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File lattice.py has 401 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import numpy as np
import random
import itertools
import sys
Severity: Minor
Found in lattice_mc/lattice.py - About 5 hrs to fix

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

                r = np.array( [ i * sqrt(3) * spacing + sqrt(3)/2 * spacing, ( j * 3 + 0.5 ) * spacing, 0.0 ] )
    Severity: Major
    Found in lattice_mc/init_lattice.py and 1 other location - About 3 hrs to fix
    lattice_mc/init_lattice.py on lines 78..78

    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 71.

    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

                r = np.array( [ i * sqrt(3) * spacing + sqrt(3)/2 * spacing, ( j * 3 + 1.5 ) * spacing, 0.0 ] )
    Severity: Major
    Found in lattice_mc/init_lattice.py and 1 other location - About 3 hrs to fix
    lattice_mc/init_lattice.py on lines 72..72

    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 71.

    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

    File simulation.py has 270 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    from lattice_mc import init_lattice, species, lookup_table

class Simulation:
    """
    Simulation class
    Severity: Minor
    Found in lattice_mc/simulation.py - About 2 hrs to fix

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

                  neighbours = [ grid[ i, j, 0 ], 
                           grid[ i, j, 2 ], 
                           np.roll( grid, -1, axis=0 )[ i, j, 0 ] ]
      Severity: Major
      Found in lattice_mc/init_lattice.py and 1 other location - About 2 hrs to fix
      lattice_mc/init_lattice.py on lines 79..81

      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 50.

      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

                  neighbours = [ grid[ i, j, 1 ],
                           grid[ i, j, 3 ],
                           np.roll( grid, -1, axis=0 )[ i, j, 3 ] ]
      Severity: Major
      Found in lattice_mc/init_lattice.py and 1 other location - About 2 hrs to fix
      lattice_mc/init_lattice.py on lines 73..75

      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 50.

      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

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

          def potential_jumps( self ):
        """
        All nearest-neighbour jumps not blocked by volume exclusion 
        (i.e. from occupied to neighbouring unoccupied sites).
      Severity: Minor
      Found in lattice_mc/lattice.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

      Similar blocks of code found in 3 locations. Consider refactoring.
      Open

              along_y = any( [ s2 in s1.p_neighbours for s1 in edges[2] for s2 in edges[3] ] )
      Severity: Major
      Found in lattice_mc/cluster.py and 2 other locations - About 1 hr to fix
      lattice_mc/cluster.py on lines 96..96
      lattice_mc/cluster.py on lines 98..98

      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 42.

      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 3 locations. Consider refactoring.
      Open

              along_x = any( [ s2 in s1.p_neighbours for s1 in edges[0] for s2 in edges[1] ] )
      Severity: Major
      Found in lattice_mc/cluster.py and 2 other locations - About 1 hr to fix
      lattice_mc/cluster.py on lines 97..97
      lattice_mc/cluster.py on lines 98..98

      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 42.

      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 3 locations. Consider refactoring.
      Open

              along_z = any( [ s2 in s1.p_neighbours for s1 in edges[4] for s2 in edges[5] ] )
      Severity: Major
      Found in lattice_mc/cluster.py and 2 other locations - About 1 hr to fix
      lattice_mc/cluster.py on lines 96..96
      lattice_mc/cluster.py on lines 97..97

      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 42.

      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

          @property
    def old_collective_correlation( self ):
        """
        Returns the collective correlation factor, f_I
      Severity: Major
      Found in lattice_mc/simulation.py and 1 other location - About 1 hr to fix
      lattice_mc/simulation.py on lines 181..201

      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 42.

      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

          @property
    def old_tracer_correlation( self ):
        """
        Deprecated tracer correlation factor for this simulation.
      Severity: Major
      Found in lattice_mc/simulation.py and 1 other location - About 1 hr to fix
      lattice_mc/simulation.py on lines 235..255

      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 42.

      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

      Function connected_sites has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
      Open

          def connected_sites( self, site_labels=None ):
        """
        Searches the lattice to find sets of sites that are contiguously neighbouring.
        Mutually exclusive sets of contiguous sites are returned as Cluster objects.
      Severity: Minor
      Found in lattice_mc/lattice.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 generate_nearest_neighbour_lookup_table has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
      Open

          def generate_nearest_neighbour_lookup_table( self ):
        """
        Construct a look-up table of relative jump probabilities for a nearest-neighbour interaction Hamiltonian.

        Args:
      Severity: Minor
      Found in lattice_mc/lookup_table.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 run has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
      Open

          def run( self, for_time=None ):
        """
        Run the simulation.

        Args:
      Severity: Minor
      Found in lattice_mc/simulation.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 enforce_periodic_boundary_conditions has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def enforce_periodic_boundary_conditions( self ):
        """
        Ensure that all lattice sites are within the central periodic image of the simulation cell.
        Sites that are outside the central simulation cell are mapped back into this cell.
      Severity: Minor
      Found in lattice_mc/lattice.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

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

                  sites.append( lattice_site.Site( grid[ i, j, 1 ], r, neighbours, 0.0, site_labels[1] ) )
      Severity: Major
      Found in lattice_mc/init_lattice.py and 3 other locations - About 45 mins to fix
      lattice_mc/init_lattice.py on lines 70..70
      lattice_mc/init_lattice.py on lines 82..82
      lattice_mc/init_lattice.py on lines 88..88

      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 35.

      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 4 locations. Consider refactoring.
      Open

                  sites.append( lattice_site.Site( grid[ i, j, 0 ], r, neighbours, 0.0, site_labels[0] ) )
      Severity: Major
      Found in lattice_mc/init_lattice.py and 3 other locations - About 45 mins to fix
      lattice_mc/init_lattice.py on lines 76..76
      lattice_mc/init_lattice.py on lines 82..82
      lattice_mc/init_lattice.py on lines 88..88

      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 35.

      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 4 locations. Consider refactoring.
      Open

                  sites.append( lattice_site.Site( grid[ i, j, 3 ], r, neighbours, 0.0, site_labels[3] ) )
      Severity: Major
      Found in lattice_mc/init_lattice.py and 3 other locations - About 45 mins to fix
      lattice_mc/init_lattice.py on lines 70..70
      lattice_mc/init_lattice.py on lines 76..76
      lattice_mc/init_lattice.py on lines 82..82

      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 35.

      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

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

          def __init__( self, number, coordinates, neighbours, energy, label, cn_energies=None ):
      Severity: Minor
      Found in lattice_mc/lattice_site.py - About 45 mins to fix
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