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gillespy2/solvers/numpy/tau_hybrid_solver.py

Summary

Maintainability
F
6 days
Test Coverage
C
78%

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

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

Cognitive Complexity

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

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

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

Further reading

Function 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

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

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

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

Cognitive Complexity

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

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

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

Further reading

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

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

Cognitive Complexity

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

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

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

Further reading

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):
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 __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
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 __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):
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

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

Cyclomatic complexity is too high in method __create_diff_eqs. (18)
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 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 __integrate. (14)
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 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 __detect_events. (11)
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 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 __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

Cyclomatic complexity is too high in method __init__. (10)
Open

    def __init__(self, model=None, profile_reactions=False, constant_tau_stepsize=None):
        if model is None:
            raise SimulationError("A model is required to run the simulation.")

        name = 'TauHybridSolver'
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 __toggle_reactions. (10)
Open

    def __toggle_reactions(self, all_compiled, deterministic_reactions, dependencies,
                            curr_state, det_spec, rr_sets):
        """
        Helper method which is used to convert reaction channels into
        rate rules, and rate rules into reaction channels, as they are switched
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 __initialize_state. (9)
Open

    def __initialize_state(self, curr_state, debug):
        """
        Initialize curr_state for each trajectory.
        """
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

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

Cyclomatic complexity is too high in class TauHybridSolver. (8)
Open

class TauHybridSolver(GillesPySolver):
    """
    This solver uses a root-finding interpretation of the direct SSA method,
    along with ODE solvers to simulate ODE and Stochastic systems
    interchangeably or simultaneously.
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 __f. (8)
Open

    @staticmethod
    def __f(t, y, curr_state, species, reactions, rate_rules, propensities,
            y_map, compiled_reactions, active_rr, events, assignment_rules):
        """
        Evaluate the propensities for the reactions and the RHS of the Reactions and RateRules.
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 __flag_det_reactions. (8)
Open

    def __flag_det_reactions(self, det_spec, det_rxn, dependencies):
        """
        Helper method used to flag reactions that can be processed
        deterministically without exceeding the user-supplied tolerance.
        """
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 __update_stochastic_rxn_states. (8)
Open

    def __update_stochastic_rxn_states(self, propensities, tau_step, compiled_reactions, curr_state, only_update=None):
        """
        Helper method for updating the state of stochastic reactions.

        if 'only_update' is set to a reaction name, it will only reset that reaction, and only one firing
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

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 __update_stochastic_rxn_states has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
Open

    def __update_stochastic_rxn_states(self, propensities, tau_step, compiled_reactions, curr_state, only_update=None):
        """
        Helper method for updating the state of stochastic reactions.

        if 'only_update' is set to a reaction name, it will only reset that reaction, and only one firing
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 1 hr 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 15 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, model=None, profile_reactions=False, constant_tau_stepsize=None):
        if model is None:
            raise SimulationError("A model is required to run the simulation.")

        name = 'TauHybridSolver'
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 1 hr 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 __check_t0_events. (6)
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 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 __find_event_time. (6)
Open

    def __find_event_time(self, sol, start, end, index, depth):
        """
        Helper method providing binary search implementation for locating
        precise event times.
        """
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 __save_state_to_output. (6)
Open

    def __save_state_to_output(self, curr_time, save_index, curr_state, species, 
                                trajectory, save_times):
        """
        Helper function to save the curr_state to the trajectory output
        """
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 __map_state. (6)
Open

    def __map_state(self, species, parameters, compiled_reactions, events, curr_state):
        """
        Creates the start state vector for integration and provides a
        dictionary map to it's elements.
        """
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

Function __toggle_reactions has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def __toggle_reactions(self, all_compiled, deterministic_reactions, dependencies,
                            curr_state, det_spec, rr_sets):
        """
        Helper method which is used to convert reaction channels into
        rate rules, and rate rules into reaction channels, as they are switched
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 1 hr 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 __flag_det_reactions has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def __flag_det_reactions(self, det_spec, det_rxn, dependencies):
        """
        Helper method used to flag reactions that can be processed
        deterministically without exceeding the user-supplied tolerance.
        """
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 1 hr 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 11 (exceeds 5 allowed). Consider refactoring.
Open

    def __f(t, y, curr_state, species, reactions, rate_rules, propensities,
            y_map, compiled_reactions, active_rr, events, assignment_rules):
        """
        Evaluate the propensities for the reactions and the RHS of the Reactions and RateRules.
        Also evaluates boolean value of event triggers.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 1 hr 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_state has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def __initialize_state(self, curr_state, debug):
        """
        Initialize curr_state for each trajectory.
        """
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 1 hr 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 __save_state_to_output has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def __save_state_to_output(self, curr_time, save_index, curr_state, species, 
                                trajectory, save_times):
        """
        Helper function to save the curr_state to the trajectory output
        """
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 55 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 __map_state has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def __map_state(self, species, parameters, compiled_reactions, events, curr_state):
        """
        Creates the start state vector for integration and provides a
        dictionary map to it's elements.
        """
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py - About 35 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 __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

Missing whitespace after ','
Open

            for s,sname in enumerate(species):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Test for membership should be 'not in'
Open

            if not r in deterministic_reactions:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Negative comparison should be done using "not in" and "is not".

Okay: if x not in y:\n    pass
Okay: assert (X in Y or X is Z)
Okay: if not (X in Y):\n    pass
Okay: zz = x is not y
E713: Z = not X in Y
E713: if not X.B in Y:\n    pass
E714: if not X is Y:\n    pass
E714: Z = not X.B is Y

Expected an indented block (comment)
Open

        # Otherwise, this is a new determinstic reaction set that must be compiled
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Use indent_size (PEP8 says 4) spaces per indentation level.

For really old code that you don't want to mess up, you can continue
to use 8-space tabs.

Okay: a = 1
Okay: if a == 0:\n    a = 1
E111:   a = 1
E114:   # a = 1

Okay: for item in items:\n    pass
E112: for item in items:\npass
E115: for item in items:\n# Hi\n    pass

Okay: a = 1\nb = 2
E113: a = 1\n    b = 2
E116: a = 1\n    # b = 2

Line too long (101 > 79 characters)
Open

                        diff_eqs[self.model.listOfSpecies[dep]] += ' + {0}*({1})'.format(factor[dep],
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Test for membership should be 'not in'
Open

            if not r in inactive_reactions:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Negative comparison should be done using "not in" and "is not".

Okay: if x not in y:\n    pass
Okay: assert (X in Y or X is Z)
Okay: if not (X in Y):\n    pass
Okay: zz = x is not y
E713: Z = not X in Y
E713: if not X.B in Y:\n    pass
E714: if not X is Y:\n    pass
E714: Z = not X.B is Y

Line too long (101 > 79 characters)
Open

                        diff_eqs[self.model.listOfSpecies[dep]] += ' + {0}*({1})'.format(factor[dep],
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (85 > 79 characters)
Open

    def __toggle_reactions(self, all_compiled, deterministic_reactions, dependencies,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (85 > 79 characters)
Open

            for key, value in self.model.listOfReactions[reaction].reactants.items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                           self.model.listOfReactions[reaction].propensity_function)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (89 > 79 characters)
Open

                assignment_value = eval(ar.formula, {**eval_globals, **assignment_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Multiple spaces after operator
Open

            tmp =  self.__create_diff_eqs(deterministic_reactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Avoid extraneous whitespace around an operator.

Okay: a = 12 + 3
E221: a = 4  + 5
E222: a = 4 +  5
E223: a = 4\t+ 5
E224: a = 4 +\t5

Multiple imports on one line
Open

import random, math, sys
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Place imports on separate lines.

Okay: import os\nimport sys
E401: import sys, os

Okay: from subprocess import Popen, PIPE
Okay: from myclas import MyClass
Okay: from foo.bar.yourclass import YourClass
Okay: import myclass
Okay: import foo.bar.yourclass

Line too long (82 > 79 characters)
Open

        # Otherwise, this is a new determinstic reaction set that must be compiled
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (95 > 79 characters)
Open

        Evaluate the propensities for the reactions and the RHS of the Reactions and RateRules.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (2)
Open

        starting_curr_state = copy.deepcopy(curr_state)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (132 > 79 characters)
Open

        (invalid_state, invalid_err_message) = self.__simulate_invalid_state_check(species_modified, curr_state, compiled_reactions)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace after ','
Open

            for rname,rcnt in rxn_count.items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (85 > 79 characters)
Open

            "clear_output" specifies if display should be refreshed with each display
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (2)
Open

        self.validate_tspan(increment=increment, t=t)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (105 > 79 characters)
Open

                                                                    'increment': increment, 'seed': seed,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (91 > 79 characters)
Open

                                        'Try display \"type\" = \"text\" or \"progress\".')
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (104 > 79 characters)
Open

                display_timer = gillespy2.core.liveGraphing.RepeatTimer(live_output_options['interval'],
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace around operator
Open

                        if curr_state[0][r] > 0 and propensities[r]==0:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Continuation line under-indented for visual indent
Open

                                                                               propensities, species,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (102 > 79 characters)
Open

                if self.model.listOfSpecies[species].mode == 'dynamic' and det_spec[species] == False:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace around operator
Open

        if curr_time==0.0: #re-set cv_history
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Inline comment should start with '# '
Open

        if curr_time==0.0: #re-set cv_history
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (119 > 79 characters)
Open

    def __update_stochastic_rxn_states(self, propensities, tau_step, compiled_reactions, curr_state, only_update=None):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

At least two spaces before inline comment
Open

        CV_a = OrderedDict() # time-averaged CV (forward derivative based)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Continuation line under-indented for visual indent
Open

                    event_sensitivity, tau_step ):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (86 > 79 characters)
Open

            event_times = self.__detect_events(event_sensitivity, sol, delayed_events,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (81 > 79 characters)
Open

                CV_a[species] = sum(cv_history[species])/len(cv_history[species])
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (95 > 79 characters)
Open

    def __simulate_invalid_state_check(self, species_modified, curr_state, compiled_reactions):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (98 > 79 characters)
Open

                curr_state[assignment_rules[item].variable] = eval(assignment_rules[item].formula,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (82 > 79 characters)
Open

        :param curr_state: Contains all state variables for system at current time
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (86 > 79 characters)
Open

            triggered = eval(event.trigger.expression, {**eval_globals, **curr_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace around operator
Open

        species_modified=None
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Multiple statements on one line (colon)
Open

        if start >= mid or mid >= end or depth == 20: return end
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Compound statements (on the same line) are generally discouraged.

While sometimes it's okay to put an if/for/while with a small body
on the same line, never do this for multi-clause statements.
Also avoid folding such long lines!

Always use a def statement instead of an assignment statement that
binds a lambda expression directly to a name.

Okay: if foo == 'blah':\n    do_blah_thing()
Okay: do_one()
Okay: do_two()
Okay: do_three()

E701: if foo == 'blah': do_blah_thing()
E701: for x in lst: total += x
E701: while t < 10: t = delay()
E701: if foo == 'blah': do_blah_thing()
E701: else: do_non_blah_thing()
E701: try: something()
E701: finally: cleanup()
E701: if foo == 'blah': one(); two(); three()
E702: do_one(); do_two(); do_three()
E703: do_four();  # useless semicolon
E704: def f(x): return 2*x
E731: f = lambda x: 2*x

At least two spaces before inline comment
Open

                    curr_state[rxn] = math.log(np.random.uniform(0, 1)) #set this value, needs to be <0
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (95 > 79 characters)
Open

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (83 > 79 characters)
Open

                                                    self.model.tspan[-1], next_tau)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (95 > 79 characters)
Open

        trajectory_base = np.zeros((number_of_trajectories, timeline.size, number_species + 1))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (2)
Open

    def __simulate_negative_state_check(self, curr_state):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (131 > 79 characters)
Open

                                                                        args=(curr_state, curr_time, trajectory_base, live_output))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace around operator
Open

        loop_err_message=""
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Trailing whitespace
Open

            raise self.has_raised_exception
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Missing whitespace around operator
Open

                    rxn_times[rname] = -1* curr_state[rname] / propensities[rname]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Multiple statements on one line (colon)
Open

                if state is None: state = curr_state[0]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Compound statements (on the same line) are generally discouraged.

While sometimes it's okay to put an if/for/while with a small body
on the same line, never do this for multi-clause statements.
Also avoid folding such long lines!

Always use a def statement instead of an assignment statement that
binds a lambda expression directly to a name.

Okay: if foo == 'blah':\n    do_blah_thing()
Okay: do_one()
Okay: do_two()
Okay: do_three()

E701: if foo == 'blah': do_blah_thing()
E701: for x in lst: total += x
E701: while t < 10: t = delay()
E701: if foo == 'blah': do_blah_thing()
E701: else: do_non_blah_thing()
E701: try: something()
E701: finally: cleanup()
E701: if foo == 'blah': one(); two(); three()
E702: do_one(); do_two(); do_three()
E703: do_four();  # useless semicolon
E704: def f(x): return 2*x
E731: f = lambda x: 2*x

Inline comment should start with '# '
Open

            tau_step = min_tau #estimated time to the first stochatic reaction
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Continuation line under-indented for visual indent
Open

                                                                               curr_state[0], y0, curr_time[0],
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (106 > 79 characters)
Open

            curr_state[fd.name] = eval(f"lambda {', '.join(fd.args)}: {sanitized_function}", eval_globals)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                                               debug, det_spec, det_rxn)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Missing whitespace after ','
Open

            debug=False, profile=False, tau_tol=0.03, event_sensitivity=100,integrator_options={},
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (83 > 79 characters)
Open

                raise SimulationError("A model is required to run the simulation.")
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (121 > 79 characters)
Open

                live_grapher[0] = gillespy2.core.liveGraphing.LiveDisplayer(self.model, timeline, number_of_trajectories,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Block comment should start with '# '
Open

        #move configuration to solver init (issue #905)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Do not use bare 'except'
Open

        except:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

When catching exceptions, mention specific exceptions when possible.

Okay: except Exception:
Okay: except BaseException:
E722: except:

Line too long (85 > 79 characters)
Open

        det_rxn = {rxn: False for (rxn, value) in self.model.listOfReactions.items()}
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (114 > 79 characters)
Open

                    print("Setting Random number ", curr_state[0][r], " for ", self.model.listOfReactions[r].name)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (91 > 79 characters)
Open

                    sd[reactant.name] += (propensities[r] * (rxn.reactants[reactant] ** 2))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

The backslash is redundant between brackets
Open

                    raise SimulationError(f"Negative State detected at begining of step." \
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Avoid explicit line join between brackets.

The preferred way of wrapping long lines is by using Python's
implied line continuation inside parentheses, brackets and braces.
Long lines can be broken over multiple lines by wrapping expressions
in parentheses.  These should be used in preference to using a
backslash for line continuation.

E502: aaa = [123, \\n       123]
E502: aaa = ("bbb " \\n       "ccc")

Okay: aaa = [123,\n       123]
Okay: aaa = ("bbb "\n       "ccc")
Okay: aaa = "bbb " \\n    "ccc"
Okay: aaa = 123  # \\

Line too long (80 > 79 characters)
Open

                            curr_state[0][r] = math.log(np.random.uniform(0, 1))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace around operator
Open

        starting_tau_step=tau_step
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Missing whitespace around operator
Open

                        X+= f'{k}:{v:.2f} '
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Too many blank lines (2)
Open

        # check each reaction to see if it is >=0. If we have taken a single SSA step, this could be >0 for the non-selected reactions, check if propensity is zero and reset if so
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (114 > 79 characters)
Open

                                                                               trajectory, save_times, save_index,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                                               trajectory, save_times, save_index,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (81 > 79 characters)
Open

            log.warning('model = gillespy2.model is deprecated. Future releases '
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (113 > 79 characters)
Open

                # Solve_ivp doesn't return any results until it's finished solving so timing out early only slows
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (103 > 79 characters)
Open

                                                                    'debug': debug, 'profile': profile,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (110 > 79 characters)
Open

                                                                    'integrator_options': integrator_options})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (115 > 79 characters)
Open

            [dependencies[reaction].add(product.name) for product in self.model.listOfReactions[reaction].products]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (104 > 79 characters)
Open

                                             compiled_reactions, self.model.listOfEvents, curr_state[0])
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Comparison to false should be 'if cond is false:' or 'if not cond:'
Open

                if self.model.listOfSpecies[species].mode == 'dynamic' and det_spec[species] == False:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Comparison to singletons should use "is" or "is not".

Comparisons to singletons like None should always be done
with "is" or "is not", never the equality operators.

Okay: if arg is not None:
E711: if arg != None:
E711: if None == arg:
E712: if arg == True:
E712: if False == arg:

Also, beware of writing if x when you really mean if x is not None
-- e.g. when testing whether a variable or argument that defaults to
None was set to some other value.  The other value might have a type
(such as a container) that could be false in a boolean context!

Line too long (96 > 79 characters)
Open

                                                                               active_rr, y_map,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

At least two spaces before inline comment
Open

        history_length = 12 #cite: "Statistical rules of thumb" G Van Belle
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (81 > 79 characters)
Open

                                                        dense_range[y + 1], i, 0)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (90 > 79 characters)
Open

            execution_time = curr_time + eval(event.delay, {**eval_globals, **curr_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (103 > 79 characters)
Open

                    curr_state[rxn] = math.log(np.random.uniform(0, 1)) #set this value, needs to be <0
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (85 > 79 characters)
Open

        int_args = [curr_state, self.model.listOfSpecies, self.model.listOfReactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Over-indented
Open

            for s in self.non_negative_species:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Use indent_size (PEP8 says 4) spaces per indentation level.

For really old code that you don't want to mess up, you can continue
to use 8-space tabs.

Okay: a = 1
Okay: if a == 0:\n    a = 1
E111:   a = 1
E114:   # a = 1

Okay: for item in items:\n    pass
E112: for item in items:\npass
E115: for item in items:\n# Hi\n    pass

Okay: a = 1\nb = 2
E113: a = 1\n    b = 2
E116: a = 1\n    # b = 2

Continuation line under-indented for visual indent
Open

                    " Species involved in reactions can not be negative.")
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (85 > 79 characters)
Open

            for k in list(self.model.listOfSpecies)+list(self.model.listOfReactions):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          tau_step, det_rxn
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Missing whitespace after ','
Open

            species_modified,rxn_count = self.__update_stochastic_rxn_states(propensities, actual_tau_step, compiled_reactions, curr_state, only_update=rxn_selected)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (106 > 79 characters)
Open

        events_processed = self.__process_queued_events(event_queue, trigger_states, curr_state, det_spec)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (91 > 79 characters)
Open

                                                            rr.formula, '<string>', 'eval')
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (91 > 79 characters)
Open

        y0 = [0] * (len(species) + len(parameters) + len(compiled_reactions) + len(events))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

        :param live_output_options: contains options for live_output. By default {"interval":1}.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (111 > 79 characters)
Open

        det_spec = {species: value.mode != 'discrete' for (species, value) in self.model.listOfSpecies.items()}
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (83 > 79 characters)
Open

            propensities = OrderedDict()  # Propensities evaluated at current state
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (104 > 79 characters)
Open

                                                                               debug, det_spec, det_rxn)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                                               trigger_states,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (95 > 79 characters)
Open

        NOTE: the argument cv_history should not be passed in, this is modified by the function
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace after ','
Open

        for species,value in self.model.listOfSpecies.items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (113 > 79 characters)
Open

        next_step = {sim_end: 'end', next_tau: 'tau', next_event_trigger: 'trigger', next_delayed_event: 'delay'}
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (105 > 79 characters)
Open

        if 'only_update' is set to a reaction name, it will only reset that reaction, and only one firing
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (80 > 79 characters)
Open

        next_step, curr_time = self.__get_next_step(event_times, reaction_times,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (82 > 79 characters)
Open

                curr_time, save_index, curr_state, species, trajectory, save_times
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          delayed_events,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (105 > 79 characters)
Open

                    floored_propensities[r] = eval(compiled_reactions[r], {**eval_globals, **curr_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (136 > 79 characters)
Open

            (invalid_state, invalid_err_message) = self.__simulate_invalid_state_check(species_modified, curr_state, compiled_reactions)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (2)
Open

        save_index = self.__save_state_to_output(curr_time, save_index, curr_state, species, trajectory, save_times)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (106 > 79 characters)
Open

            compiled_reactions[r] = compile(self.model.listOfReactions[r].propensity_function, '<string>',
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

        :param tau_tol: Tolerance level for Tau leaping algorithm.  Larger tolerance values will
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

            see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.LSODA.html.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (97 > 79 characters)
Open

            # raise SimulationError("TauHybridSolver must be instantiated to run the simulation")
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (119 > 79 characters)
Open

                mn, sd, CV = self.__calculate_statistics(curr_time[0], propensities, curr_state[0], tau_step, det_spec)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                                               delayed_events,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Blank line contains whitespace
Open
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Line too long (80 > 79 characters)
Open

            for key, value in model.listOfReactions[reaction].reactants.items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Blank line contains whitespace
Open
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Line too long (100 > 79 characters)
Open

                trajectory[trajectory_index][species.index(ar.variable.name) + 1] = assignment_value
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (108 > 79 characters)
Open

                diff_eqs[self.model.listOfSpecies[spec]] = self.model.listOfRateRules[rr_vars[spec]].formula
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

At least two spaces before inline comment
Open

        rr_sets[comb] = rate_rules # save values
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (96 > 79 characters)
Open

    Uses integrators from scipy.integrate.ode to perform calculations used to produce solutions.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (109 > 79 characters)
Open

    def __calculate_statistics(self, curr_time, propensities, curr_state, tau_step, det_spec, cv_history={}):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (81 > 79 characters)
Open

        Calculates Mean, Standard Deviation, and Coefficient of Variance for each
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

At least two spaces before inline comment
Open

        if curr_time==0.0: #re-set cv_history
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (84 > 79 characters)
Open

                    mn[reactant.name] -= (propensities[r] * rxn.reactants[reactant])
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (88 > 79 characters)
Open

                    sd[product.name] += (propensities[r] * (rxn.products[product] ** 2))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Inline comment should start with '# '
Open

        history_length = 12 #cite: "Statistical rules of thumb" G Van Belle
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Missing whitespace after ','
Open

        for species,value in self.model.listOfSpecies.items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Missing whitespace around operator
Open

        if len(self.model.listOfRateRules)==0:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Line too long (80 > 79 characters)
Open

                    event_time = self.__find_event_time(sol, dense_range[y - 1],
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (83 > 79 characters)
Open

            bool_res = [x > 0 for x in solutions[i - len(self.model.listOfEvents)]]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Inline comment should start with '# '
Open

                    cv_history[species].pop(0) #remove the first item
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Whitespace before ')'
Open

                    event_sensitivity, tau_step ):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Avoid extraneous whitespace.

Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.

Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })

E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x

Line too long (114 > 79 characters)
Open

                    curr_state[product.name] += self.model.listOfReactions[rxn].products[product] * rxn_count[rxn]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (98 > 79 characters)
Open

                                                                   {**eval_globals, **curr_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Whitespace before ')'
Open

                    event_sensitivity, tau_step, det_rxn ):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Avoid extraneous whitespace.

Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.

Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })

E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x

Line too long (92 > 79 characters)
Open

                            propensities, y_map, compiled_reactions, active_rr, event_queue,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                    active_rr, event_queue,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (88 > 79 characters)
Open

                            delayed_events, trigger_states, event_sensitivity, tau_step)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (101 > 79 characters)
Open

            heapq.heappush(event_queue, (eval(self.model.listOfEvents[event[1]].priority), event[1]))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Do not assign a lambda expression, use a def
Open

        rhs = lambda t, y: TauHybridSolver.__f(t, y, *int_args)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Compound statements (on the same line) are generally discouraged.

While sometimes it's okay to put an if/for/while with a small body
on the same line, never do this for multi-clause statements.
Also avoid folding such long lines!

Always use a def statement instead of an assignment statement that
binds a lambda expression directly to a name.

Okay: if foo == 'blah':\n    do_blah_thing()
Okay: do_one()
Okay: do_two()
Okay: do_three()

E701: if foo == 'blah': do_blah_thing()
E701: for x in lst: total += x
E701: while t < 10: t = delay()
E701: if foo == 'blah': do_blah_thing()
E701: else: do_non_blah_thing()
E701: try: something()
E701: finally: cleanup()
E701: if foo == 'blah': one(); two(); three()
E702: do_one(); do_two(); do_three()
E703: do_four();  # useless semicolon
E704: def f(x): return 2*x
E731: f = lambda x: 2*x

Continuation line under-indented for visual indent
Open

                    delayed_events, trigger_states,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Continuation line under-indented for visual indent
Open

                            propensities, y_map, compiled_reactions, active_rr, event_queue,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Too many blank lines (2)
Open

        # Update states of all species based on changes made to species through
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Continuation line under-indented for visual indent
Open

                                          y0, curr_time, propensities, y_map,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Missing whitespace after ','
Open

        species_modified,rxn_count = self.__update_stochastic_rxn_states(propensities, actual_tau_step, compiled_reactions, curr_state)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Continuation line under-indented for visual indent
Open

                                          active_rr,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (85 > 79 characters)
Open

                                               trigger_states, curr_time, curr_state)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          event_queue,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Continuation line under-indented for visual indent
Open

                                          delayed_events,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (91 > 79 characters)
Open

                    raise SimulationError(f"Negative State detected at begining of step." \
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (87 > 79 characters)
Open

            # Redo this step, with a smaller Tau such that a single SSA reaction occurs
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (84 > 79 characters)
Open

                                        event_queue, trigger_states, delayed_events)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (199 > 79 characters)
Open

                    raise SimulationError('Error calculation propensity for {0}.\nReason: {1}\nfloored_propensities={2}\ncompiled_reactions={3}'.format(r, e, floored_propensities,compiled_reactions))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          compiled_reactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

At least two spaces before inline comment
Open

            tau_step = min_tau #estimated time to the first stochatic reaction
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (90 > 79 characters)
Open

                compiled_rate_rules[rr.variable] = compile(rr.formula, '<string>', 'eval')
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (89 > 79 characters)
Open

            curr_time, actual_tau_step = self.__integrate(integrator_options, curr_state,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (80 > 79 characters)
Open

                    log.warning('timeouts not supported by continuous species.')
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Closing bracket does not match visual indentation
Open

                                          )
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (83 > 79 characters)
Open

                gillespy2.core.liveGraphing.valid_graph_params(live_output_options)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (165 > 79 characters)
Open

            species_modified,rxn_count = self.__update_stochastic_rxn_states(propensities, actual_tau_step, compiled_reactions, curr_state, only_update=rxn_selected)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line over-indented for visual indent
Open

                                                        dependencies, curr_state[0], det_spec, rr_sets)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (117 > 79 characters)
Open

        objects and will inherit those parameters which are passed with the model as the arguments this run function.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (135 > 79 characters)
Open

        species_modified,rxn_count = self.__update_stochastic_rxn_states(propensities, actual_tau_step, compiled_reactions, curr_state)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

                                                                        live_grapher[0].display,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                                               event_sensitivity, tau_step,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Continuation line under-indented for visual indent
Open

                                          active_rr,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (87 > 79 characters)
Open

            y_map[event] = i + len(species) + len(parameters) + len(compiled_reactions)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (86 > 79 characters)
Open

                triggered = eval(e.trigger.expression, {**eval_globals, **curr_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (82 > 79 characters)
Open

            steps/save points for event detection. Default event_sensitivity = 100
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Expected 2 blank lines, found 1
Open

def __piecewise(*args):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (85 > 79 characters)
Open

                compiled_rate_rules[self.model.listOfSpecies[rr.variable]] = compile(
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (80 > 79 characters)
Open

    def __save_state_to_output(self, curr_time, save_index, curr_state, species,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (83 > 79 characters)
Open

        :param timeout: If set, if simulation takes longer than timeout, will exit.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

        :returns: Tuple of strings, denoting all keyword argument for this solvers run() method.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (85 > 79 characters)
Open

        # curr_time and curr_state are list of len 1 so that __run receives reference
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line over-indented for visual indent
Open

                                trajectory, save_times):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (111 > 79 characters)
Open

                                                                               curr_state[0], y0, curr_time[0],
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (113 > 79 characters)
Open

                    log.warning('timeouts not fully supported by dynamic species. If timeout is triggered during'
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (101 > 79 characters)
Open

                                                                               propensities, species,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace after ','
Open

        for s,d in det_spec.items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (87 > 79 characters)
Open

                                                                    'tau_tol': tau_tol,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (120 > 79 characters)
Open

                                                           self.model.listOfReactions[reaction].ode_propensity_function)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (107 > 79 characters)
Open

                                                                    'event_sensitivity': event_sensitivity,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (100 > 79 characters)
Open

            output_rules[spec] = compile(gillespy2.RateRule(spec, rate).formula, '<string>', 'eval')
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

                                                                            live_output_options)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (87 > 79 characters)
Open

                state_change[y_map[s.name]] += eval(rr, {**eval_globals, **curr_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (91 > 79 characters)
Open

                # Calculate sd and CV for hybrid switching and flag deterministic reactions
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (89 > 79 characters)
Open

            propensities[r] = eval(compiled_reactions[r], {**eval_globals, **curr_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (88 > 79 characters)
Open

        solutions = np.diff(sol.sol(dense_range)[-len(self.model.listOfEvents) + index])
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (80 > 79 characters)
Open

        next_step, curr_time = self.__get_next_step(event_times, reaction_times,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (95 > 79 characters)
Open

                                                    self.model.tspan[-1], curr_time + tau_step)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (82 > 79 characters)
Open

                    rxn_times[rname] = -1* curr_state[rname] / propensities[rname]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Multiple statements on one line (colon)
Open

            if rxn_selected is None: raise SimulationError(f"Negative State detected in step, and no reaction found to fire. error_message={invalid_err_message}")
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Compound statements (on the same line) are generally discouraged.

While sometimes it's okay to put an if/for/while with a small body
on the same line, never do this for multi-clause statements.
Also avoid folding such long lines!

Always use a def statement instead of an assignment statement that
binds a lambda expression directly to a name.

Okay: if foo == 'blah':\n    do_blah_thing()
Okay: do_one()
Okay: do_two()
Okay: do_three()

E701: if foo == 'blah': do_blah_thing()
E701: for x in lst: total += x
E701: while t < 10: t = delay()
E701: if foo == 'blah': do_blah_thing()
E701: else: do_non_blah_thing()
E701: try: something()
E701: finally: cleanup()
E701: if foo == 'blah': one(); two(); three()
E702: do_one(); do_two(); do_three()
E703: do_four();  # useless semicolon
E704: def f(x): return 2*x
E731: f = lambda x: 2*x

Closing bracket does not match visual indentation
Open

                                          )
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (100 > 79 characters)
Open

        :param profile: Set to True to provide information about step size (tau) taken at each step.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Blank line contains whitespace
Open
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Line too long (107 > 79 characters)
Open

                raise SpeciesError('Species mode can only be \'continuous\', \'dynamic\',\'discrete\', or '
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (82 > 79 characters)
Open

                    for i, s in enumerate(list(self.model._listOfSpecies.keys())):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (90 > 79 characters)
Open

                active_rr = self.__toggle_reactions(all_compiled, deterministic_reactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (88 > 79 characters)
Open

    def __init__(self, model=None, profile_reactions=False, constant_tau_stepsize=None):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (3)
Open

    def __save_state_to_output(self, curr_time, save_index, curr_state, species,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Continuation line under-indented for visual indent
Open

                                                           self.model.listOfReactions[reaction].ode_propensity_function)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (117 > 79 characters)
Open

                    curr_state[reactant.name] -= self.model.listOfReactions[rxn].reactants[reactant] * rxn_count[rxn]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Blank line contains whitespace
Open
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Continuation line under-indented for visual indent
Open

                                          tau_step, det_rxn
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (107 > 79 characters)
Open

                print("Setting Random number ", curr_state[r], " for ", self.model.listOfReactions[r].name)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (91 > 79 characters)
Open

        :param event_sensitivity: Number of data points to be inspected between integration
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (95 > 79 characters)
Open

            # For multi trajectories, live_grapher needs to be informed of trajectory increment
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (101 > 79 characters)
Open

                        propensities[r] = eval(compiled_propensities[r], eval_globals, curr_state[0])
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (94 > 79 characters)
Open

                            # This is an edge case, that might happen after a single SSA step.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (187 > 79 characters)
Open

                    tau_step = Tau.select(HOR, reactants, mu_i, sigma_i, g_i, epsilon_i, tau_tol, critical_threshold, self.model, propensities, curr_state[0], curr_time[0], save_times[0])
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (100 > 79 characters)
Open

                deterministic_reactions = self.__flag_det_reactions(det_spec, det_rxn, dependencies)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

At least two spaces before inline comment
Open

                rr_sets = {frozenset() : compiled_rate_rules} # base rr set
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (94 > 79 characters)
Open

                                                                               delayed_events,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (94 > 79 characters)
Open

                                                                               trigger_states,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                                               parameters, compiled_reactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (82 > 79 characters)
Open

            time = save_times.pop(0) # remove the value from the front of the list
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (86 > 79 characters)
Open

        # loop through each det reaction and concatenate it's diff eq for each species
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (2)
Open

    def __toggle_reactions(self, all_compiled, deterministic_reactions, dependencies,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (90 > 79 characters)
Open

                elif bool_res[y] and dense_range[y] != curr_time and bool_res[y - 1] == 0:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (89 > 79 characters)
Open

                        execution_time = eval(e.delay, {**eval_globals, **initial_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line over-indented for visual indent
Open

                            curr_state, det_spec, rr_sets):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (99 > 79 characters)
Open

from gillespy2.core import GillesPySolver, log, Event, RateRule, AssignmentRule, FunctionDefinition
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                    propensities, y_map, compiled_reactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (116 > 79 characters)
Open

                                                           self.model.listOfReactions[reaction].propensity_function)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (85 > 79 characters)
Open

            for k in list(self.model.listOfSpecies)+list(self.model.listOfReactions):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Trailing whitespace
Open

        Integreate one step, skip ODE integrator as all species are
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Line too long (81 > 79 characters)
Open

                assign_value = eval(a.expression, eval_globals, assignment_state)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Blank line contains whitespace
Open
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

At least two spaces before inline comment
Open

            time = save_times.pop(0) # remove the value from the front of the list
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (114 > 79 characters)
Open

                            initial_state[a.variable.name] = eval(a.expression, {**eval_globals, **initial_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          compiled_reactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (81 > 79 characters)
Open

        # Determine if each rxn would be deterministic apart from other reactions
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (95 > 79 characters)
Open

            sanitized_function = fd.sanitized_function(sanitized_species, sanitized_parameters)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace around operator
Open

        elif len(self.model.listOfRateRules)==0:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Line too long (81 > 79 characters)
Open

                    mn[product.name] += (propensities[r] * rxn.products[product])
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (84 > 79 characters)
Open

        :param seed: The random seed for the simulation. Optional, defaults to None.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                            delayed_events, trigger_states, event_sensitivity, tau_step)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (89 > 79 characters)
Open

                t0_firing = eval(e.trigger.expression, {**eval_globals, **initial_state})
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Block comment should start with '# '
Open

        #next_tau = curr_time + tau_step
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (103 > 79 characters)
Open

        :param integrator_options:  contains options to the scipy integrator. by default, this includes
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

                                ' integration, total solve time could be longer than expected.')
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Inline comment should start with '# '
Open

                    curr_state[rxn] = math.log(np.random.uniform(0, 1)) #set this value, needs to be <0
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Multiple statements on one line (colon)
Open

            while self.result is None: pass
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Compound statements (on the same line) are generally discouraged.

While sometimes it's okay to put an if/for/while with a small body
on the same line, never do this for multi-clause statements.
Also avoid folding such long lines!

Always use a def statement instead of an assignment statement that
binds a lambda expression directly to a name.

Okay: if foo == 'blah':\n    do_blah_thing()
Okay: do_one()
Okay: do_two()
Okay: do_three()

E701: if foo == 'blah': do_blah_thing()
E701: for x in lst: total += x
E701: while t < 10: t = delay()
E701: if foo == 'blah': do_blah_thing()
E701: else: do_non_blah_thing()
E701: try: something()
E701: finally: cleanup()
E701: if foo == 'blah': one(); two(); three()
E702: do_one(); do_two(); do_three()
E703: do_four();  # useless semicolon
E704: def f(x): return 2*x
E731: f = lambda x: 2*x

Continuation line under-indented for visual indent
Open

                                          event_sensitivity,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (81 > 79 characters)
Open

    def __integrate_constant(self, integrator_options, curr_state, y0, curr_time,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (105 > 79 characters)
Open

    def ___run(self, curr_state, curr_time, timeline, trajectory_base, initial_state, live_grapher, t=20,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (104 > 79 characters)
Open

            self.__run(curr_state, curr_time, timeline, trajectory_base, initial_state, live_grapher, t,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Over-indented (comment)
Open

            # check each species to see if they are negative
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Use indent_size (PEP8 says 4) spaces per indentation level.

For really old code that you don't want to mess up, you can continue
to use 8-space tabs.

Okay: a = 1
Okay: if a == 0:\n    a = 1
E111:   a = 1
E114:   # a = 1

Okay: for item in items:\n    pass
E112: for item in items:\npass
E115: for item in items:\n# Hi\n    pass

Okay: a = 1\nb = 2
E113: a = 1\n    b = 2
E116: a = 1\n    # b = 2

Line too long (85 > 79 characters)
Open

            # Record Highest Order reactant for each reaction and set error tolerance
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (107 > 79 characters)
Open

            compiled_reactions, compiled_rate_rules, compiled_inactive_reactions, compiled_propensities = \
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (116 > 79 characters)
Open

        save_index = self.__save_state_to_output(curr_time, save_index, curr_state, species, trajectory, save_times)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace after ','
Open

                    for k,v in curr_state[0].items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (98 > 79 characters)
Open

            debug=False, profile=False, tau_tol=0.03, event_sensitivity=100,integrator_options={},
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace around operator
Open

        err_message=""
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Too many blank lines (2)
Open

                # Process switching if used
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Missing whitespace around operator
Open

        rxn_count=None
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Line too long (113 > 79 characters)
Open

        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 pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (179 > 79 characters)
Open

        # check each reaction to see if it is >=0. If we have taken a single SSA step, this could be >0 for the non-selected reactions, check if propensity is zero and reset if so
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (95 > 79 characters)
Open

        :param debug: Set to True to provide additional debug information about the simulation.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          event_queue,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (98 > 79 characters)
Open

                You should use `gillespy2.Model.run(solver=TauHybridSolver(model=gillespy2.Model))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (107 > 79 characters)
Open

                                                                               event_sensitivity, tau_step,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          trigger_states,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (101 > 79 characters)
Open

                log.warning('Unsupported keyword argument to {0} solver: {1}'.format(self.name, key))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (108 > 79 characters)
Open

                                      args=(curr_state, curr_time, timeline, trajectory_base, initial_state,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (117 > 79 characters)
Open

                                                                    'number_of_trajectories': number_of_trajectories,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Missing whitespace after ','
Open

                    raise SimulationError('Error calculation propensity for {0}.\nReason: {1}\nfloored_propensities={2}\ncompiled_reactions={3}'.format(r, e, floored_propensities,compiled_reactions))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (112 > 79 characters)
Open

                            log.warning('display \"type\" = \"graph\" not recommended with continuous species. '
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          event_sensitivity,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (133 > 79 characters)
Open

                raise SimulationError(f"Negative State detected in step, after single SSA step. error_message={invalid_err_message}")
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (106 > 79 characters)
Open

        events_processed = self.__process_queued_events(event_queue, trigger_states, curr_state, det_spec)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Trailing whitespace
Open

    def __save_state_to_output(self, curr_time, save_index, curr_state, species,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Missing whitespace around operator
Open

        while len(save_times)>0 and save_times[0] <= curr_time:
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Line too long (107 > 79 characters)
Open

        return ('model', 't', 'number_of_trajectories', 'increment', 'seed', 'debug', 'profile', 'tau_tol',
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line over-indented for visual indent
Open

                                            dependencies, rr_sets, rate_rules)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (113 > 79 characters)
Open

        :param number_of_trajectories: Number of trajectories to simulate. By default number_of_trajectories = 1.
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (84 > 79 characters)
Open

            for key, value in self.model.listOfReactions[reaction].products.items():
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (104 > 79 characters)
Open

    def __run(self, curr_state, curr_time, timeline, trajectory_base, initial_state, live_grapher, t=20,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (89 > 79 characters)
Open

                    CV[species] = 1  # value chosen to guarantee species will be discrete
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (118 > 79 characters)
Open

            [dependencies[reaction].add(reactant.name) for reactant in self.model.listOfReactions[reaction].reactants]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

At least two spaces before inline comment
Open

                    cv_history[species].pop(0) #remove the first item
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (108 > 79 characters)
Open

            trajectory = trajectory_base[trajectory_num]  # NumPy array containing this simulation's results
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (86 > 79 characters)
Open

        dense_range = np.linspace(sol.t[0], sol.t[-1], len(sol.t) * event_sensitivity)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Whitespace before ':'
Open

                rr_sets = {frozenset() : compiled_rate_rules} # base rr set
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Avoid extraneous whitespace.

Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.

Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })

E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x

Line too long (80 > 79 characters)
Open

            fired_event = self.model.listOfEvents[heapq.heappop(event_queue)[1]]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Too many blank lines (3)
Open

    def __integrate(self, integrator_options, curr_state, y0, curr_time,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

Line too long (103 > 79 characters)
Open

                                                        dependencies, curr_state[0], det_spec, rr_sets)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (91 > 79 characters)
Open

            return self.__integrate_constant(integrator_options, curr_state, y0, curr_time,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (105 > 79 characters)
Open

                curr_state[0], curr_time[0], save_times, save_index = self.__simulate(integrator_options,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (80 > 79 characters)
Open

                                    event_queue, trigger_states, delayed_events)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (85 > 79 characters)
Open

        curr_time, actual_tau_step = self.__integrate(integrator_options, curr_state,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (162 > 79 characters)
Open

            if rxn_selected is None: raise SimulationError(f"Negative State detected in step, and no reaction found to fire. error_message={invalid_err_message}")
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                          y0, curr_time, propensities, y_map,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Continuation line under-indented for visual indent
Open

                                          trigger_states,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (106 > 79 characters)
Open

        return compiled_reactions, compiled_rate_rules, compiled_inactive_reactions, compiled_propensities
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (87 > 79 characters)
Open

    def __map_state(self, species, parameters, compiled_reactions, events, curr_state):
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (101 > 79 characters)
Open

            y0[i + len(species) + len(parameters) + len(compiled_reactions)] = curr_state[event.name]
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (112 > 79 characters)
Open

        :param live_output: The type of output to be displayed by solver. Can be "progress", "text", or "graph".
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (93 > 79 characters)
Open

        t0_delayed_events, species_modified_by_events = self.__check_t0_events(initial_state)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (115 > 79 characters)
Open

            HOR, reactants, mu_i, sigma_i, g_i, epsilon_i, critical_threshold = Tau.initialize(self.model, tau_tol)
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (140 > 79 characters)
Open

                        raise SimulationError('Error calculation propensity for {0}.\nReason: {1}\ncurr_state={2}'.format(r, e, curr_state))
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (110 > 79 characters)
Open

                                                                               parameters, compiled_reactions,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                                                                               active_rr, y_map,
Severity: Minor
Found in gillespy2/solvers/numpy/tau_hybrid_solver.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

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