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

    for node in nodes:
        for i in range(len(node.children)-1):
            if getattr(node.children[i],'data','')=='multiply' and getattr(node.children[i+1],'data','')=='term':
                collapsible = True
                insert_this = node.children[i+1].children
Severity: Major
Found in wc_rules/expressions/parse.py and 1 other location - About 3 days to fix
wc_rules/expressions/parse.py on lines 140..159

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 319.

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

    for node in nodes:
        for i in range(len(node.children)-1):
            if getattr(node.children[i],'data','')=='add' and getattr(node.children[i+1],'data','')=='sum':
                collapsible = True
                insert_this = node.children[i+1].children
Severity: Major
Found in wc_rules/expressions/parse.py and 1 other location - About 3 days to fix
wc_rules/expressions/parse.py on lines 105..124

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 319.

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 simplify_tree has a Cognitive Complexity of 77 (exceeds 5 allowed). Consider refactoring.
Open

def simplify_tree(tree): 
    '''
    # PURPOSE: simplify and standardize expressions using arithmetic rules
    # Rules for simplification
    # parent ->factor -> noflip,item ==> parent -> item AKA +x ==> x
Severity: Minor
Found in wc_rules/expressions/parse.py - About 1 day 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 2 locations. Consider refactoring.
Open

def build_receptor(contents=['alpha', 'beta', 'gamma']):
    classes, names, edges = [Receptor], ['receptor'], []
    if 'alpha' in contents:
        classes.append(Alpha)
        names.append('alpha')
Severity: Major
Found in examples/fceri_ji/submodels2/graphs.py and 1 other location - About 1 day to fix
examples/fceri_ji/submodels2/graphs.py on lines 36..50

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 163.

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

def build_Syk(contents=['tsh2','linker','aloop']):
    classes, names, edges = [Syk], ['syk'], []
    if 'tsh2' in contents:
        classes.append(TandemSH2)
        names.append('tsh2')
Severity: Major
Found in examples/fceri_ji/submodels2/graphs.py and 1 other location - About 1 day to fix
examples/fceri_ji/submodels2/graphs.py on lines 17..31

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 163.

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

def directed_square():
    k = [K(x) for x in 'abcd']
    for i in range(-1,len(k)-1):
        k[i].x = k[i+1]
    seed_node,nsyms = k[0], len('abcd')
Severity: Major
Found in wc_rules/graph/examples.py and 1 other location - About 6 hrs to fix
wc_rules/graph/examples.py on lines 69..76

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 107.

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

def directed_wheel():
    #edges: a->b->c->d->e->a
    k = [K(x) for x in 'abcde']
    for i in range(-1,len(k)-1):
        k[i].x = k[i+1]
Severity: Major
Found in wc_rules/graph/examples.py and 1 other location - About 6 hrs to fix
wc_rules/graph/examples.py on lines 53..59

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 107.

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 attach_edgeattr_methods has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
Open

    def attach_edgeattr_methods(self,attr):
        def add_edge_fn(self,*args):
            targets = deque()
            for arg in args:
                if isinstance(arg,list):
Severity: Minor
Found in wc_rules/schema/actions.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

BaseClass has 25 functions (exceeds 20 allowed). Consider refactoring.
Open

class BaseClass(core.Model,ActionMixin):
    ''' Base class for building objects '''
    id = IdAttribute()

    def __init__(self, *args, **kwargs):
Severity: Minor
Found in wc_rules/schema/base.py - About 2 hrs to fix

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

                    if spare[0] in big and spare[3] in small:
                    new_tour = self.link(big,small,spare[0],spare[3])
    Severity: Major
    Found in wc_rules/graph/euler_tour.py and 1 other location - About 2 hrs to fix
    wc_rules/graph/euler_tour.py on lines 239..240

    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 59.

    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 spare[3] in big and spare[0] in small:
                    new_tour = self.link(big,small,spare[3],spare[0])
    Severity: Major
    Found in wc_rules/graph/euler_tour.py and 1 other location - About 2 hrs to fix
    wc_rules/graph/euler_tour.py on lines 237..238

    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 59.

    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 actions.py has 279 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    from dataclasses import dataclass
from collections import deque, ChainMap
from types import MethodType
from abc import ABC, abstractmethod
from obj_tables import core
    Severity: Minor
    Found in wc_rules/schema/actions.py - About 2 hrs to fix

      File collections.py has 275 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      """
:Author: John Sekar <johnarul.sekar@gmail.com>
:Date: 2017-12-13
:Copyright: 2017, Karr Lab
:License: MIT
      Severity: Minor
      Found in wc_rules/utils/collections.py - About 2 hrs to fix

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

            for node in nodes:
        if getattr(node.children[0],'data','') not in ['add','subtract']:
            node.children.insert(0,Tree(data='add',children=[]))
        Severity: Major
        Found in wc_rules/expressions/parse.py and 1 other location - About 2 hrs to fix
        wc_rules/expressions/parse.py on lines 96..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 54.

        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

            for node in nodes:
        if getattr(node.children[0],'data','') not in ['multiply','divide']:
            node.children.insert(0,Tree(data='multiply',children=[]))
        Severity: Major
        Found in wc_rules/expressions/parse.py and 1 other location - About 2 hrs to fix
        wc_rules/expressions/parse.py on lines 130..132

        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 54.

        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

            def peek(self):
        if len(self.events) > 0:
            event,time = self.events.topitem()
            return event,time
        return None, float('inf')
        Severity: Major
        Found in wc_rules/simulator/scheduler.py and 1 other location - About 2 hrs to fix
        wc_rules/simulator/scheduler.py on lines 33..37

        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

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

            def pop(self):
        if len(self.events) > 0:
            event,time = self.events.popitem()
            return event,time
        return None, float('inf')
        Severity: Major
        Found in wc_rules/simulator/scheduler.py and 1 other location - About 2 hrs to fix
        wc_rules/simulator/scheduler.py on lines 19..23

        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

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

        def canonical_label(g):

    partition = initialize_partition(g)
    opp = ordered_partition_pair(partition,partition)
    orbindex = initialize_orbindex(partition)
        Severity: Minor
        Found in wc_rules/graph/canonical_labeling.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 get_attribute_calls has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_attribute_calls(self):
        attrcalls = defaultdict(SortedSet)
        for c in self.execs:
            for k,v in c.deps.attribute_calls.items():
                attrcalls[k].update(v)
        Severity: Minor
        Found in wc_rules/expressions/executable.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 simulate has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
        Open

            def simulate(self,start=0.0,end=1.0,period=1,write_location=None):
        global CURRENT_ACTION_RECORD
        print(f'Simulating from time={start} to time={end}.')
        time = start
        sch = CoordinatedScheduler([
        Severity: Minor
        Found in wc_rules/simulator/simulator.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

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