File mrna_and_proteins_using_several_methods.py has 743 lines of code (exceeds 250 allowed). Consider refactoring.

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""" Stochastic simulation tutorial
 
:Author: Jonathan Karr <jonrkarr@gmail.com>
:Date: 2017-08-30
:Copyright: 2017, Karr Lab

File model.py has 671 lines of code (exceeds 250 allowed). Consider refactoring.

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'''
Reads models specified in Excel into a Python object
 
@author Jonathan Karr, karr@mssm.edu
@date 3/22/2016

File model_composition.py has 614 lines of code (exceeds 250 allowed). Consider refactoring.

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""" Model composition tutorial
 
- Glycolysis model (Teusink et al., 2000)
- Glycerol synthesis model (Cronwright et al., 2002)
 
 

Function getModelFromExcel has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring.

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def getModelFromExcel(filename):
    # Reads model from Excel file into a Python object
 
    with warnings.catch_warnings():
        warnings.filterwarnings("ignore", "Discarded range with reserved name", UserWarning)

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GlycolysisModel has 35 functions (exceeds 20 allowed). Consider refactoring.

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class GlycolysisModel(object):
    """ Glycolysis model (Teusink et al., 2000)
 
    Based on the `version from JWS Online <http://jjj.biochem.sun.ac.za/models/teusink/>`_
 
 

Function simulate has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.

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def simulate(mdl):
    # simulates model
 
    # Get metabolism submodel
    submdl = mdl.getComponentById('Metabolism')

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Function simulate has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

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def simulate(mdl):
    # simulates model
 
    # Get FBA, SSA submodels
    ssaSubmodels = []

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Function main has 69 lines of code (exceeds 25 allowed). Consider refactoring.

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def main(examples_dir=os.path.join(os.path.dirname(__file__), 'examples')):
 
    ################################################################
    # This code is used by literalinclude commands in wc_lang_tutorial.rst
    # It contains many separate examples, each prefixed by a comment that delineates the

Function setupSimulation has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

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    def setupSimulation(self):
        '''setup reaction participant, enzyme counts matrices'''
        Submodel.setupSimulation(self)
 
        '''Setup FBA'''

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Function run has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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    def run(self, value_init=5, time_max=10):
        """ Runs a simulation for `time_max` seconds starting with `value_init` molecules
 
        Args:
            value_init (:obj:`float`, optional): initial number of species

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Function get_steady_state has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

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    def get_steady_state(self):
        """ Calculate the steady state probability distribution
 
        Returns:
            :obj:`numpy.array`: steay-state probability of each (mRNA, protein) state (dimensionless)

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Function dp_dt has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

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    def dp_dt(self, p_part_vec):
        """ Calculate the time derivative of the probability of each (mRNA, protein) state
 
        Args:
            p_part_vec (:obj:`numpy.array`): vector of probability of each (mRNA, protein) state (dimensionless)

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Function main has 44 lines of code (exceeds 25 allowed). Consider refactoring.

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def main():
    # seed random number generator
    numpy.random.seed(0)
 
    # simulate

Function main has 41 lines of code (exceeds 25 allowed). Consider refactoring.

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def main():
    # create a figure with 2x1 subplots
    fig, axes = pyplot.subplots(nrows=2, ncols=1)
 
    # plot data on the subplots

Function main has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

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def main(init_concs=None):
    """ Run dFBA simsulation, plot results, and save plots
 
    Args:
        init_concs (:obj:`dict`, optional): initial concentrations

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Function main has 37 lines of code (exceeds 25 allowed). Consider refactoring.

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def main(init_concs=None):
    """ Run dFBA simsulation, plot results, and save plots
 
    Args:
        init_concs (:obj:`dict`, optional): initial concentrations

Function __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self, id='', name='', submodel='', reversible=None, participants=[],

Function main has 33 lines of code (exceeds 25 allowed). Consider refactoring.

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def main(out_dir=None):
    """ Simulate individual models and combined model, plot results, and save plots
 
    Args:
        out_dir (:obj:`str`, optional): path to directory to save results

Function insert_records has 33 lines of code (exceeds 25 allowed). Consider refactoring.

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def insert_records(session):
    # create homo sapiens organism with one reaction
    organism = Organism(ncbi_id=9606, name='Homo sapiens')
    session.add(organism)
 
 

Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(self, id='', name='', structure='', empiricalFormula='', molecularWeight=None,