import numpy as np
from numpy.random import Generator
SEED: int = 180319 # Seed for reproducibility
RANDOM_GENERATOR: Generator = np.random.default_rng(SEED)
[docs]
def set_random_seed(seed: int = SEED) -> None:
"""
Set the random seed for reproducibility.
Parameters
----------
seed : int, optional
Seed value to set, by default SEED
"""
global RANDOM_GENERATOR
RANDOM_GENERATOR = np.random.default_rng(seed)
print(f"Random seed set to {seed}.")
class MyoGenSetupError(Exception):
"""Exception raised when MyoGen setup fails."""
pass
def _setup_myogen(quiet: bool = False, force_rebuild: bool = False, strict: bool = False) -> bool:
"""
Set up MyoGen with NEURON mechanism compilation and loading.
This function handles the compilation and loading of NMODL files required for
neural simulations. It also compiles Cython extensions if they are not already
available (typically only needed in development mode).
Parameters
----------
quiet : bool, optional
If True, suppress most output messages, by default False
force_rebuild : bool, optional
If True, force recompilation of Cython extensions even if they appear
to be already compiled, by default False
strict : bool, optional
If True, raise exceptions on errors instead of returning False.
Recommended for CI/CD pipelines and production deployments.
Returns
-------
bool
True if setup completed successfully, False otherwise
Raises
------
MyoGenSetupError
If strict=True and setup fails
"""
def error(msg):
"""Handle errors based on strict mode."""
if strict:
raise MyoGenSetupError(msg)
else:
print(f"ERROR: {msg}")
return False
# Check if Cython extensions are already compiled (from installed package)
cython_modules = [
"myogen.simulator.neuron._cython._spindle",
"myogen.simulator.neuron._cython._hill",
"myogen.simulator.neuron._cython._gto",
"myogen.simulator.neuron._cython._poisson_process_generator",
"myogen.simulator.neuron._cython._gamma_process_generator",
"myogen.simulator.neuron._cython._simulate_fiber",
]
all_compiled = True
if not force_rebuild:
for module_name in cython_modules:
try:
__import__(module_name)
except ImportError:
all_compiled = False
break
else:
all_compiled = False
# Only compile Cython extensions if not already available
if not all_compiled:
if not quiet:
print("Compiling Cython extensions (development mode)...")
import os
from pathlib import Path
# Check if .pyx files exist (development install)
myogen_root = Path(__file__).parent
pyx_files_exist = (
myogen_root / "simulator" / "neuron" / "_cython" / "_spindle.pyx"
).exists()
if not pyx_files_exist:
if not quiet:
print("Cython source files not found. This is expected for installed packages.")
print("Cython extensions should have been compiled during installation.")
# Try importing again to give a clearer error if truly missing
try:
from myogen.simulator.neuron._cython import _spindle
if not quiet:
print("Cython extensions are available.")
except ImportError as e:
return error(
f"Cython extensions are not available: {e}\n"
"Please reinstall MyoGen or run setup from a development clone."
)
else:
# Development mode: compile in-place
from Cython.Build import cythonize
from setuptools import Extension, setup
setup(
ext_modules=cythonize(
[
Extension(
"myogen.simulator.neuron._cython._spindle",
["myogen/simulator/neuron/_cython/_spindle.pyx"],
extra_compile_args=["-O2", "-march=native", "-ffast-math"],
),
Extension(
"myogen.simulator.neuron._cython._hill",
["myogen/simulator/neuron/_cython/_hill.pyx"],
extra_compile_args=["-O2", "-march=native"],
),
Extension(
"myogen.simulator.neuron._cython._gto",
["myogen/simulator/neuron/_cython/_gto.pyx"],
extra_compile_args=["-O2", "-march=native", "-ffast-math"],
),
Extension(
"myogen.simulator.neuron._cython._poisson_process_generator",
["myogen/simulator/neuron/_cython/_poisson_process_generator.pyx"],
extra_compile_args=["-O2", "-march=native", "-ffast-math"],
),
Extension(
"myogen.simulator.neuron._cython._gamma_process_generator",
["myogen/simulator/neuron/_cython/_gamma_process_generator.pyx"],
extra_compile_args=["-O2", "-march=native", "-ffast-math"],
),
Extension(
"myogen.simulator.neuron._cython._simulate_fiber",
["myogen/simulator/neuron/_cython/_simulate_fiber.pyx"],
extra_compile_args=["-O2", "-march=native", "-ffast-math"],
),
],
compiler_directives={"embedsignature": True},
nthreads=4,
),
script_args=["build_ext", "--inplace"],
include_dirs=[np.get_include()],
)
if not quiet:
print("Cython extensions compiled successfully.")
elif not quiet:
print("Cython extensions already available.")
# Compile NMODL files for NEURON
try:
from pathlib import Path
import platform
# Check if NMODL files are already compiled
myogen_root = Path(__file__).parent
nmodl_path = myogen_root / "simulator" / "nmodl_files"
# Check for compiled NMODL libraries
nmodl_compiled = False
if platform.system() == "Windows":
# On Windows, look for nrnmech.dll
nmodl_compiled = any(nmodl_path.glob("*nrnmech.dll"))
else:
# On Unix, look for libnrnmech.so or x86_64 directory
nmodl_compiled = (nmodl_path / "x86_64").exists() or any(nmodl_path.glob("*nrnmech.so"))
if nmodl_compiled and not force_rebuild:
if not quiet:
print("NMODL mechanisms already compiled.")
return True
else:
if not quiet:
print("Compiling NMODL mechanisms...")
from myogen.utils.nmodl import compile_nmodl_files
result = compile_nmodl_files(quiet=quiet)
if result and not quiet:
print("NMODL mechanisms compiled successfully.")
return result
except ImportError as e:
return error(f"NEURON not available, cannot compile mechanisms: {e}")
except Exception as e:
return error(f"MyoGen setup failed: {e}")
from myogen.utils.nmodl import (
load_nmodl_mechanisms,
NMODLLoadError,
get_mechanism_parameters,
validate_mechanism_parameter,
set_mechanism_param,
)
# Auto-load NMODL mechanisms when MyoGen is imported
# quiet=True suppresses success messages, but warnings are still shown
# Use strict=True in your code to raise exceptions on failure
_nmodl_loaded = load_nmodl_mechanisms(quiet=True, strict=False)
__all__ = [
"RANDOM_GENERATOR",
"SEED",
"set_random_seed",
"load_nmodl_mechanisms",
"NMODLLoadError",
"MyoGenSetupError",
"get_mechanism_parameters",
"validate_mechanism_parameter",
"set_mechanism_param",
"_setup_myogen",
]
