Function run
has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring. Open
def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, integrator='lsoda',
integrator_options={}, live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):
"""
:param model: The model on which the solver will operate. (Deprecated)
:type model: gillespy2.Model
- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Cyclomatic complexity is too high in method run. (26) Open
def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, integrator='lsoda',
integrator_options={}, live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):
"""
:param model: The model on which the solver will operate. (Deprecated)
:type model: gillespy2.Model
- Read upRead up
- Exclude checks
Cyclomatic Complexity
Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.
Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:
Construct | Effect on CC | Reasoning |
---|---|---|
if | +1 | An if statement is a single decision. |
elif | +1 | The elif statement adds another decision. |
else | +0 | The else statement does not cause a new decision. The decision is at the if. |
for | +1 | There is a decision at the start of the loop. |
while | +1 | There is a decision at the while statement. |
except | +1 | Each except branch adds a new conditional path of execution. |
finally | +0 | The finally block is unconditionally executed. |
with | +1 | The with statement roughly corresponds to a try/except block (see PEP 343 for details). |
assert | +1 | The assert statement internally roughly equals a conditional statement. |
Comprehension | +1 | A list/set/dict comprehension of generator expression is equivalent to a for loop. |
Boolean Operator | +1 | Every boolean operator (and, or) adds a decision point. |
Cyclomatic complexity is too high in method __run. (17) Open
def __run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
number_of_trajectories=1, increment=0.05, integrator='lsoda',
integrator_options={}, resume=None, **kwargs):
timeStopped = 0
- Read upRead up
- Exclude checks
Cyclomatic Complexity
Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.
Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:
Construct | Effect on CC | Reasoning |
---|---|---|
if | +1 | An if statement is a single decision. |
elif | +1 | The elif statement adds another decision. |
else | +0 | The else statement does not cause a new decision. The decision is at the if. |
for | +1 | There is a decision at the start of the loop. |
while | +1 | There is a decision at the while statement. |
except | +1 | Each except branch adds a new conditional path of execution. |
finally | +0 | The finally block is unconditionally executed. |
with | +1 | The with statement roughly corresponds to a try/except block (see PEP 343 for details). |
assert | +1 | The assert statement internally roughly equals a conditional statement. |
Comprehension | +1 | A list/set/dict comprehension of generator expression is equivalent to a for loop. |
Boolean Operator | +1 | Every boolean operator (and, or) adds a decision point. |
Function __run
has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring. Open
def __run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
number_of_trajectories=1, increment=0.05, integrator='lsoda',
integrator_options={}, resume=None, **kwargs):
timeStopped = 0
- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Cyclomatic complexity is too high in class ODESolver. (9) Open
class ODESolver(GillesPySolver):
"""
This solver produces the deterministic continuous solution via Ordinary Differential Equations.
Uses integrators from scipy.integrate.ode to perform calculations used to produce solutions.
- Read upRead up
- Exclude checks
Cyclomatic Complexity
Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.
Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:
Construct | Effect on CC | Reasoning |
---|---|---|
if | +1 | An if statement is a single decision. |
elif | +1 | The elif statement adds another decision. |
else | +0 | The else statement does not cause a new decision. The decision is at the if. |
for | +1 | There is a decision at the start of the loop. |
while | +1 | There is a decision at the while statement. |
except | +1 | Each except branch adds a new conditional path of execution. |
finally | +0 | The finally block is unconditionally executed. |
with | +1 | The with statement roughly corresponds to a try/except block (see PEP 343 for details). |
assert | +1 | The assert statement internally roughly equals a conditional statement. |
Comprehension | +1 | A list/set/dict comprehension of generator expression is equivalent to a for loop. |
Boolean Operator | +1 | Every boolean operator (and, or) adds a decision point. |
Function __f
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def __f(t, y, curr_state, model, c_prop):
"""
The right hand side of the differential equation, uses scipy.integrate ode
:param t: time as a numpy array
- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Blank line contains whitespace Open
- Read upRead up
- Exclude checks
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 (116 > 79 characters) Open
:param integrator: integrator to be used from scipy.integrate.ode. Options include 'vode', 'zvode', 'lsoda',
- Read upRead up
- Exclude checks
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
:param integrator_options: a dictionary containing options to the scipy integrator. for a list of options,
- Read upRead up
- Exclude checks
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
see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html
- Read upRead up
- Exclude checks
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
"clear_output" specifies if display should be refreshed with each display.
- Read upRead up
- Exclude checks
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
:param live_output_options: dictionary contains options for live_output. By default {"interval":1}.
- Read upRead up
- Exclude checks
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
The right hand side of the differential equation, uses scipy.integrate ode
- Read upRead up
- Exclude checks
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
:param number_of_trajectories: Number of trajectories to simulate. By default number_of_trajectories = 1.
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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 (91 > 79 characters) Open
# raise SimulationError("ODESolver must be instantiated to run the simulation")
- Read upRead up
- Exclude checks
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 (99 > 79 characters) Open
This solver produces the deterministic continuous solution via Ordinary Differential Equations.
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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
Blank line contains whitespace Open
- Read upRead up
- Exclude checks
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
Blank line contains whitespace Open
- Read upRead up
- Exclude checks
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 (112 > 79 characters) Open
:param live_output: The type of output to be displayed by solver. Can be "progress", "text", or "graph".
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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
Multiple spaces after operator Open
state_change = OrderedDict()
- Read upRead up
- Exclude checks
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
Line too long (96 > 79 characters) Open
:returns: Tuple of strings, denoting all keyword argument for this solvers run() method.
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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
log.warning('model = gillespy2.model is deprecated. Future releases '
- Read upRead up
- Exclude checks
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
integrator_options={}, live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):
- Read upRead up
- Exclude checks
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.
- Read upRead up
- Exclude checks
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
return ('model', 't', 'number_of_trajectories', 'increment', 'integrator', 'integrator_options',
- Read upRead up
- Exclude checks
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
see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html.
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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 (92 > 79 characters) Open
You should use `gillespy2.Model.run(solver=ODESolver(model=gillespy2.Model))
- Read upRead up
- Exclude checks
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
Uses integrators from scipy.integrate.ode to perform calculations used to produce solutions.
- Read upRead up
- Exclude checks
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=None, model=None, t=None, number_of_trajectories=1, increment=None, integrator='lsoda',
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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 (83 > 79 characters) Open
raise SimulationError("A model is required to run the simulation.")
- Read upRead up
- Exclude checks
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
live_output_options, resume=resumeTest)
- Read upRead up
- Exclude checks
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
self.__run(curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t,
- Read upRead up
- Exclude checks
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 (92 > 79 characters) Open
rhs.set_initial_value(y0, curr_time[0]).set_f_params(curr_state, self.model, c_prop)
- Read upRead up
- Exclude checks
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
sim_thread = Thread(target=self.___run, args=(curr_state, curr_time, timeline, trajectory_base,
- Read upRead up
- Exclude checks
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,
- Read upRead up
- Exclude checks
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 (92 > 79 characters) Open
resumeTest = True # If resuming, relay this information to live_grapher
- Read upRead up
- Exclude checks
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
tmpSpecies, live_grapher,), kwargs={'t': t,
- Read upRead up
- Exclude checks
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
'increment': increment,
- Read upRead up
- Exclude checks
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
timeline, species, resume=resume)
- Read upRead up
- Exclude checks
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
integrator_options, })
- Read upRead up
- Exclude checks
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
number_of_trajectories, increment, integrator, integrator_options, resume,
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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
'resume': resume,
- Read upRead up
- Exclude checks
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
'integrator_options':
- Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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 (112 > 79 characters) Open
"'t' must be greater than previous simulations end time, or set in the run() method as the "
- Read upRead up
- Exclude checks
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 (102 > 79 characters) Open
def ___run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
- Read upRead up
- Exclude checks
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
def __run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
- Read upRead up
- Exclude checks
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
gillespy2.core.liveGraphing.valid_graph_params(live_output_options)
- Read upRead up
- Exclude checks
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
log.warning('Unsupported keyword argument to {0} solver: {1}'.format(self.name, key))
- Read upRead up
- Exclude checks
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
c_prop[r_name] = compile(reaction.ode_propensity_function, '<string>', 'eval')
- Read upRead up
- Exclude checks
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
f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
- Read upRead up
- Exclude checks
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
log.warning("Generating duplicate trajectories for model with ODE Solver. "
- Read upRead up
- Exclude checks
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,
- Read upRead up
- Exclude checks
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 (130 > 79 characters) Open
args=(curr_state, curr_time, trajectory_base,live_output))
- Read upRead up
- Exclude checks
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,
- Read upRead up
- Exclude checks
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
args=(curr_state, curr_time, trajectory_base,live_output))
- Read upRead up
- Exclude checks
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 (81 > 79 characters) Open
rhs = ode(ODESolver.__f).set_integrator(integrator, **integrator_options)
- Read upRead up
- Exclude checks
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
'integrator': integrator,
- Read upRead up
- Exclude checks
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'],
- Read upRead up
- Exclude checks
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
raise gillespyError.ModelError('When resuming, one must not alter the model being resumed.')
- Read upRead up
- Exclude checks
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
trajectory_base, tmpSpecies = nputils.numpy_trajectory_base_initialization(self.model, number_of_trajectories,
- Read upRead up
- Exclude checks
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
'number_of_trajectories':
- Read upRead up
- Exclude checks
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.