"""
AMICI
-----
The AMICI Python module provides functionality for importing SBML or PySB
models and turning them into C++ Python extensions.
"""
import contextlib
import importlib
import os
import re
import sys
from pathlib import Path
from types import ModuleType as ModelModule
from typing import Any
from collections.abc import Callable
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 currentframe, getouterframes
from os import sep
# 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"
) or frame_path.endswith(f"{sep}setuptools{sep}build_meta.py"):
return True
return False
# Initialize AMICI paths
#: absolute root path of the amici repository or Python package
amici_path = _get_amici_path()
#: absolute path of the amici swig directory
amiciSwigPath = os.path.join(amici_path, "swig")
#: absolute path of the amici source directory
amiciSrcPath = os.path.join(amici_path, "src")
#: absolute root path of the amici module
amiciModulePath = os.path.dirname(__file__)
#: boolean indicating if this is the full package with swig interface or
# the raw package without extension
has_clibs: bool = any(
os.path.isfile(os.path.join(amici_path, wrapper))
for wrapper in ["amici.py", "amici_without_hdf5.py"]
)
#: boolean indicating if amici was compiled with hdf5 support
hdf5_enabled: bool = 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()
# These modules require the swig interface and other dependencies
from .numpy import ExpDataView, ReturnDataView # noqa: F401
from .pandas import *
from .swig_wrappers import *
# These modules don't require the swig interface
from typing import Protocol, runtime_checkable
from .de_export import DEExporter # noqa: F401
from .sbml_import import ( # noqa: F401
SbmlImporter,
assignmentRules2observables,
)
[docs]
@runtime_checkable
class ModelModule(Protocol): # noqa: F811
"""Type of AMICI-generated model modules.
To enable static type checking."""
[docs]
def getModel(self) -> amici.Model:
"""Create a model instance."""
...
[docs]
def get_model(self) -> amici.Model:
"""Create a model instance."""
...
[docs]
class add_path:
"""Context manager for temporarily changing PYTHONPATH"""
[docs]
def __init__(self, path: 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):
with contextlib.suppress(ValueError):
sys.path.remove(self.path)
[docs]
def import_model_module(
module_name: str, module_path: Path | str
) -> 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)
[docs]
class AmiciVersionError(RuntimeError):
"""Error thrown if an AMICI model is loaded that is incompatible with
the installed AMICI base package"""
pass
def _get_default_argument(func: Callable, arg: str) -> Any:
"""Get the default value of the given argument in the given function."""
import inspect
signature = inspect.signature(func)
if (
default := signature.parameters[arg].default
) is not inspect.Parameter.empty:
return default
raise ValueError(f"No default value for argument {arg} of {func}.")