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Marcello-Sega/pytim

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pytim/observables/local_frame.py

Summary

Maintainability
A
1 hr
Test Coverage

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

    def compute(self, inp, kargs=None):
        """ Compute the local reference frame

            :param AtomGroup inp:  the group of atoms that define the surface
            :returns:              a (len(inp),3,3) set of coordinates defining
Severity: Minor
Found in pytim/observables/local_frame.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 compute has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def compute(self, inp, kargs=None):
        """ Compute the local reference frame

            :param AtomGroup inp:  the group of atoms that define the surface
            :returns:              a (len(inp),3,3) set of coordinates defining
Severity: Minor
Found in pytim/observables/local_frame.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 _compute_local_coords has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def _compute_local_coords(self, box):
        local_coords = []
        for i, patch in enumerate(self.patches):
            p = self.tree.data[patch].copy()
            p = self.remove_pbc(p, box)
Severity: Minor
Found in pytim/observables/local_frame.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

TODO found
Open

        # TODO write a version that does not depend on passing an AtomGroup
Severity: Minor
Found in pytim/observables/local_frame.py by fixme

Do not use bare 'except'
Open

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

When catching exceptions, mention specific exceptions when possible.

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

Line too long (84 > 79 characters)
Open

        ...     print(np.array_str((val+1e3)-1e3, precision=2, suppress_small=True))
Severity: Minor
Found in pytim/observables/local_frame.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.

Trailing whitespace
Open

        line with opposite signs for x and y. Could be an instability of
Severity: Minor
Found in pytim/observables/local_frame.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

Ambiguous variable name 'i'
Open

            I = -np.tensordot(dr[:], dr[:], axes=(0, 0)) + \
Severity: Minor
Found in pytim/observables/local_frame.py by pep8

Never use the characters 'l', 'O', or 'I' as variable names.

In some fonts, these characters are indistinguishable from the
numerals one and zero. When tempted to use 'l', use 'L' instead.

Okay: L = 0
Okay: o = 123
Okay: i = 42
E741: l = 0
E741: O = 123
E741: I = 42

Variables can be bound in several other contexts, including class
and function definitions, 'global' and 'nonlocal' statements,
exception handlers, and 'with' and 'for' statements.
In addition, we have a special handling for function parameters.

Okay: except AttributeError as o:
Okay: with lock as L:
Okay: foo(l=12)
Okay: for a in foo(l=12):
E741: except AttributeError as O:
E741: with lock as l:
E741: global I
E741: nonlocal l
E741: def foo(l):
E741: def foo(l=12):
E741: l = foo(l=12)
E741: for l in range(10):
E742: class I(object):
E743: def l(x):

Do not use bare 'except'
Open

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

When catching exceptions, mention specific exceptions when possible.

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

Line too long (80 > 79 characters)
Open

                                   the local axes, with the slice [:2:] defining
Severity: Minor
Found in pytim/observables/local_frame.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("Warning: without having a PYTIM interface or passing")
Severity: Minor
Found in pytim/observables/local_frame.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/local_frame.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/local_frame.py by pep8

When catching exceptions, mention specific exceptions when possible.

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

Trailing whitespace
Open

                UU[2] = -UU[2]
Severity: Minor
Found in pytim/observables/local_frame.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 (87 > 79 characters)
Open

        ...     curv = pytim.observables.Curvature(cutoff=1.,warning=False).compute(pp)
Severity: Minor
Found in pytim/observables/local_frame.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/local_frame.py by pep8

When catching exceptions, mention specific exceptions when possible.

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

There are no issues that match your filters.

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