"""
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
"""
import importlib
import os
import re
import sys
from pathlib import Path
from types import ModuleType as ModelModule
from typing import Optional, Union
def _get_amici_path():
"""
Determine package installation path, or, if used directly from git
repository, get repository root
"""
basedir = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
if os.path.exists(os.path.join(basedir, '.git')):
return os.path.abspath(basedir)
return os.path.dirname(__file__)
def _get_commit_hash():
"""Get commit hash from file"""
basedir = os.path.dirname(os.path.dirname(os.path.dirname(amici_path)))
commitfile = next(
(
file for file in [
os.path.join(basedir, '.git', 'FETCH_HEAD'),
os.path.join(basedir, '.git', 'ORIG_HEAD'), ]
if os.path.isfile(file)
),
None
)
if commitfile:
with open(commitfile) as f:
return str(re.search(r'^([\w]*)', f.read().strip()).group())
return 'unknown'
def _imported_from_setup() -> bool:
"""Check whether this module is imported from `setup.py`"""
from inspect import getouterframes, currentframe
# in case we are imported from setup.py, this will be the AMICI package
# root directory (otherwise it is most likely the Python library directory,
# we are not interested in)
package_root = os.path.realpath(os.path.dirname(os.path.dirname(__file__)))
for frame in getouterframes(currentframe(), context=0):
# Need to compare the full path, in case a user tries to import AMICI
# from a module `*setup.py`. Will still cause trouble if some package
# requires the AMICI extension during its installation, but seems
# unlikely...
frame_path = os.path.realpath(os.path.expanduser(frame.filename))
if frame_path == os.path.join(package_root, 'setup.py'):
return True
return False
# Initialize AMICI paths
amici_path = _get_amici_path()
amiciSwigPath = os.path.join(amici_path, 'swig')
amiciSrcPath = os.path.join(amici_path, 'src')
amiciModulePath = os.path.dirname(__file__)
has_clibs = any([os.path.isfile(os.path.join(amici_path, wrapper))
for wrapper in ['amici.py', 'amici_without_hdf5.py']])
hdf5_enabled = False
# Get version number from file
with open(os.path.join(amici_path, 'version.txt')) as f:
__version__ = f.read().strip()
__commit__ = _get_commit_hash()
# Import SWIG module and swig-dependent submodules if required and available
if not _imported_from_setup():
if has_clibs:
from . import amici
from .amici import *
# has to be done before importing readSolverSettingsFromHDF5
# from .swig_wrappers
hdf5_enabled = 'readSolverSettingsFromHDF5' in dir()
from .swig_wrappers import *
# These modules require the swig interface and other dependencies
from .numpy import ReturnDataView, ExpDataView
from .pandas import *
# These modules don't require the swig interface
from .sbml_import import SbmlImporter, assignmentRules2observables
from .ode_export import ODEModel, ODEExporter
from typing import Protocol
[docs] class ModelModule(Protocol):
"""Enable Python static type checking for AMICI-generated model
modules"""
[docs] def getModel(self) -> amici.Model:
pass
[docs]class add_path:
"""Context manager for temporarily changing PYTHONPATH"""
[docs] def __init__(self, path: Union[str, Path]):
self.path: str = str(path)
def __enter__(self):
if self.path:
sys.path.insert(0, self.path)
def __exit__(self, exc_type, exc_value, traceback):
try:
sys.path.remove(self.path)
except ValueError:
pass
[docs]def import_model_module(
module_name: str,
module_path: Optional[Union[Path, str]] = None
) -> ModelModule:
"""
Import Python module of an AMICI model
:param module_name:
Name of the python package of the model
:param module_path:
Absolute or relative path of the package directory
:return:
The model module
"""
module_path = str(module_path)
# ensure we will find the newly created module
importlib.invalidate_caches()
if not os.path.isdir(module_path):
raise ValueError(f"module_path '{module_path}' is not a directory.")
module_path = os.path.abspath(module_path)
# module already loaded?
if module_name in sys.modules:
# if a module with that name is already in sys.modules, we remove it,
# along with all other modules from that package. otherwise, there
# will be trouble if two different models with the same name are to
# be imported.
del sys.modules[module_name]
# collect first, don't delete while iterating
to_unload = {loaded_module_name for loaded_module_name in
sys.modules.keys() if
loaded_module_name.startswith(f"{module_name}.")}
for m in to_unload:
del sys.modules[m]
with add_path(module_path):
return importlib.import_module(module_name)
class AmiciVersionError(RuntimeError):
"""Error thrown if an AMICI model is loaded that is incompatible with
the installed AMICI base package"""
pass