Sign upLogin

Marcello-Sega/pytim

View on GitHub
Star
pytim/datafiles/__init__.py

Summary

Maintainability
A
3 hrs
Test Coverage

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

    def _vdwradii_gmx(self, filename):
        with open(filename) as f:
            input_type = 'sigeps'
            content = f.read()
            if re.match('.*name.*c6 *c12.*', content.replace('\n', ' ')):
Severity: Minor
Found in pytim/datafiles/__init__.py by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

File __init__.py has 262 lines of code (exceeds 250 allowed). Consider refactoring.
Open

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Location of data files for Pytim examples and tests
====================================================
Severity: Minor
Found in pytim/datafiles/__init__.py - About 2 hrs to fix

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

    @staticmethod
    def fetch(name, tmpdir=None):
        """ Fetch a sample trajectory from the github repository.

            Have a look at https://github.com/Marcello-Sega/pytim/raw/extended_datafiles/files/
Severity: Minor
Found in pytim/datafiles/__init__.py by radon

Cyclomatic Complexity

Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

Construct Effect on CC Reasoning
if +1 An if statement is a single decision.
elif +1 The elif statement adds another decision.
else +0 The else statement does not cause a new decision. The decision is at the if.
for +1 There is a decision at the start of the loop.
while +1 There is a decision at the while statement.
except +1 Each except branch adds a new conditional path of execution.
finally +0 The finally block is unconditionally executed.
with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
assert +1 The assert statement internally roughly equals a conditional statement.
Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

Source: http://radon.readthedocs.org/en/latest/intro.html

Function _vdwradii_gmx has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def _vdwradii_gmx(self, filename):
        with open(filename) as f:
            input_type = 'sigeps'
            content = f.read()
            if re.match('.*name.*c6 *c12.*', content.replace('\n', ' ')):
Severity: Minor
Found in pytim/datafiles/__init__.py - About 1 hr to fix

Cognitive Complexity

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

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

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

Further reading

Remove this commented out code.
Open

        #labels = [label for label, val in self.type.iteritems() if val == name]
Severity: Major
Found in pytim/datafiles/__init__.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Line too long (81 > 79 characters)
Open

    "AMBER03_TOP",  # AMBER03 nonbonded parameters, from the gromacs distribution
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (103 > 79 characters)
Open

        urlbase_md5 = 'https://raw.githubusercontent.com/Marcello-Sega/pytim/extended_datafiles/files/'
Severity: Minor
Found in pytim/datafiles/__init__.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)
Open

        #labels = [label for label, val in self.type.iteritems() if val == name]
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

WATER_DROPLET_CYLINDRICAL_XTC = resource_filename('pytim', 'data/water_droplet_cylindrical.xtc')
Severity: Minor
Found in pytim/datafiles/__init__.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 (95 > 79 characters)
Open

            Have a look at https://github.com/Marcello-Sega/pytim/raw/extended_datafiles/files/
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (89 > 79 characters)
Open

# NOTE: to add a new datafile, make sure it is listed in setup.py (in the root directory)
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Do not use bare 'except'
Open

except:
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

When catching exceptions, mention specific exceptions when possible.

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

Line too long (105 > 79 characters)
Open

pytim_data.add('ANTAGONISTIC_GRO', 'conf', 'GRO', '3-Methylpyridine, Sodium Tetraphenylborate and water')
Severity: Minor
Found in pytim/datafiles/__init__.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

    "G43A1_TOP",  # GROMOS 43a1 nonbonded parameters, from the gromacs distribution
Severity: Minor
Found in pytim/datafiles/__init__.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 (90 > 79 characters)
Open

            checking presence of a cached copy... not found. Fetching remote file... done.
Severity: Minor
Found in pytim/datafiles/__init__.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

        #labels = [label for label, val in self.type.iteritems() if val == name]
Severity: Minor
Found in pytim/datafiles/__init__.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 (84 > 79 characters)
Open

    "METHANOL_GRO",  # methanol/vapour interface with molecules in the  vapour phase
Severity: Minor
Found in pytim/datafiles/__init__.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 (100 > 79 characters)
Open

    "WATER_DROPLET_CYLINDRICAL_XTC",  # GROMACS 2 frames trajectory, SPC/E water droplet on graphite
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (81 > 79 characters)
Open

    "WATER_LMP_DATA",  # LAMMPS topology for WATER_LAMMPS, water/vapour interface
Severity: Minor
Found in pytim/datafiles/__init__.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

    "CHARMM27_TOP",  # CHARM27 nonbonded parameters, from the gromacs distribution
Severity: Minor
Found in pytim/datafiles/__init__.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

        urlbase = 'https://github.com/Marcello-Sega/pytim/raw/extended_datafiles/files/'
Severity: Minor
Found in pytim/datafiles/__init__.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

    "WATER_DROPLET_CYLINDRICAL_GRO",  # GROMACS single frame, SPC/E water droplet on graphite
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (81 > 79 characters)
Open

    "WATER_520K_GRO",  # GROMACS single frame, SPC/E water/vapour interface,520 K
Severity: Minor
Found in pytim/datafiles/__init__.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

WATER_DROPLET_CYLINDRICAL_GRO = resource_filename('pytim', 'data/water_droplet_cylindrical.gro')
Severity: Minor
Found in pytim/datafiles/__init__.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

    "CCL4_WATER_GRO",  # GROMACS single frame, carbon tetrachloride / water interface
Severity: Minor
Found in pytim/datafiles/__init__.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 (95 > 79 characters)
Open

            >>> WATERSMALL_TRR = pytim.datafiles.pytim_data.fetch('WATERSMALL_TRR',tmpdir='./')
Severity: Minor
Found in pytim/datafiles/__init__.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.

There are no issues that match your filters.

Category
Status