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tree_lib/node.py

Summary

Maintainability
F
3 days
Test Coverage

File node.py has 367 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import sys
import pdb
import math
import multitree
import branch
Severity: Minor
Found in tree_lib/node.py - About 4 hrs to fix

    node has 31 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class node:

    def __init__(self,raw_name,arbre):
        # remove any leading angled brackets
        raw_name = raw_name.lstrip(">")
    Severity: Minor
    Found in tree_lib/node.py - About 3 hrs to fix

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

          def DistTo(this_node,that_node,this_branch=None,dist=0):
        # what to do at the end
        if this_node is that_node:
            return True, dist
        # if not ...
      Severity: Minor
      Found in tree_lib/node.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 imposeHierarchy has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
      Open

          def imposeHierarchy(self):
    '''find all the child nodes that have yet to be visited and
    assign their children'''

    for kid_branch in self.child_branches:
      Severity: Minor
      Found in tree_lib/node.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 __init__ has 28 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def __init__(self,raw_name,arbre):
        # remove any leading angled brackets
        raw_name = raw_name.lstrip(">")

        # handle mixed underscore and dot environment
      Severity: Minor
      Found in tree_lib/node.py - About 1 hr to fix

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

            def GetChildLeaves(this_node,parent_node,other_nodes):

        merge_list = []
        for kid_node in other_nodes:
            if parent_node in this_node.leaf_dict:
        Severity: Minor
        Found in tree_lib/node.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 GetNodeLinkDict has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
        Open

            def GetNodeLinkDict(this_node,node_link_dict):

        this_node.link_dict_visited = True
        leaf_dict = this_node.leaf_dict
        Severity: Minor
        Found in tree_lib/node.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 UnrootedLeaving has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
        Open

            def UnrootedLeaving(this_node):

        other_nodes = this_node.GetOtherNodes()
        for parent_node in other_nodes:
            child_nodes = list(set(other_nodes).difference(set([parent_node])))
        Severity: Minor
        Found in tree_lib/node.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 treePrint has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

            def treePrint(self,newickString):

    count = 0
        # implement sorting so that you can compare trees in a quick
        # and dirty way
        Severity: Minor
        Found in tree_lib/node.py - About 45 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 subtreeMap has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

            def subtreeMap(self,species_node):

    # do the children of the current species node possess the
    # relevant genes?  if so, follow that child.  if not, return
    # the current node
        Severity: Minor
        Found in tree_lib/node.py - About 45 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

        Avoid deeply nested control flow statements.
        Open

                                if found is True:
                            was_found = found
                            found_dist = new_dist
        Severity: Major
        Found in tree_lib/node.py - About 45 mins to fix

          Avoid deeply nested control flow statements.
          Open

                      if child_branch is not kid_branch:
                node.child_branches.append(child_branch)
                node.imposeHierarchy()

    # recursively label the roots of subtrees w/ the leaves contained
          Severity: Major
          Found in tree_lib/node.py - About 45 mins to fix

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

                def GetHeights(self):
        ''' get MEDIAN distance to leaves at all internal nodes on the
        tree '''

        # get distances from leaves
            Severity: Minor
            Found in tree_lib/node.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 Find_Subnodes has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

                def Find_Subnodes(self):

        for kid_nodes in self.kid_nodes.keys():
            new_dict = kid_nodes.Find_Subnodes()
            for k in new_dict.keys():
            Severity: Minor
            Found in tree_lib/node.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

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

                def ValidTransfer(self,other_node):
        ''' return boolean regarding whether or not the parent
        branches of the queried nodes overlap temporally '''

        # no auto-transfer
            Severity: Minor
            Found in tree_lib/node.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

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

                def FindDists(self):
        ''' recursively enumerate all pairwise distances on the
        species tree '''

        dist_dict = self.tree.dist_dict
            Severity: Minor
            Found in tree_lib/node.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

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

                def FindLCA(self,node1,node2):
        ''' find the last common ancestor of two nodes.  will descend
        from the subroot (self) looking to see which children possess
        both nodes.  if neither children possess both nodes, return
        current node '''
            Severity: Minor
            Found in tree_lib/node.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

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

                def GetOtherNodes(this_node):

        # fill out the leaf dictionary
        other_nodes = []
        for branch in this_node.branch_list:
            Severity: Minor
            Found in tree_lib/node.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

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

                def __ne__(self,other):

    if self is None or other is None:
        return True
    elif self.serial == other.serial:
            Severity: Major
            Found in tree_lib/node.py and 1 other location - About 2 hrs to fix
            tree_lib/node.py on lines 67..73

            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 53.

            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 __eq__(self,other):
    if self is None or other is None:
        return False
    elif self.serial == other.serial:
        return True
            Severity: Major
            Found in tree_lib/node.py and 1 other location - About 2 hrs to fix
            tree_lib/node.py on lines 76..83

            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 53.

            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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