Showing 2,350 of 2,350 total issues
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.
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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.
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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
- Read upRead up
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
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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. (26) 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
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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. |
Cyclomatic complexity is too high in method __run. (26) 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):
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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. |
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(
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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. (25) 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.
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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. |
Cyclomatic complexity is too high in method run. (25) 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.
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- Exclude checks
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. |
Cyclomatic complexity is too high in method run. (25) 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.
- Read upRead up
- Exclude checks
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. |
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()
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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 function select. (24) 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
- Read upRead up
- Exclude checks
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. |
Cyclomatic complexity is too high in method display. (24) 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.
- Read upRead up
- Exclude checks
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. |
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.
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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 add. (23) 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.
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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. |
Cyclomatic complexity is too high in method __calculate_statistics. (22) 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
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- Exclude checks
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. |
Cyclomatic complexity is too high in method __simulate. (22) 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):
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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. |
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.
"""
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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 __create_options. (21) 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.
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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. |
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.
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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"