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Function __run has a Cognitive Complexity of 147 (exceeds 5 allowed). Consider refactoring.
Open

    def __run(self, curr_state, total_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
              number_of_trajectories=1, increment=0.05, seed=None, debug=False, profile=False,
              resume=None, tau_tol=0.03, **kwargs):

        # for use with resume, determines how much excess data to cut off due to
Severity: Minor
Found in gillespy2/solvers/numpy/tau_leaping_solver.py - About 2 days to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function validate has a Cognitive Complexity of 147 (exceeds 5 allowed). Consider refactoring.
Open

    def validate(self, reactants=None, products=None, propensity_function=None,
                 ode_propensity_function=None, marate=None, annotation=None, coverage="build"):
        """
        Check if the reaction is properly formatted.
        Does nothing on sucesss, raises and error on failure.
Severity: Minor
Found in gillespy2/core/reaction.py - About 2 days to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __run has a Cognitive Complexity of 142 (exceeds 5 allowed). Consider refactoring.
Open

    def __run(self, curr_state, total_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
              number_of_trajectories=1, increment=0.05, seed=None, debug=False, profile=False, timeout=None,
              resume=None, tau_tol=0.03, **kwargs):

        # for use with resume, determines how much excess data to cut off due to
Severity: Minor
Found in gillespy2/solvers/numpy/CLE_solver.py - About 2 days to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __run has a Cognitive Complexity of 94 (exceeds 5 allowed). Consider refactoring.
Open

    def __run(self, curr_state, total_time, timeline, trajectory_base, live_grapher, t=20,
              number_of_trajectories=1, increment=0.05, seed=None, debug=False,
              resume=None,):

        # for use with resume, determines how much excess data to cut off due to
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py - About 1 day to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function to_model has a Cognitive Complexity of 60 (exceeds 5 allowed). Consider refactoring.
Open

    def to_model(self, name):
        """ Instantiates a Model object from a StochMLDocument. """

        # Empty model
        model = Model(name=name)
Severity: Minor
Found in gillespy2/core/model.py - About 1 day to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __run has a Cognitive Complexity of 54 (exceeds 5 allowed). Consider refactoring.
Open

    def __run(self, curr_state, curr_time, timeline, trajectory_base, initial_state, live_grapher, t=20,
              number_of_trajectories=1, increment=0.05, seed=None,
              debug=False, profile=False,
              tau_tol=0.03, event_sensitivity=100,
              integrator_options={}, **kwargs):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 1 day to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function validate has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.
Open

    def validate(self, initial_value=None, coverage="all"):
        """
        Validate the species.

        :param initial_value: Initial population (discrete) or concentration (continuous) of this species.
Severity: Minor
Found in gillespy2/core/species.py - About 6 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function dependency_grapher has a Cognitive Complexity of 41 (exceeds 5 allowed). Consider refactoring.
Open

def dependency_grapher(model, reactions):
    """
    This function returns a dependency graph for a models reactions in the form of a
    dictionary containing {species name: {'dependencies'}:[list of reaction names]}.
Severity: Minor
Found in gillespy2/solvers/utilities/solverutils.py - About 6 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring.
Open

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None,
            debug=False, profile=False, tau_tol=0.03, event_sensitivity=100,integrator_options={},
            live_output=None, live_output_options={}, timeout=None, **kwargs):
        """
        Function calling simulation of the model. This is typically called by the run function in GillesPy2 model
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 6 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.
Open

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, integrator='lsoda',
            integrator_options={}, live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):
        """
        :param model: The model on which the solver will operate. (Deprecated)
        :type model: gillespy2.Model
Severity: Minor
Found in gillespy2/solvers/numpy/ode_solver.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
Open

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None, debug=False,
            live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):

        """
        Run the SSA algorithm. Uses a NumPy array for storing results and for generating the timeline.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
Open

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None,
            debug=False, profile=False,  live_output=None, live_output_options={},
            timeout=None, resume=None, tau_tol=0.03, **kwargs):
        """
        Function calling simulation of the model.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_leaping_solver.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __simulate has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
Open

    def __simulate(self, integrator_options, curr_state, y0, curr_time,
                   propensities, species, parameters, compiled_reactions,
                   active_rr, y_map, trajectory, save_times, save_index,
                   delayed_events, trigger_states, event_sensitivity,
                   tau_step, debug, det_spec, det_rxn):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
Open

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None,
            debug=False, profile=False,  live_output=None, live_output_options={},
            timeout=None, resume=None, tau_tol=0.03, **kwargs):
        """
        Function calling simulation of the model.
Severity: Minor
Found in gillespy2/solvers/numpy/CLE_solver.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function display has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.
Open

    def display(self, curr_state, curr_time, trajectory_base, finished=False):
        '''
        Display the output for the live grapher.

        :param curr_state: Current state of the simulation. Should be a list of len 1 to get reference.
Severity: Minor
Found in gillespy2/core/liveGraphing.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function select has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.
Open

def select(*tau_args):
    """
    Tau Selection method based on Cao, Y.; Gillespie, D. T.; Petzold, L. R. (2006).
    "Efficient step size selection for the tau-leaping simulation method" (PDF).
    The Journal of Chemical Physics. 124 (4): 044109. Bibcode:2006JChPh.124d4109C. doi:10.1063/1.2159468. PMID 16460151
Severity: Minor
Found in gillespy2/solvers/utilities/Tau.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __calculate_statistics has a Cognitive Complexity of 35 (exceeds 5 allowed). Consider refactoring.
Open

    def __calculate_statistics(self, curr_time, propensities, curr_state, tau_step, det_spec, cv_history={}):
        """
        Calculates Mean, Standard Deviation, and Coefficient of Variance for each
        dynamic species, then set if species can be represented determistically
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __init__ has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, name=None, reactants=None, products=None, propensity_function=None,
                 ode_propensity_function=None, rate=None, annotation=None, massaction=None):
        if massaction is not None:
            from gillespy2.core import log # pylint: disable=import-outside-toplevel
            log.warning(
Severity: Minor
Found in gillespy2/core/reaction.py - About 5 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __get_reactions has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

def __get_reactions(sbml_model, gillespy_model, errors):
    # reactions
    for i in range(sbml_model.getNumReactions()):
        reaction = sbml_model.getReaction(i)
        name = reaction.getId()
Severity: Minor
Found in gillespy2/sbml/SBMLimport.py - About 4 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function plotplotly has a Cognitive Complexity of 32 (exceeds 5 allowed). Consider refactoring.
Open

    def plotplotly(self, index=None, xaxis_label="Time", yaxis_label="Value", title=None,
                   show_title=False, show_legend=True, multiple_graphs=False, included_species_list=[],
                   return_plotly_figure=False,  **layout_args):
        """ Plots the Results using plotly. Can only be viewed in a Jupyter Notebook.
Severity: Minor
Found in gillespy2/core/results.py - About 4 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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