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pytim/sanity_check.py

Summary

Maintainability
B
4 hrs
Test Coverage

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

    def assign_radii(self, radii_dict=None):

        if radii_dict is not None:
            self.interface.radii_dict = radii_dict.copy()
        else:
Severity: Minor
Found in pytim/sanity_check.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 assign_universe. (8)
Open

    def assign_universe(self, universe, analysis_group):
        """ Assign the universe and the analysis_group
        """
        self.interface._mode = self._check_universe(universe)
        if self.interface._mode is None:
Severity: Minor
Found in pytim/sanity_check.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 _check_universe. (7)
Open

    def _check_universe(self, input_obj):
        """ Check whether instead of a universe,
            the input_obj is one of the following,
            and act accordingly:
            - MDAnalysis.core.universe.Universe
Severity: Minor
Found in pytim/sanity_check.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 assign_cluster_params. (7)
Open

    def assign_cluster_params(self,
                              cluster_cut,
                              cluster_threshold_density,
                              extra_cluster_groups):
        elements = 0
Severity: Minor
Found in pytim/sanity_check.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 assign_radii has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def assign_radii(self, radii_dict=None):

        if radii_dict is not None:
            self.interface.radii_dict = radii_dict.copy()
        else:
Severity: Minor
Found in pytim/sanity_check.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 assign_universe has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def assign_universe(self, universe, analysis_group):
        """ Assign the universe and the analysis_group
        """
        self.interface._mode = self._check_universe(universe)
        if self.interface._mode is None:
Severity: Minor
Found in pytim/sanity_check.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 assign_cluster_params has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def assign_cluster_params(self,
                              cluster_cut,
                              cluster_threshold_density,
                              extra_cluster_groups):
        elements = 0
Severity: Minor
Found in pytim/sanity_check.py - About 45 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

Avoid too many return statements within this function.
Open

        return None
Severity: Major
Found in pytim/sanity_check.py - About 30 mins to fix

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

    def assign_normal(self, normal):
        interface = self.interface
        if not (interface.symmetry == 'planar'):
            raise ValueError(" wrong symmetry for normal assignement")
        if interface.analysis_group is None:
Severity: Minor
Found in pytim/sanity_check.py - About 25 mins to fix

Cognitive Complexity

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

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

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

Further reading

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

    def _check_universe(self, input_obj):
        """ Check whether instead of a universe,
            the input_obj is one of the following,
            and act accordingly:
            - MDAnalysis.core.universe.Universe
Severity: Minor
Found in pytim/sanity_check.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

TODO found
Open

    # TODO: rename
Severity: Minor
Found in pytim/sanity_check.py by fixme

Merge this if statement with the enclosing one.
Open

                if self.interface.cluster_cut is None:
Severity: Major
Found in pytim/sanity_check.py by sonar-python

Merging collapsible if statements increases the code's readability.

Noncompliant Code Example

if condition1:
    if condition2:
        # ...

Compliant Solution

if condition1 and condition2:
    # ...

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