Sign upLogin

GillesPy2/GillesPy2

View on GitHub
Star

Showing 115 of 2,350 total issues

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

    def __create_diff_eqs(self, comb, dependencies, rr_sets, rate_rules):
        """
        Helper method used to convert stochastic reaction descriptions into
        differential equations, used dynamically throught the simulation.
        """
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.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 plot has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.
Open

    def plot(self, index=None, xaxis_label="Time", xscale='linear', yscale='linear', yaxis_label="Value",
             style="default", title=None, show_title=False, show_legend=True, multiple_graphs=False,
             included_species_list=[], save_png=False, figsize=(18, 10)):
        """
        Plots the Results using matplotlib.
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

Function __str__ has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
Open

    def __str__(self):
        divider = '\n**********\n'

        def decorate(header):
            return '\n' + divider + header + divider
Severity: Minor
Found in gillespy2/core/model.py - About 3 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 __resolve_evals has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

def __resolve_evals(gillespy_model, init_state):
    while True:
        successful = []
        if len(postponed_evals):
            for var, expr in postponed_evals.items():
Severity: Minor
Found in gillespy2/sbml/SBMLimport.py - About 3 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_species has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

def __get_species(sbml_model, gillespy_model, errors):

    for i in range(sbml_model.getNumSpecies()):
        species = sbml_model.getSpecies(i)
        name = species.getId()
Severity: Minor
Found in gillespy2/sbml/SBMLimport.py - About 3 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 24 (exceeds 5 allowed). Consider refactoring.
Open

    def __run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
              number_of_trajectories=1, increment=0.05, integrator='lsoda',
              integrator_options={}, resume=None, **kwargs):

        timeStopped = 0
Severity: Minor
Found in gillespy2/solvers/numpy/ode_solver.py - About 3 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 __create_options has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
Open

    def __create_options(self, sanitized_model: "SanitizedModel") -> "SanitizedModel":
        """
        Populate the given list of species modes into a set of template macro definitions.
        Generated options are specific to the Tau Hybrid solver,
        and get passed as custom definitions to the build engine.
Severity: Minor
Found in gillespy2/solvers/cpp/tau_hybrid_c_solver.py - About 3 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 __str__ has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
Open

    def __str__(self):
        print_string = self.name
        if len(self.reactants):
            print_string += '\n\tReactants'
            for reactant, stoich in self.reactants.items():
Severity: Minor
Found in gillespy2/core/reaction.py - About 2 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 __integrate has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

    def __integrate(self, integrator_options, curr_state, y0, curr_time,
                    propensities, y_map, compiled_reactions,
                    active_rr, event_queue,
                    delayed_events, trigger_states,
                    event_sensitivity, tau_step, det_rxn ):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 2 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_rules has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

def __get_rules(sbml_model, gillespy_model, errors):
    for i in range(sbml_model.getNumRules()):
        rule = sbml_model.getRule(i)

        # If the SBML object does not contain an ID attribute create a unique rule_name from the variable name.
Severity: Minor
Found in gillespy2/sbml/SBMLimport.py - About 2 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 18 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, name="", delay=None, assignments=[], priority="0", trigger=None,
                 use_values_from_trigger_time=False):

        # Events can contain any number of assignments
        self.assignments = []
Severity: Minor
Found in gillespy2/core/events.py - About 2 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 add has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

    def add(self, components):
        """
        Adds a component, or list of components to the model. If a list is provided, Species
        and Parameters are added before other components.  Lists may contain any combination
        of accepted types other than lists and do not need to be in any particular order.
Severity: Minor
Found in gillespy2/core/model.py - About 2 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_mean_stdev has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    def plotplotly_mean_stdev(self, xaxis_label="Time", yaxis_label="Value", title=None,
                                 show_title=False, show_legend=True, included_species_list=[],
                                 return_plotly_figure=False, ddof=0, **layout_args):
        """
        Plot a plotly graph depicting the mean and standard deviation of a results object
Severity: Minor
Found in gillespy2/core/results.py - About 2 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 add_rate_rule has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    def add_rate_rule(self, rate_rule):
        """
        Adds a rate rule, or list of rate rules to the model.

        :param rate_rule: The rate rule or list of rate rules to be added to the model object.
Severity: Minor
Found in gillespy2/core/model.py - About 2 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 to_csv has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    def to_csv(self, path=".", nametag=None, stamp=None, postfix=".odf", verbose=False):
        """
        Outputs the Results to one or more .csv files in a new directory.

        :param nametag: allows the user to optionally "tag" the directory and included files. Defaults to the model
Severity: Minor
Found in gillespy2/core/results.py - About 2 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 __detect_events has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    def __detect_events(self, event_sensitivity, sol, delayed_events,
                        trigger_states, curr_time, curr_state):
        """
        Helper method to locate precise time of event firing.  This method
        first searches for any instance of an event using event_sensitivity to
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 2 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 __check_t0_events has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

    def __check_t0_events(self, initial_state):
        """
        Helper method for firing events who reach a trigger condition at start
        of simulation, time == 0.
        """
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 2 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 initialize has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

def initialize(model, epsilon):
    """
    This method initailizes the state for tau-leaping selections to be made.
    Based on Cao, Y.; Gillespie, D. T.; Petzold, L. R. (2006). "Efficient step size selection for the tau-leaping
    simulation method" (PDF).
Severity: Minor
Found in gillespy2/solvers/utilities/Tau.py - About 2 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 stddev_ensemble has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

    def stddev_ensemble(self, ddof=0):
        """
        Generate a single Results object with a Trajectory that is made of the sample standard deviations of all
        trajectories' outputs.
Severity: Minor
Found in gillespy2/core/results.py - About 2 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 validate has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

    def validate(self, expression=None, coverage="all"):
        """
        Validate the parameter.

        :param expression: String for a function calculating parameter values. Should be
Severity: Minor
Found in gillespy2/core/parameter.py - About 2 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

Severity
Category
Status
Source
Language