amici

AMICI

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

Module Attributes

amici_path

absolute root path of the amici repository or Python package

amiciSwigPath

absolute path of the amici swig directory

amiciSrcPath

absolute path of the amici source directory

amiciModulePath

absolute root path of the amici module

hdf5_enabled

boolean indicating if amici was compiled with hdf5 support

Functions

import_model_module(module_name, module_path)

Import Python module of an AMICI model

Classes

ModelModule(*args, **kwargs)

Type of AMICI-generated model modules.

add_path(path)

Context manager for temporarily changing PYTHONPATH

Exceptions

AmiciVersionError

Error thrown if an AMICI model is loaded that is incompatible with the installed AMICI base package

exception amici.AmiciVersionError[source]

Error thrown if an AMICI model is loaded that is incompatible with the installed AMICI base package

class amici.ModelModule(*args, **kwargs)[source]

Type of AMICI-generated model modules.

To enable static type checking.

__init__(*args, **kwargs)
getModel()[source]

Create a model instance.

Return type:

amici.amici.Model

get_model()[source]

Create a model instance.

Return type:

amici.amici.Model

class amici.add_path(path)[source]

Context manager for temporarily changing PYTHONPATH

__init__(path)[source]
amici.amiciModulePath = '/home/docs/checkouts/readthedocs.org/user_builds/amici/checkouts/develop/python/sdist/amici'

absolute root path of the amici module

amici.amiciSrcPath = '/home/docs/checkouts/readthedocs.org/user_builds/amici/checkouts/develop/python/sdist/amici/src'

absolute path of the amici source directory

amici.amiciSwigPath = '/home/docs/checkouts/readthedocs.org/user_builds/amici/checkouts/develop/python/sdist/amici/swig'

absolute path of the amici swig directory

amici.amici_path = '/home/docs/checkouts/readthedocs.org/user_builds/amici/checkouts/develop/python/sdist/amici'

absolute root path of the amici repository or Python package

amici.hdf5_enabled: bool = False

boolean indicating if amici was compiled with hdf5 support

amici.import_model_module(module_name, module_path)[source]

Import Python module of an AMICI model

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

  • module_path (typing.Union[pathlib.Path, str]) – Absolute or relative path of the package directory

Return type:

amici.ModelModule

Returns:

The model module