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trajpy/trajpy.py

Summary

Maintainability
C
7 hrs
Test Coverage

File trajpy.py has 414 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import numpy as np
from scipy.stats import linregress
import trajpy.auxiliar_functions as aux
from typing import Union, List, Dict, Tuple
import warnings
Severity: Minor
Found in trajpy/trajpy.py - About 5 hrs to fix

    Function __init__ has 28 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def __init__(self, trajectory: np.ndarray=np.zeros((1, 2)), box_length: int = None, **params) -> None:
        """
        Initialization function that can be left blank for using staticmethods.
        It can be initialized with an array with shape (N, dim)
        where dim is the number of spatial dimensions plus the time component.
    Severity: Minor
    Found in trajpy/trajpy.py - About 1 hr to fix

      Comparison to none should be 'if cond is not none:'
      Open

              if box_length != None:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Comparison to singletons should use "is" or "is not".

      Comparisons to singletons like None should always be done
with "is" or "is not", never the equality operators.

Okay: if arg is not None:
E711: if arg != None:
E711: if None == arg:
E712: if arg == True:
E712: if False == arg:

Also, beware of writing if x when you really mean if x is not None
-- e.g. when testing whether a variable or argument that defaults to
None was set to some other value.  The other value might have a type
(such as a container) that could be false in a boolean context!

      Line too long (116 > 79 characters)
      Wontfix

              self.vacf = self.stationary_velocity_correlation_(self.velocity, self._t,np.arange(int(len(self.velocity))))
      Severity: Minor
      Found in trajpy/trajpy.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 (102 > 79 characters)
      Open

              #self.confinement_probability = self.confinement_probability_(2,self.diffusivity, self._t[-1])
      Severity: Minor
      Found in trajpy/trajpy.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.

      Too many blank lines (2)
      Open

              features = (str(np.round(self.anomalous_exponent, 4)) + ',' +
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Separate top-level function and class definitions with two blank lines.

      Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

      Line too long (87 > 79 characters)
      Wontfix

                  msd[n] = np.sum(np.power(spatial_components[n] - spatial_components[0], 2))
      Severity: Minor
      Found in trajpy/trajpy.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 (80 > 79 characters)
      Wontfix

              # calculating the distance between each pair of points in the trajectory
      Severity: Minor
      Found in trajpy/trajpy.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 (88 > 79 characters)
      Open

          def gyration_radius_(trajectory: np.ndarray) -> Dict[str, Union[np.ndarray, float]]:
      Severity: Minor
      Found in trajpy/trajpy.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

                                  'eigenvectors':eigenvectors}
      Severity: Minor
      Found in trajpy/trajpy.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 (85 > 79 characters)
      Open

                                       (2. * np.power(eigenvalues[0] + eigenvalues[1], 2)))
      Severity: Minor
      Found in trajpy/trajpy.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 (80 > 79 characters)
      Wontfix

                  raise IndexError("This function is meant for 2D trajectories only.")
      Severity: Minor
      Found in trajpy/trajpy.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

                  return velocity_description: returns a dictionary where the values are bounded
      Severity: Minor
      Found in trajpy/trajpy.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

      Trailing whitespace
      Open

              standard_deviation = np.std(velocity,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              ran = np.abs(np.max(velocity,axis=0) - np.min(velocity,axis=0))
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace around operator
      Open

                  if max(vel_freq)==1:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Surround operators with a single space on either side.

      - Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

      Continuation line under-indented for visual indent
      Open

                      'mode':mode,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Missing whitespace after ':'
      Open

                      'variance':variance,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Whitespace before ']'
      Open

          def frequency_spectrum_(position: np.ndarray, time: np.ndarray) -> Dict[str, Union[np.ndarray, float] ]:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Avoid extraneous whitespace.

      Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.

Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })

E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x

      Trailing whitespace
      Open

              limit = np.arange(1,np.floor(n/2),dtype='int')
      Severity: Minor
      Found in trajpy/trajpy.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

      Trailing whitespace
      Open

              power = power[1:max(limit),:]
      Severity: Minor
      Found in trajpy/trajpy.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

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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 (120 > 79 characters)
      Wontfix

              :math:`m` and :math:`n` assume the values of the corresponding coordinates along the directions :math:`x, y, z`.
      Severity: Minor
      Found in trajpy/trajpy.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.

      Inline comment should start with '# '
      Open

              g_radius = np.sqrt(np.abs(r_gyr/trajectory.size)) #gyration radius tensor
      Severity: Minor
      Found in trajpy/trajpy.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

      At least two spaces before inline comment
      Open

              return gyration_radius #dictionary
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              self.kurtosis = self.kurtosis_(self._r, self.eigenvectors[:,0])
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Trailing whitespace
      Open

              Takes the eigenvalues of the gyration radius tensor
      Severity: Minor
      Found in trajpy/trajpy.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 (148 > 79 characters)
      Open

              where :math:`N` is the number of segments of the trajectory, :math:`\\mathbf{r}_i` is the :math:`i`-th position vector along the trajectory,
      Severity: Minor
      Found in trajpy/trajpy.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

                  eigenvalues[::-1].sort() # the eigenvalues must the in the descending order
      Severity: Minor
      Found in trajpy/trajpy.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 (93 > 79 characters)
      Open

              eigenvectors = eigenvectors[:,id] #eigenvectors corresponding to the descending order
      Severity: Minor
      Found in trajpy/trajpy.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

          def green_kubo_(velocity: np.ndarray, t:np.ndarray, vacf:np.ndarray) -> float:
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

              eigenvectors = eigenvectors[:,id] #eigenvectors corresponding to the descending order
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Inline comment should start with '# '
      Open

              eigenvectors = eigenvectors[:,id] #eigenvectors corresponding to the descending order
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              mean = np.mean(velocity,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (82 > 79 characters)
      Wontfix

                  summation += np.sqrt(np.dot(trajectory[i_pos] - trajectory[i_pos - 1],
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

              skewness = (sum((velocity[:,:]-mean)**3)/len(velocity))/((sum((velocity[:,:]-mean)**2)/len(velocity))**1.5)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (137 > 79 characters)
      Wontfix

              where :math:`\\langle r^p \\rangle` is the mean position of the projected trajectory and :math:`\\sigma_{r^p}^2` is the variance.
      Severity: Minor
      Found in trajpy/trajpy.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

                  along with the frequency spectrum and their amplituded
      Severity: Minor
      Found in trajpy/trajpy.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 (92 > 79 characters)
      Wontfix

              The kurtosis measures the peakiness of the distribution of points in the trajectory.
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ':'
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (97 > 79 characters)
      Open

          def velocity_description_(velocity: np.ndarray) -> Dict[str, Union[np.ndarray, float, str] ]:
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

              median = np.median(velocity,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              kurtosis = (sum((velocity[:,:]-mean)**4)/len(velocity))/(standard_deviation**4) - 3
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

                  vel_values, vel_freq = np.unique(np.round(velocity[:,col],2), return_counts=True,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Continuation line under-indented for visual indent
      Open

                      'median':median,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Continuation line under-indented for visual indent
      Open

                      'variance':variance,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Continuation line under-indented for visual indent
      Open

                      'skewness':skewness}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              self.diffusivity = self.green_kubo_(self.velocity,self._t,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (102 > 79 characters)
      Wontfix

          def msd_time_averaged_(spatial_components: np.ndarray, tau: Union[np.ndarray, int]) -> np.ndarray:
      Severity: Minor
      Found in trajpy/trajpy.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.

      Inline comment should start with '# '
      Open

              eigenvalues,eigenvectors = np.linalg.eig(g_radius) #computes the eigenvalues and eigenvectors
      Severity: Minor
      Found in trajpy/trajpy.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

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Trailing whitespace
      Open

                  return frequency_spectrum: returns a dictionary containing the dominant amplitude and the associated frequency
      Severity: Minor
      Found in trajpy/trajpy.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

      Continuation line under-indented for visual indent
      Open

                                  self.stationary_velocity_correlation_(self.velocity, self._t,np.arange(int(len(self.velocity)))))
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ':'
      Open

                                  'eigenvalues':eigenvalues,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              kurtosis = (1./N) * np.sum(np.power(r_projection,4))/np.power(std_, 4)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau)+tau,axis=0),
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau),axis=0)))+
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Whitespace before ']'
      Open

          def velocity_description_(velocity: np.ndarray) -> Dict[str, Union[np.ndarray, float, str] ]:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Avoid extraneous whitespace.

      Avoid extraneous whitespace in these situations:
- Immediately inside parentheses, brackets or braces.
- Immediately before a comma, semicolon, or colon.

Okay: spam(ham[1], {eggs: 2})
E201: spam( ham[1], {eggs: 2})
E201: spam(ham[ 1], {eggs: 2})
E201: spam(ham[1], { eggs: 2})
E202: spam(ham[1], {eggs: 2} )
E202: spam(ham[1 ], {eggs: 2})
E202: spam(ham[1], {eggs: 2 })

E203: if x == 4: print x, y; x, y = y , x
E203: if x == 4: print x, y ; x, y = y, x
E203: if x == 4 : print x, y; x, y = y, x

      Continuation line under-indented for visual indent
      Open

                      'kurtosis':kurtosis,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Line too long (117 > 79 characters)
      Open

                  Computes the frequency spectrum for each spatial coordinate by using the Fast Fourier Transform algorithm
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

              limit = np.arange(1,np.floor(n/2),dtype='int')
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (106 > 79 characters)
      Open

          def __init__(self, trajectory: np.ndarray=np.zeros((1, 2)), box_length: int = None, **params) -> None:
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      At least two spaces before inline comment
      Open

              eigenvalues,eigenvectors = np.linalg.eig(g_radius) #computes the eigenvalues and eigenvectors
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ':'
      Open

              gyration_radius = {'gyration tensor':g_radius,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Trailing whitespace
      Open

              return gyration_radius #dictionary
      Severity: Minor
      Found in trajpy/trajpy.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 (83 > 79 characters)
      Wontfix

                                              trajectory[i_pos] - trajectory[i_pos - 1]))
      Severity: Minor
      Found in trajpy/trajpy.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 (80 > 79 characters)
      Wontfix

                                            trajectory[-1] - trajectory[0]))/summation
      Severity: Minor
      Found in trajpy/trajpy.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 (110 > 79 characters)
      Open

          def stationary_velocity_correlation_(velocity: np.ndarray, t: np.ndarray, taus: np.ndarray) -> np.ndarray:
      Severity: Minor
      Found in trajpy/trajpy.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

              :param taus: single or array of non-negative integer values representing the time lag
      Severity: Minor
      Found in trajpy/trajpy.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

                  :return diffusivity: diffusion constant obtained by the Green-Kubo relation
      Severity: Minor
      Found in trajpy/trajpy.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 (91 > 79 characters)
      Wontfix

              kurtosis = (sum((velocity[:,:]-mean)**4)/len(velocity))/(standard_deviation**4) - 3
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ':'
      Open

                      'mode':mode,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              fourier = np.fft.fft(position,axis=0,n=n)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Trailing whitespace
      Open

              power = 2*np.abs(fourier)/n
      Severity: Minor
      Found in trajpy/trajpy.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

      Trailing whitespace
      Open

              dominant_frequency = f[np.argmax(power[:max(limit)],axis=0)]
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ':'
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace around parameter equals
      Open

          def __init__(self, trajectory: np.ndarray=np.zeros((1, 2)), box_length: int = None, **params) -> None:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Don't use spaces around the '=' sign in function arguments.

      Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

      Line too long (131 > 79 characters)
      Open

              where :math:`\\tau` is the time interval (time lag) between the two positions and :math:`T is total trajectory time length.
      Severity: Minor
      Found in trajpy/trajpy.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)
      Wontfix

              d_max = np.sqrt(np.max(dr))  # maximum distance between any two points of the trajectory
      Severity: Minor
      Found in trajpy/trajpy.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 (104 > 79 characters)
      Open

              diffusivity :math:`D` being trapped in the interval :math:`[-r0, +r0]` after a period of time t.
      Severity: Minor
      Found in trajpy/trajpy.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

                  Calculates the efficiency of the movement, a measure that is related to
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              skewness = (sum((velocity[:,:]-mean)**3)/len(velocity))/((sum((velocity[:,:]-mean)**2)/len(velocity))**1.5)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              mode = np.empty(velocity.shape[1],dtype=object)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (82 > 79 characters)
      Wontfix

              :param spatial_components: array containing trajectory spatial coordinates
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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 (89 > 79 characters)
      Wontfix

                                           + np.log(d_max * np.power(length, -1))), decimals=2)
      Severity: Minor
      Found in trajpy/trajpy.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 (91 > 79 characters)
      Wontfix

                      dr[n_distance] = np.sum(np.power(trajectory[i_pos] - trajectory[j_pos], 2))
      Severity: Minor
      Found in trajpy/trajpy.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

              f = (1/(dt*n))*np.arange(n)
      Severity: Minor
      Found in trajpy/trajpy.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

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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 (114 > 79 characters)
      Wontfix

              :return gyration_radius: gyration_radius dictionary containing the tensor, eigenvalues in descending order
      Severity: Minor
      Found in trajpy/trajpy.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.

      Continuation line under-indented for visual indent
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau)+tau,axis=0),
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Line too long (84 > 79 characters)
      Open

                  asymmetry = - np.log(1. - np.power(eigenvalues[0] - eigenvalues[1], 2) /
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau),axis=0)))+
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

                  eigenvalues =  np.concatenate((eigenvalues,np.array([0.0])),axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (115 > 79 characters)
      Wontfix

              skewness = (sum((velocity[:,:]-mean)**3)/len(velocity))/((sum((velocity[:,:]-mean)**2)/len(velocity))**1.5)
      Severity: Minor
      Found in trajpy/trajpy.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 (85 > 79 characters)
      Open

          def confinement_probability_(r0: int, D: float, t: float, N: int = 100) -> float:
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace around operator
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau),axis=0)))+
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Surround operators with a single space on either side.

      - Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

      Line too long (100 > 79 characters)
      Wontfix

                  vel_values, vel_freq = np.unique(np.round(velocity[:,col],2), return_counts=True,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

                  vel_values, vel_freq = np.unique(np.round(velocity[:,col],2), return_counts=True,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

                  vel_values, vel_freq = np.unique(np.round(velocity[:,col],2), return_counts=True,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (120 > 79 characters)
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ':'
      Open

                      'standard_deviation':standard_deviation,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ':'
      Open

                      'skewness':skewness}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              fourier = np.fft.fft(position,axis=0,n=n)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Trailing whitespace
      Open

              dominant_amp = np.max(power[:max(limit)],axis=0)
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              dominant_amp = np.max(power[:max(limit)],axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ':'
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (84 > 79 characters)
      Open

              self.gyration_radius = self.gyration_radius_(self._r).get('gyration tensor')
      Severity: Minor
      Found in trajpy/trajpy.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 (125 > 79 characters)
      Open

                                  self.stationary_velocity_correlation_(self.velocity, self._t,np.arange(int(len(self.velocity)))))
      Severity: Minor
      Found in trajpy/trajpy.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.

      Block comment should start with '# '
      Open

              #self.confinement_probability = self.confinement_probability_(2,self.diffusivity, self._t[-1])
      Severity: Minor
      Found in trajpy/trajpy.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 (143 > 79 characters)
      Open

              where :math:`N` is the number of trajectories,  :math:`\\mathbf{r}_n(t)` is the position of the trajectory :math:`n` at time :math:`t`.
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ':'
      Open

                                  'eigenvectors':eigenvectors}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (138 > 79 characters)
      Open

                  a^2 = 1 - 3 \\frac{\\lambda_1\\lambda_2 + \\lambda_2 \\lambda_3 + \\lambda_3\\lambda_1 }{(\\lambda_1+\\lambda_2+\\lambda_3)^2}
      Severity: Minor
      Found in trajpy/trajpy.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 (146 > 79 characters)
      Wontfix

              We obtain the kurtosis by projecting each position of the trajectory along the main principal eigenvector of the radius of gyration tensor
      Severity: Minor
      Found in trajpy/trajpy.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.

      Too many blank lines (2)
      Open

              return kurtosis
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Separate top-level function and class definitions with two blank lines.

      Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

      Line too long (81 > 79 characters)
      Wontfix

                  g(n) = \\frac{ \\langle r_n^4 \\rangle }{2 \\langle r_n^2 \\rangle^2}
      Severity: Minor
      Found in trajpy/trajpy.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

                      np.take(a=velocity,indices=np.arange(0,N-tau),axis=0)))+
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              standard_deviation = np.std(velocity,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              ran = np.abs(np.max(velocity,axis=0) - np.min(velocity,axis=0))
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (108 > 79 characters)
      Open

          def frequency_spectrum_(position: np.ndarray, time: np.ndarray) -> Dict[str, Union[np.ndarray, float] ]:
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

                                  self.stationary_velocity_correlation_(self.velocity, self._t,np.arange(int(len(self.velocity)))))
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (82 > 79 characters)
      Wontfix

              :param spatial_components: array containing trajectory spatial coordinates
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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 (116 > 79 characters)
      Open

                  \\beta = \\frac{  \\partial \\log{ \\left( \\langle x^2 \\rangle   \\right)} }{ \\partial (\\log{(t)}) }
      Severity: Minor
      Found in trajpy/trajpy.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

              eigenvalues[::-1].sort() # the eigenvalues must the in the descending order
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau),axis=0)))+
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ':'
      Open

          def green_kubo_(velocity: np.ndarray, t:np.ndarray, vacf:np.ndarray) -> float:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ':'
      Open

              velocity_description = {'mean':mean,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Trailing whitespace
      Open

              fourier = np.fft.fft(position,axis=0,n=n)
      Severity: Minor
      Found in trajpy/trajpy.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

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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 (95 > 79 characters)
      Wontfix

                  \\langle r^2 \\rangle_{\\tau_1, \\tau_2} = \\frac{\\langle r^2 \\rangle_{\\tau_1 }}
      Severity: Minor
      Found in trajpy/trajpy.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

              g_radius = np.sqrt(np.abs(r_gyr/trajectory.size)) #gyration radius tensor
      Severity: Minor
      Found in trajpy/trajpy.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 (101 > 79 characters)
      Open

              eigenvalues,eigenvectors = np.linalg.eig(g_radius) #computes the eigenvalues and eigenvectors
      Severity: Minor
      Found in trajpy/trajpy.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

              eigenvectors = eigenvectors[:,id] #eigenvectors corresponding to the descending order
      Severity: Minor
      Found in trajpy/trajpy.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

      Inline comment should start with '# '
      Open

              return gyration_radius #dictionary
      Severity: Minor
      Found in trajpy/trajpy.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 (97 > 79 characters)
      Open

              Calculates the trajectory anisotropy using the eigenvalues of the gyration radius tensor.
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau)+tau,axis=0),
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace around operator
      Open

                      mode[col] = vel_values[np.where(vel_freq==max(vel_freq))]
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Surround operators with a single space on either side.

      - Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ':'
      Open

                      'range':ran,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (84 > 79 characters)
      Wontfix

                  self._t, self._r = np.asarray(trajectory[0]), np.asarray(trajectory[1:])
      Severity: Minor
      Found in trajpy/trajpy.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

              self._r0 = None  # maximum distance between any two points of the trajectory
      Severity: Minor
      Found in trajpy/trajpy.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 (80 > 79 characters)
      Wontfix

              self.anomalous_exponent = self.anomalous_exponent_(self.msd_ea, self._t)
      Severity: Minor
      Found in trajpy/trajpy.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.

      Too many blank lines (2)
      Open

          @staticmethod
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Separate top-level function and class definitions with two blank lines.

      Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

      Line too long (80 > 79 characters)
      Wontfix

                      dx.append(spatial_components[n + value] - spatial_components[n])
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              eigenvalues,eigenvectors = np.linalg.eig(g_radius) #computes the eigenvalues and eigenvectors
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Continuation line over-indented for visual indent
      Open

                                  'eigenvalues':eigenvalues,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Line too long (94 > 79 characters)
      Open

               :math:`r_i^p = \\mathbf{r} \\cdot \\hat{e}_1` and then calculating the quartic moment
      Severity: Minor
      Found in trajpy/trajpy.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 (85 > 79 characters)
      Open

                  Computes the stationary velocity autocorrelation function by time average
      Severity: Minor
      Found in trajpy/trajpy.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.

      Missing whitespace after ','
      Open

                      np.take(a=velocity,indices=np.arange(0,N-tau)+tau,axis=0),
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Trailing whitespace
      Open

                  :return diffusivity: diffusion constant obtained by the Green-Kubo relation
      Severity: Minor
      Found in trajpy/trajpy.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 (90 > 79 characters)
      Open

                  return velocity_description: returns a dictionary where the values are bounded
      Severity: Minor
      Found in trajpy/trajpy.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.

      Continuation line under-indented for visual indent
      Open

                      'standard_deviation':standard_deviation,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Line too long (83 > 79 characters)
      Wontfix

                  raise TypeError('trajectory receives an array or a filename as input.')
      Severity: Minor
      Found in trajpy/trajpy.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 (91 > 79 characters)
      Open

                  msd[time_lag] = np.sum(np.power(dx, 2)) / (spatial_components.size - value + 1)
      Severity: Minor
      Found in trajpy/trajpy.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)
      Wontfix

              g_radius = np.sqrt(np.abs(r_gyr/trajectory.size)) #gyration radius tensor
      Severity: Minor
      Found in trajpy/trajpy.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.

      Inline comment should start with '# '
      Open

              eigenvalues = eigenvalues[id] #eigenvalues in descending order
      Severity: Minor
      Found in trajpy/trajpy.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 (87 > 79 characters)
      Wontfix

                  eigenvalues[::-1].sort() # the eigenvalues must the in the descending order
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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 (83 > 79 characters)
      Open

              eigenvalues[::-1].sort() # the eigenvalues must the in the descending order
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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 (99 > 79 characters)
      Open

                  Computes the main features of the velocity distribuition: mean, median, mode, variance,
      Severity: Minor
      Found in trajpy/trajpy.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.

      Continuation line under-indented for visual indent
      Open

                      'range':ran,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Missing whitespace after ','
      Open

              limit = np.arange(1,np.floor(n/2),dtype='int')
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ','
      Open

              dominant_frequency = f[np.argmax(power[:max(limit)],axis=0)]
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace after ':'
      Open

              frequency_spectrum = {'dominant frequency':dominant_frequency,'dominant amplitude':dominant_amp,'x':f,'y':power}
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Missing whitespace around parameter equals
      Open

          def __init__(self, trajectory: np.ndarray=np.zeros((1, 2)), box_length: int = None, **params) -> None:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Don't use spaces around the '=' sign in function arguments.

      Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

      Missing whitespace after ','
      Open

              self.vacf = self.stationary_velocity_correlation_(self.velocity, self._t,np.arange(int(len(self.velocity))))
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (143 > 79 characters)
      Open

                  \\langle \\mathbf{r}_{\\tau}^2 \\rangle = \\frac{1}{T-\\tau} \\sum_{t=1}^{N-\\tau} |\\mathbf{x}_{t+\\tau} - \\mathbf{x}_{\\tau} |^2
      Severity: Minor
      Found in trajpy/trajpy.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 (158 > 79 characters)
      Open

                  R_{mn} =  \\frac{1}{2N^2} \\sum_{i=1}^N \\sum_{j=1}^N \\left( r_{m}^{(i)} -  r_{m}^{(j)}  \\right)\\left( r_{n}^{(i)} -  r_{n}^{(j)} \\right)\\, ,
      Severity: Minor
      Found in trajpy/trajpy.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

              id = eigenvalues.argsort()[::-1]
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

                  eigenvalues =  np.concatenate((eigenvalues,np.array([0.0])),axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Multiple spaces after operator
      Open

                  eigenvalues =  np.concatenate((eigenvalues,np.array([0.0])),axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Avoid extraneous whitespace around an operator.

      Okay: a = 12 + 3
E221: a = 4  + 5
E222: a = 4 +  5
E223: a = 4\t+ 5
E224: a = 4 +\t5

      Line too long (122 > 79 characters)
      Open

                  K = \\frac{1}{N} \\sum_{i=1}^N \\frac{ \\left(r_i^p - \\langle r^p \\rangle \\right)^4}{\\sigma_{r^p}^4} \\, ,
      Severity: Minor
      Found in trajpy/trajpy.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 (85 > 79 characters)
      Wontfix

              :return time_averaged_corr_velocity: velocity autocorrelation function output
      Severity: Minor
      Found in trajpy/trajpy.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.

      Expected 2 blank lines, found 1
      Open

      class Trajectory(object):
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Separate top-level function and class definitions with two blank lines.

      Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

      Missing whitespace after ':'
      Open

          def green_kubo_(velocity: np.ndarray, t:np.ndarray, vacf:np.ndarray) -> float:
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (112 > 79 characters)
      Wontfix

                  \\langle \\mathbf{r}^2 \\rangle (t) = \\frac{1}{N-1} \\sum_{n=1}^N |\\mathbf{x}_{n}-\\mathbf{x}_0|^2
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Trailing whitespace
      Open

              mean = np.mean(velocity,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.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

      At least two spaces before inline comment
      Open

              eigenvalues = eigenvalues[id] #eigenvalues in descending order
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              variance = np.var(velocity,axis=0)
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (115 > 79 characters)
      Open

                  a = - \\log{ \\left(1 - \\frac{ ( \\lambda_1 - \\lambda_2)^2}{2 ( \\lambda_1 + \\lambda_2)^2} \\right)}
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Trailing whitespace
      Open

              mode = np.empty(velocity.shape[1],dtype=object)
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ':'
      Open

                      'median':median,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ':'
      Open

                      'kurtosis':kurtosis,
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      Line too long (122 > 79 characters)
      Wontfix

                  return frequency_spectrum: returns a dictionary containing the dominant amplitude and the associated frequency
      Severity: Minor
      Found in trajpy/trajpy.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.

      Blank line contains whitespace
      Open
      Severity: Minor
      Found in trajpy/trajpy.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

      Missing whitespace after ','
      Open

              power = power[1:max(limit),:]
      Severity: Minor
      Found in trajpy/trajpy.py by pep8

      Each comma, semicolon or colon should be followed by whitespace.

      Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

      There are no issues that match your filters.

      Category
      Status