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gillespy2/solvers/numpy/ssa_solver.py

Summary

Maintainability
D
2 days
Test Coverage
C
75%

Function __run has a Cognitive Complexity of 94 (exceeds 5 allowed). Consider refactoring.
Open

    def __run(self, curr_state, total_time, timeline, trajectory_base, live_grapher, t=20,
              number_of_trajectories=1, increment=0.05, seed=None, debug=False,
              resume=None,):

        # for use with resume, determines how much excess data to cut off due to
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py - About 1 day to fix

Cognitive Complexity

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

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

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

Further reading

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

    def __run(self, curr_state, total_time, timeline, trajectory_base, live_grapher, t=20,
              number_of_trajectories=1, increment=0.05, seed=None, debug=False,
              resume=None,):

        # for use with resume, determines how much excess data to cut off due to
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py by radon

Cyclomatic Complexity

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

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

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

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

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

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None, debug=False,
            live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):

        """
        Run the SSA algorithm. Uses a NumPy array for storing results and for generating the timeline.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py - About 5 hrs to fix

Cognitive Complexity

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

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

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

Further reading

Cyclomatic complexity is too high in method run. (25)
Open

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None, debug=False,
            live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):

        """
        Run the SSA algorithm. Uses a NumPy array for storing results and for generating the timeline.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py by radon

Cyclomatic Complexity

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

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

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

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

Cyclomatic complexity is too high in class NumPySSASolver. (13)
Open

class NumPySSASolver(GillesPySolver):

    """
    This solver produces simulations of systems via Stochastic Simulation Algorithm.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py by radon

Cyclomatic Complexity

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

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

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

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

Line too long (114 > 79 characters)
Open

                                                                                                       live_output
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                    "'t' must be greater than previous simulations end time, or set in the run() method as the "
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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

                You should use `gillespy2.Model.run(solver=NumPySSASolver(model=gillespy2.Model))
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                                             live_output_options,resume = resumeTest)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 (127 > 79 characters)
Open

                                        - self.model.listOfReactions[reaction].reactants.get(self.model.listOfSpecies[spec], 0)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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('species_changes: {0},i={1}, j={2}... {3}'.format(species, i, j, species_changes[i][j]))
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

        return ('model', 't', 'number_of_trajectories', 'increment', 'seed', 'debug', 'timeout')
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 (94 > 79 characters)
Open

                f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 (92 > 79 characters)
Open

                while entry_count < timeline.size and timeline[entry_count] <= curr_time[0]:
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

    This solver produces simulations of systems via Stochastic Simulation Algorithm.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 (114 > 79 characters)
Open

                                                                        live_grapher[0].display, args=(curr_state,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

               number_of_trajectories=1, increment=0.05, seed=None, debug=False, resume=None,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                    propensity_sums[i] = propensity_functions[reactions[i]][0](species_states)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 (119 > 79 characters)
Open

                                                                                                       trajectory_base,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                raise ModelError('When resuming, one must not alter the model being resumed.')
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

        # create mapping of reactions, and which reactions depend on their reactants/products
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

            live_output=None, live_output_options={}, timeout=None, resume=None, **kwargs):
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

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

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

                log.warning('Unsupported keyword argument to {0} solver: {1}'.format(self.name, key))
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

        # for use with resume, determines how much excess data to cut off due to
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py by 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/ssa_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 i,spec in enumerate(self.model.listOfSpecies):
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 (96 > 79 characters)
Open

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

            # raise SimulationError("NumPySSASolver must be instantiated to run the simulation")
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 over-indented for visual indent
Open

                                                                             live_output_options,resume = resumeTest)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

        # curr_time and curr_state are list of len 1 so that __run receives reference
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

            self.__run(curr_state, total_time, timeline, trajectory_base, live_grapher, t, number_of_trajectories,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 (101 > 79 characters)
Open

                                                                              number_of_trajectories,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 (112 > 79 characters)
Open

        species_mappings, species, parameter_mappings, number_species = nputils.numpy_initialization(self.model)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                                              'resume': resume, })
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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

Unexpected spaces around keyword / parameter equals
Open

                                                                             live_output_options,resume = resumeTest)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Line too long (118 > 79 characters)
Open

        trajectory_base, tmpSpecies = nputils.numpy_trajectory_base_initialization(self.model, number_of_trajectories,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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.

Unexpected spaces around keyword / parameter equals
Open

                                                                             live_output_options,resume = resumeTest)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Line too long (104 > 79 characters)
Open

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

                                                                                                       )
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                            propensity_sums[propensity_functions[i][1]] = propensity_functions[i][0](species_states)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

    def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, seed=None, debug=False,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

    def __run(self, curr_state, total_time, timeline, trajectory_base, live_grapher, t=20,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 (102 > 79 characters)
Open

        Run the SSA algorithm. Uses a NumPy array for storing results and for generating the timeline.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_solver.py 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/ssa_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_state[0][spec] += species_changes[potential_reaction][i]
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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

        sim_thread = Thread(target=self.___run, args=(curr_state, total_time, timeline, trajectory_base,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 (92 > 79 characters)
Open

                    resumeTest = True  # If resuming, relay this information to live_grapher
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                                                                       total_time,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

        # create dictionary of all constant parameters for propensity evaluation
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 (102 > 79 characters)
Open

            propensity_functions[reaction] = [eval('lambda S:' + self.model.listOfReactions[reaction].
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 (83 > 79 characters)
Open

                gillespy2.core.liveGraphing.valid_graph_params(live_output_options)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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 (126 > 79 characters)
Open

                species_changes[i][j] = self.model.listOfReactions[reaction].products.get(self.model.listOfSpecies[spec], 0) \
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

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

        :param number_of_trajectories: Number of trajectories to simulate. By default number_of_trajectories = 1.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                                              'increment': increment,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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/ssa_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

                                                                              'seed': seed, 'debug': debug,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                                                   timeline, species, resume=resume)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                    curr_state[0][spec] = self.model.listOfSpecies[spec].initial_value
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                   sanitized_propensity_function(species_mappings, parameter_mappings),
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                print('new propensity sum: ', propensity_sums[i])
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 and curr_state are list of len 1 so that __run receives reference
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

            simulation_data = nputils.numpy_resume(timeStopped, simulation_data, resume=resume)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

        :param live_output_options: dictionary contains options for live_output. By default {"interval":1}.
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                      live_grapher,), kwargs={'t': t, 'number_of_trajectories':
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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

                                                                             live_output_options,resume = resumeTest)
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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 (91 > 79 characters)
Open

    def ___run(self, curr_state, total_time, timeline, trajectory_base, live_grapher, t=20,
Severity: Minor
Found in gillespy2/solvers/numpy/ssa_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.

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