Marcello-Sega/pytim

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pytim/interface.py

Summary

Maintainability
D
2 days
Test Coverage

File interface.py has 569 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
from abc import ABCMeta, abstractmethod
import numpy as np
from .properties import _create_property
Severity: Major
Found in pytim/interface.py - About 1 day to fix

Cyclomatic complexity is too high in method _center. (9)
Open

    @staticmethod
    def _center(group, direction, halfbox_shift=False):
        """
        Centers the liquid slab in the simulation box.

Severity: Minor
Found in pytim/interface.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

Interface has 21 functions (exceeds 20 allowed). Consider refactoring.
Open

class Interface(object):
    """ The Interface metaclass. Classes for interfacial determination
        (ITIM, GITIM,...) are derived from this one
    """
    __metaclass__ = ABCMeta
Severity: Minor
Found in pytim/interface.py - About 2 hrs to fix

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

    def label_group(self,
                    group,
                    beta=None,
                    layer=None,
                    cluster=None,
Severity: Minor
Found in pytim/interface.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 _define_cluster_group has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

    def _define_cluster_group(self):
        self.universe.atoms.pack_into_box()
        self.cluster_group = self.universe.atoms[:0]  # empty
        if (self.cluster_cut is not None):
            cluster_cut = float(self.cluster_cut[0])
Severity: Minor
Found in pytim/interface.py - About 2 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 _define_cluster_group. (7)
Open

    def _define_cluster_group(self):
        self.universe.atoms.pack_into_box()
        self.cluster_group = self.universe.atoms[:0]  # empty
        if (self.cluster_cut is not None):
            cluster_cut = float(self.cluster_cut[0])
Severity: Minor
Found in pytim/interface.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 _center has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def _center(group, direction, halfbox_shift=False):
        """
        Centers the liquid slab in the simulation box.

        The algorithm tries to avoid problems with the definition
Severity: Minor
Found in pytim/interface.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 center_system has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def center_system(symmetry, group, direction, planar_to_origin=False):
        if symmetry == 'planar':
            utilities.centerbox(group.universe, center_direction=direction)
            Interface._center(group, direction, halfbox_shift=True)
            utilities.centerbox(group.universe, center_direction=direction)
Severity: Minor
Found in pytim/interface.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 label_group has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def label_group(self,
                    group,
                    beta=None,
                    layer=None,
                    cluster=None,
Severity: Minor
Found in pytim/interface.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

Function label_group has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def label_group(self,
Severity: Minor
Found in pytim/interface.py - About 35 mins to fix

Function writepdb has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def writepdb(self,
Severity: Minor
Found in pytim/interface.py - About 35 mins to fix

Function label_planar_sides has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def label_planar_sides(self):
        """ Assign to all layers a label (the beta tempfactor)
            that can be used in pdb files. Additionally, set
            the new layers and sides.
        """
Severity: Minor
Found in pytim/interface.py - About 35 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

Refactor this function to reduce its Cognitive Complexity from 16 to the 15 allowed.
Open

    def _define_cluster_group(self):
Severity: Critical
Found in pytim/interface.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

TODO found
Open

    # TODO: does this belong here ?
Severity: Minor
Found in pytim/interface.py by fixme

Line too long (93 > 79 characters)
Open

        ...     interface = method(u,group=DPC,molecular=False,alpha=2.5,_noextrapoints=True)
Severity: Minor
Found in pytim/interface.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 (120 > 79 characters)
Open

        >>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=False, molecular=True)
Severity: Minor
Found in pytim/interface.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

                    x_labels, x_counts, _ = utilities.do_cluster_analysis_dbscan(
Severity: Minor
Found in pytim/interface.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

        >>> interface = pytim.ITIM(u, alpha=1.5,group=oxygens, max_layers=1,multiproc=False,molecular=False)
Severity: Minor
Found in pytim/interface.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

        ...         if not np.all(np.isclose(inter.atoms.positions[0], ref.atoms.positions[0])):
Severity: Minor
Found in pytim/interface.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

        ...     interface = method(u,group=DPC,molecular=False,alpha=2.5,_noextrapoints=True)
Severity: Minor
Found in pytim/interface.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

        >>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True)
Severity: Minor
Found in pytim/interface.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

        ...         raise RuntimeError("mdtraj available, but a general exception happened")
Severity: Minor
Found in pytim/interface.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 (103 > 79 characters)
Open

        Warning: the option biggest_cluster_only has no effect without setting cluster_cut, ignoring it
Severity: Minor
Found in pytim/interface.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

        ...     interface = method(u,group=oxygens,molecular=False,alpha=2.5,_noextrapoints=True)
Severity: Minor
Found in pytim/interface.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

        ...     interface = method(u,group=oxygens,molecular=False,alpha=2.5,_noextrapoints=True)
Severity: Minor
Found in pytim/interface.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

                         "(float) distance cut to calculate the surface clusters")
Severity: Minor
Found in pytim/interface.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.

At least two spaces before inline comment
Open

        if len(self._layers) == 0: return self._layers # an empty atom group
Severity: Minor
Found in pytim/interface.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

Line too long (80 > 79 characters)
Open

        ...         _a = u.trajectory[1] # we make sure we load the second frame
Severity: Minor
Found in pytim/interface.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 (87 > 79 characters)
Open

        ...             print("MDAnalysis and mdtraj atomic positions do not coincide")
Severity: Minor
Found in pytim/interface.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.

Multiple statements on one line (colon)
Open

        if len(self._layers) == 0: return self._layers # an empty atom group
Severity: Minor
Found in pytim/interface.py by pep8

Compound statements (on the same line) are generally discouraged.

While sometimes it's okay to put an if/for/while with a small body
on the same line, never do this for multi-clause statements.
Also avoid folding such long lines!

Always use a def statement instead of an assignment statement that
binds a lambda expression directly to a name.

Okay: if foo == 'blah':\n    do_blah_thing()
Okay: do_one()
Okay: do_two()
Okay: do_three()

E701: if foo == 'blah': do_blah_thing()
E701: for x in lst: total += x
E701: while t < 10: t = delay()
E701: if foo == 'blah': do_blah_thing()
E701: else: do_non_blah_thing()
E701: try: something()
E701: finally: cleanup()
E701: if foo == 'blah': one(); two(); three()
E702: do_one(); do_two(); do_three()
E703: do_four();  # useless semicolon
E704: def f(x): return 2*x
E731: f = lambda x: 2*x

Line too long (90 > 79 characters)
Open

        >>> # check that using the biggest_cluster_only option without setting cluster_cut
Severity: Minor
Found in pytim/interface.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

        >>> interface = pytim.ITIM(u, alpha=100000.0, max_layers=1,multiproc=False)
Severity: Minor
Found in pytim/interface.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 (99 > 79 characters)
Open

        >>> interface = pytim.ITIM(oxygens, alpha=1.5,max_layers=1,multiproc=False,molecular=False)
Severity: Minor
Found in pytim/interface.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

        ...                 print ("MDAnalysis and mdtraj surface atoms do not coincide")
Severity: Minor
Found in pytim/interface.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

            else: # we still filter out molecules which do not belong to any cluster
Severity: Minor
Found in pytim/interface.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.

At least two spaces before inline comment
Open

            else: # we still filter out molecules which do not belong to any cluster
Severity: Minor
Found in pytim/interface.py by pep8

Separate inline comments by at least two spaces.

An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

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