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pytim/observables/profile.py

Summary

Maintainability
B
7 hrs
Test Coverage

File profile.py has 299 lines of code (exceeds 250 allowed). Consider refactoring.
Open

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: Profile
    ===============
"""
Severity: Minor
Found in pytim/observables/profile.py - About 3 hrs to fix

Cyclomatic complexity is too high in method sample. (8)
Open

    def sample(self, group, **kargs):
        # TODO: implement progressive averaging to handle very long trajs
        # TODO: implement memory cleanup
        if not isinstance(group, AtomGroup):
            raise TypeError("The first argument passed to "
Severity: Minor
Found in pytim/observables/profile.py by radon

Cyclomatic Complexity

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

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

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

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

Cyclomatic complexity is too high in method get_values. (7)
Open

    def get_values(self, binwidth=None, nbins=None):
        if self.sampled_values is None:
            print("Warning no profile sampled so far")
        # we use the largest box (largest number of bins) as reference.
        # Statistics will be poor at the boundaries, but like that we don't
Severity: Minor
Found in pytim/observables/profile.py by radon

Cyclomatic Complexity

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

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

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

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

Cyclomatic complexity is too high in method __init__. (6)
Open

    def __init__(self,
                 direction=None,
                 observable=None,
                 interface=None,
                 symmetry='default',
Severity: Minor
Found in pytim/observables/profile.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 sample has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

    def sample(self, group, **kargs):
        # TODO: implement progressive averaging to handle very long trajs
        # TODO: implement memory cleanup
        if not isinstance(group, AtomGroup):
            raise TypeError("The first argument passed to "
Severity: Minor
Found in pytim/observables/profile.py - About 1 hr to fix

Cognitive Complexity

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

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

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

Further reading

Function __init__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self,
                 direction=None,
                 observable=None,
                 interface=None,
                 symmetry='default',
Severity: Minor
Found in pytim/observables/profile.py - About 55 mins to fix

Cognitive Complexity

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

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

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

Further reading

Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self,
Severity: Major
Found in pytim/observables/profile.py - About 50 mins to fix

Function get_values has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def get_values(self, binwidth=None, nbins=None):
        if self.sampled_values is None:
            print("Warning no profile sampled so far")
        # we use the largest box (largest number of bins) as reference.
        # Statistics will be poor at the boundaries, but like that we don't
Severity: Minor
Found in pytim/observables/profile.py - About 25 mins to fix

Cognitive Complexity

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

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

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

Further reading

Method "__init__" has 8 parameters, which is greater than the 7 authorized.
Open

    def __init__(self,
                 direction=None,
                 observable=None,
                 interface=None,
                 symmetry='default',
Severity: Major
Found in pytim/observables/profile.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

TODO found
Open

        # TODO: implement progressive averaging to handle very long trajs
Severity: Minor
Found in pytim/observables/profile.py by fixme

TODO found
Open

        # TODO: implement memory cleanup
Severity: Minor
Found in pytim/observables/profile.py by fixme

Line too long (83 > 79 characters)
Open

    >>> # Go through the trajectory, center the liquid slab and sample the profiles
Severity: Minor
Found in pytim/observables/profile.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

    Note the missing point at position = 0, this is the delta-function contirbution.
Severity: Minor
Found in pytim/observables/profile.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

    Negative positions are within the liquid phase, while positive ones are in the vapour
Severity: Minor
Found in pytim/observables/profile.py by pep8

Limit all lines to a maximum of 79 characters.

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

Reports error E501.

Line too long (82 > 79 characters)
Open

    >>> # Note that by default Profile() uses the number of atoms as an observable
Severity: Minor
Found in pytim/observables/profile.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

    ...         # this shifts the system so that the center of mass of the liquid slab
Severity: Minor
Found in pytim/observables/profile.py by pep8

Limit all lines to a maximum of 79 characters.

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

Reports error E501.

Line too long (105 > 79 characters)
Open

    This results in the following profile (sampling more often and zooming close to the interface border)
Severity: Minor
Found in pytim/observables/profile.py by pep8

Limit all lines to a maximum of 79 characters.

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

Reports error E501.

Do not use bare 'except'
Open

        except:
Severity: Minor
Found in pytim/observables/profile.py by pep8

When catching exceptions, mention specific exceptions when possible.

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

Do not use bare 'except'
Open

            except:
Severity: Minor
Found in pytim/observables/profile.py by pep8

When catching exceptions, mention specific exceptions when possible.

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

Line too long (81 > 79 characters)
Open

    >>> inter = pytim.ITIM(u,group=g,max_layers=4,centered=True, molecular=False)
Severity: Minor
Found in pytim/observables/profile.py by pep8

Limit all lines to a maximum of 79 characters.

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

Reports error E501.

Line too long (106 > 79 characters)
Open

    >>> np.savetxt('profile.dat',list(zip(low,up,density[0],density[1],density[2],density[3],density[4])))
Severity: Minor
Found in pytim/observables/profile.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

                self.interface, symmetry=self.symmetry, mode=self.mode).compute(group)
Severity: Minor
Found in pytim/observables/profile.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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