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pytim/chacon_tarazona.py

Summary

Maintainability
A
3 hrs
Test Coverage

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

    def _assign_one_side(self, side):
        """ Calculate the interfacial molecules on one side of the box.
        """
        # TODO add successive layers
        box = self.universe.dimensions[:3]
Severity: Minor
Found in pytim/chacon_tarazona.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 __init__ has 14 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self,
Severity: Major
Found in pytim/chacon_tarazona.py - About 1 hr to fix

Function _assign_one_side has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def _assign_one_side(self, side):
        """ Calculate the interfacial molecules on one side of the box.
        """
        # TODO add successive layers
        box = self.universe.dimensions[:3]
Severity: Minor
Found in pytim/chacon_tarazona.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

Method "__init__" has 15 parameters, which is greater than the 7 authorized.
Open

    def __init__(self,
                 universe,
                 alpha=2.0,
                 tau=1.5,
                 group=None,
Severity: Major
Found in pytim/chacon_tarazona.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 parallelize
Severity: Minor
Found in pytim/chacon_tarazona.py by fixme

TODO found
Open

        # TODO add successive layers
Severity: Minor
Found in pytim/chacon_tarazona.py by fixme

TODO found
Open

        # TODO other directions
Severity: Minor
Found in pytim/chacon_tarazona.py by fixme

TODO found
Open

        # TODO implement cluster group
Severity: Minor
Found in pytim/chacon_tarazona.py by fixme

TODO found
Open

            # TODO handle failure
Severity: Minor
Found in pytim/chacon_tarazona.py by fixme

Identical blocks of code found in 2 locations. Consider refactoring.
Open

        if self.do_center is False:
            self.universe.atoms.positions = self.original_positions
        else:
            self._shift_positions_to_middle()
Severity: Minor
Found in pytim/chacon_tarazona.py and 1 other location - About 35 mins to fix
pytim/itim.py on lines 416..422

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 33.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Line too long (98 > 79 characters)
Open

        >> interface = pytim.ChaconTarazona(u,alpha=2.,tau=1.5,group=g,info=False,molecular=False)
Severity: Minor
Found in pytim/chacon_tarazona.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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