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src/tools/DumpConfigurations.py

Summary

Maintainability
F
4 days
Test Coverage

File DumpConfigurations.py has 335 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#  Copyright (C) 2016
#      Max Planck Institute for Polymer Research & JGU Mainz
#  Copyright (C) 2012,2013
#      Max Planck Institute for Polymer Research
#  Copyright (C) 2008,2009,2010,2011
Severity: Minor
Found in src/tools/DumpConfigurations.py - About 4 hrs to fix

    Function xyzfilewrite has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
    Open

    def xyzfilewrite(filename, system, append=False, atomtypes={0:'Fe',1:'O',2:'C'}, velocities=False, charge=False):
    """

    This method creates a xyz file with the data from a specific system:
    1. row:         number of the atoms
    Severity: Minor
    Found in src/tools/DumpConfigurations.py - About 3 hrs to fix

    Cognitive Complexity

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

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

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

    Further reading

    Function readxyzr has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

    def readxyzr(filename):
    """
    """

    file = open(filename)
    Severity: Minor
    Found in src/tools/DumpConfigurations.py - About 2 hrs to fix

    Cognitive Complexity

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

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

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

    Further reading

    Function writexyz has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def writexyz(filename, system, velocities = True, unfolded = False, append = False):
    """
    """
    if append:
        file = open(filename,'a')
    Severity: Minor
    Found in src/tools/DumpConfigurations.py - About 1 hr to fix

    Cognitive Complexity

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

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

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

    Further reading

    Function readxyz has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def readxyz(filename):
    """
    """
    file = open(filename)
    line = file.readline()
    Severity: Minor
    Found in src/tools/DumpConfigurations.py - About 55 mins to fix

    Cognitive Complexity

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

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

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

    Further reading

    Function fastwritexyz has 6 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def fastwritexyz(filename, system, velocities = True, unfolded = True, append = False, scale=1.0):
    Severity: Minor
    Found in src/tools/DumpConfigurations.py - About 45 mins to fix

      Function xyzfilewrite has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def xyzfilewrite(filename, system, append=False, atomtypes={0:'Fe',1:'O',2:'C'}, velocities=False, charge=False):
      Severity: Minor
      Found in src/tools/DumpConfigurations.py - About 45 mins to fix

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

        def writexyz(filename, system, velocities = True, unfolded = False, append = False):
        Severity: Minor
        Found in src/tools/DumpConfigurations.py - About 35 mins to fix

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

          def fastwritexyz(filename, system, velocities = True, unfolded = True, append = False, scale=1.0):
    """
    """

    if append:
          Severity: Minor
          Found in src/tools/DumpConfigurations.py - About 35 mins to fix

          Cognitive Complexity

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

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

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

          Further reading

          Function fastreadxyz has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
          Open

          def fastreadxyz(filename):
    """
    """

    file = open(filename)
          Severity: Minor
          Found in src/tools/DumpConfigurations.py - About 25 mins to fix

          Cognitive Complexity

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

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

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

          Further reading

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

              if len(line) == 3:
        Lx = float(line[0])
        Ly = float(line[1])
        Lz = float(line[2])
    else:
          Severity: Major
          Found in src/tools/DumpConfigurations.py and 1 other location - About 6 hrs to fix
          src/tools/DumpConfigurations.py on lines 251..258

          Duplicated Code

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

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

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

          Tuning

          This issue has a mass of 105.

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

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

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

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

          Refactorings

          Further Reading

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

              if len(line) == 3:
        Lx = float(line[0])
        Ly = float(line[1])
        Lz = float(line[2])
    else:
          Severity: Major
          Found in src/tools/DumpConfigurations.py and 1 other location - About 6 hrs to fix
          src/tools/DumpConfigurations.py on lines 110..117

          Duplicated Code

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

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

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

          Tuning

          This issue has a mass of 105.

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

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

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

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

          Refactorings

          Further Reading

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

                  if len(line) > 5:
            xvel.append(float(line[5]))
            yvel.append(float(line[6]))
            zvel.append(float(line[7]))
          Severity: Major
          Found in src/tools/DumpConfigurations.py and 1 other location - About 2 hrs to fix
          src/tools/DumpConfigurations.py on lines 182..185

          Duplicated Code

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

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

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

          Tuning

          This issue has a mass of 58.

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

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

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

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

          Refactorings

          Further Reading

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

                  if len(line) > 5 and len(line) <= 8 and len(line) != 6:
            xvel.append(float(line[5]))
            yvel.append(float(line[6]))
            zvel.append(float(line[7]))
          Severity: Major
          Found in src/tools/DumpConfigurations.py and 1 other location - About 2 hrs to fix
          src/tools/DumpConfigurations.py on lines 136..139

          Duplicated Code

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

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

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

          Tuning

          This issue has a mass of 58.

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

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

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

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

          Refactorings

          Further Reading

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

                      if unfolded == False:
                xpos   = particle.pos[0]
                ypos   = particle.pos[1]
                zpos   = particle.pos[2]
            else:
          Severity: Major
          Found in src/tools/DumpConfigurations.py and 1 other location - About 2 hrs to fix
          src/tools/io_extended.py on lines 146..154

          Duplicated Code

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

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

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

          Tuning

          This issue has a mass of 52.

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

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

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

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

          Refactorings

          Further Reading

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

                  if len(line) == 7 or len(line)==4:
            line.insert(1,'0')
          Severity: Major
          Found in src/tools/DumpConfigurations.py and 1 other location - About 1 hr to fix
          src/tools/DumpConfigurations.py on lines 267..268

          Duplicated Code

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

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

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

          Tuning

          This issue has a mass of 39.

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

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

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

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

          Refactorings

          Further Reading

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

                  if len(line) == 7 or len(line)==4:
            line.insert(1,'0')
          Severity: Major
          Found in src/tools/DumpConfigurations.py and 1 other location - About 1 hr to fix
          src/tools/DumpConfigurations.py on lines 129..130

          Duplicated Code

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

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

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

          Tuning

          This issue has a mass of 39.

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

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

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

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

          Refactorings

          Further Reading

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