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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

Cyclomatic complexity is too high in method validate. (72)
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 by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

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

Cyclomatic complexity is too high in method __run. (46)
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 by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

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

Cyclomatic complexity is too high in method __run. (45)
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 by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

Cyclomatic complexity is too high in method __run. (38)
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 by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

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

Cyclomatic complexity is too high in method to_model. (32)
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 by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

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

Cyclomatic complexity is too high in method run. (29)
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 by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

Cyclomatic complexity is too high in method validate. (29)
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 by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

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

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