Source code for bmtk.simulator.bionet

# Copyright 2017. Allen Institute. All rights reserved
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from bmtk.simulator.bionet.pyfunction_cache import synapse_model, synaptic_weight, cell_model, add_weight_function, model_processing, \
    spikes_generator
from bmtk.simulator.bionet.config import Config
from bmtk.simulator.bionet.bionetwork import BioNetwork
from bmtk.simulator.bionet.biosimulator import BioSimulator
from bmtk.simulator.bionet.nrn import reset

import sys
import argparse
import copy




class ArgumentParser(argparse.ArgumentParser):
    """A Helper class for using argparse when calling script through nrniv, eg
      $ nrniv -python run_bionet.py

    or
      $ mpirun -np 2 nrniv -mpi -python run_bionet.py
      
    
    """


    def parse_known_args(self, args=None, namespace=None):
        if args is None:
            args = copy.copy(sys.argv)
        args = ArgumentParser.parse_nrniv_arg(args)[1:]

        return super().parse_known_args(args, namespace)




    @staticmethod
    def parse_nrniv_arg(sys_argv):
        if sys_argv[0].endswith('nrniv') or sys_argv[0].endswith('nrniv.exe'):
            for i, cmd_opt in enumerate(sys_argv):
                if cmd_opt == '-python':
                    return sys_argv[i+1:]
        else:
            return sys_argv