

Keys are AMICI model attributes, values are attribute values.

amici.import_model_module(module_name, module_path=None)

Import Python module of an AMICI model

Parameters

• module_name (str) – Name of the python package of the model

• module_path (typing.Optional[str]) – Absolute or relative path of the package directory

Return type

amici.ModelModule

Returns

The model module

amici.readSolverSettingsFromHDF5(file, solver, location='solverSettings')

Convenience wrapper for amici.readSolverSettingsFromHDF5()

Parameters

• file (str) – hdf5 filename

• solver (typing.Union[amici.amici.Solver, amici.amici.SolverPtr]) – Solver instance to which settings will be transferred

• location (typing.Optional[str]) – location of solver settings in hdf5 file

Return type

None

amici.runAmiciSimulation(model, solver, edata=None)

Convenience wrapper around amici.amici.runAmiciSimulation() (generated by swig)

param model

Model instance

` :param solver:

Solver instance, must be generated from amici.amici.Model.getSolver()

param edata

ExpData instance (optional)

returns

ReturnData object with simulation results

Return type

amici.numpy.ReturnDataView

amici.runAmiciSimulations(model, solver, edata_list, failfast=True, num_threads=1)

Convenience wrapper for loops of amici.runAmiciSimulation

Parameters

• model (typing.Union[amici.amici.Model, amici.amici.ModelPtr]) – Model instance

• solver (typing.Union[amici.amici.Solver, amici.amici.SolverPtr]) – Solver instance, must be generated from Model.getSolver()

• edata_list (typing.Union[amici.amici.ExpDataPtrVector, typing.Sequence[typing.Union[amici.amici.ExpData, amici.amici.ExpDataPtr]]]) – list of ExpData instances

• failfast (bool) – returns as soon as an integration failure is encountered

• num_threads (int) – number of threads to use (only used if compiled with openmp)

Return type

typing.List[amici.numpy.ReturnDataView]

Returns

list of simulation results

amici.set_model_settings(model, settings)

Set model settings.

Parameters

• model (typing.Union[amici.amici.Model, amici.amici.ModelPtr]) – The AMICI model instance.

• settings (typing.Dict[str, typing.Any]) – Keys are callable attributes (setters) of an AMICI model, values are provided to the setters.

Return type

None

amici.writeSolverSettingsToHDF5(solver, file, location='solverSettings')

Convenience wrapper for amici.amici.writeSolverSettingsToHDF5()

Parameters

• file (typing.Union[str, object]) – hdf5 filename, can also be object created by amici.amici.createOrOpenForWriting()

• solver (typing.Union[amici.amici.Solver, amici.amici.SolverPtr]) – Solver instance from which settings will stored

• location (typing.Optional[str]) – location of solver settings in hdf5 file

Return type

None