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Function __get_reactions has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __get_reactions(self, step, curr_state, curr_time, save_time, propensities, reactions):
        """
        Helper Function to get reactions fired from t to t+tau.  
        :returns: Three values:
            rxn_count - dict with key=Reaction channel value=number of times fired
Severity: Minor
Found in gillespy2/solvers/numpy/tau_leaping_solver.py - About 25 mins 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 linspace has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def linspace(cls, t=20, num_points=None):
        """
        Creates a timespan using the form np.linspace(0, <t>, <num_points, inclusive>).

        :param t: End time for the simulation.
Severity: Minor
Found in gillespy2/core/timespan.py - About 25 mins 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 prepare has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def prepare(self, model: "Union[Model, template_gen.SanitizedModel]", variable=False) -> str:
        """
        Prepare the template directory for compilation.
        The following operations will be performed:
            1. If no cached object files are found, prebuild them.
Severity: Minor
Found in gillespy2/solvers/cpp/build/build_engine.py - About 25 mins 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 __piecewise has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def __piecewise(*args):
    # Eval entry for piecewise functions
    args = list(args)
    solution = None
    if len(args) % 2:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 25 mins 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 __process_queued_events has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __process_queued_events(self, event_queue, trigger_states,
                                curr_state, det_spec):
        """
        Helper method which processes the events queue. Method is primarily for
        evaluating assignments at the designated state (trigger time or event
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 25 mins 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 piecewise has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def piecewise(*args):
    args = list(args)
    sol = None
    if len(args) % 2:
        args.append(True)
Severity: Minor
Found in gillespy2/sbml/SBMLimport.py - About 25 mins 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 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __get_reactions(self, step, curr_state, curr_time, save_time, propensities, reactions):
        """
        Helper Function to get reactions fired from t to t+tau.  
        
        In the equation:
Severity: Minor
Found in gillespy2/solvers/numpy/CLE_solver.py - About 25 mins 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_initial_assignments has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def __get_initial_assignments(sbml_model, gillespy_model):

    for i in range(sbml_model.getNumInitialAssignments()):
        init_assign = sbml_model.getInitialAssignment(i)
        variable = init_assign.getId()
Severity: Minor
Found in gillespy2/sbml/SBMLimport.py - About 25 mins 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 __f has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __f(t, y, curr_state, model, c_prop):
        """
        The right hand side of the differential equation, uses scipy.integrate ode

        :param t: time as a numpy array
Severity: Minor
Found in gillespy2/solvers/numpy/ode_solver.py - About 25 mins 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 __set_seed has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __set_seed(self, seed):
        # Set seed if supplied
        if seed is not None:
            if not isinstance(seed, int):
                seed = int(seed)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 25 mins 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 _resolve_rule has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _resolve_rule(self, rule):
        def validate(rule):
            from gillespy2.core.gillespyError import RateRuleError, AssignmentRuleError # pylint: disable=import-outside-toplevel
            errors = {"RateRule": RateRuleError, "AssignmentRule": AssignmentRuleError}
            error_class = errors[type(rule).__name__]
Severity: Minor
Found in gillespy2/core/model.py - About 25 mins 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 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, name="", population=True, volume=1.0, tspan=None, annotation="model"):
        """ Create an empty model. """

        # The name that the model is referenced by (should be a String)
        self.name = name
Severity: Minor
Found in gillespy2/core/model.py - About 25 mins 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 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, expression=None, initial_value = False, persistent = False):

        if isinstance(expression, str):
            self.expression = expression
        else:
Severity: Minor
Found in gillespy2/core/events.py - About 25 mins 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 compile_prep has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def compile_prep(self):
        """
        Prepare the model for export or simulation.
        """
        for _, species in self.listOfSpecies.items():
Severity: Minor
Found in gillespy2/core/model.py - About 25 mins 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 add_reactant has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def add_reactant(self, species, stoichiometry):
        """
        Add a reactant to this reaction

        :param species: reactant Species object
Severity: Minor
Found in gillespy2/core/reaction.py - About 25 mins 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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