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
- var capture_cstdout
context to redirect C/C++ stdout to python stdout if python stdout was redirected (doing nothing if not redirected).
Classes
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Context manager for temporarily changing PYTHONPATH |
Functions Summary
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Convenience wrapper for |
|
Import Python module of an AMICI model |
|
Convenience wrapper for |
|
Convenience wrapper around |
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Convenience wrapper for loops of amici.runAmiciSimulation |
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Convenience wrapper for |
Functions
-
amici.
ExpData
(*args)[source]¶ Convenience wrapper for
amici.amici.ExpData
constructors- Parameters
args – arguments
- Return type
- Returns
ExpData Instance
-
amici.
import_model_module
(module_name, module_path=None)[source]¶ Import Python module of an AMICI model
- Parameters
module_name (
str
) – Name of the python package of the modelmodule_path (
typing.Optional
[str
]) – Absolute or relative path of the package directory
- Return type
module
- Returns
The model module
-
amici.
readSolverSettingsFromHDF5
(file, solver, location='solverSettings')[source]¶ Convenience wrapper for
amici.readSolverSettingsFromHDF5()
- Parameters
file (
str
) – hdf5 filenamesolver (
typing.Union
[amici.amici.Solver
,amici.amici.SolverPtr
]) – Solver instance to which settings will be transferredlocation (
typing.Optional
[str
]) – location of solver settings in hdf5 file
- Return type
-
amici.
runAmiciSimulation
(model, solver, edata=None)[source]¶ 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)[source]¶ Convenience wrapper for loops of amici.runAmiciSimulation
- Parameters
model (
typing.Union
[amici.amici.Model
,amici.amici.ModelPtr
]) – Model instancesolver (
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 instancesfailfast (
bool
) – returns as soon as an integration failure is encounterednum_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.
writeSolverSettingsToHDF5
(solver, file, location='solverSettings')[source]¶ Convenience wrapper for
amici.amici.writeSolverSettingsToHDF5()
- Parameters
file (
typing.Union
[str
,object
]) – hdf5 filename, can also be object created byamici.amici.createOrOpenForWriting()
solver (
typing.Union
[amici.amici.Solver
,amici.amici.SolverPtr
]) – Solver instance from which settings will storedlocation (
typing.Optional
[str
]) – location of solver settings in hdf5 file
- Return type