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BjornFJohansson/pydna

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src/pydna/assembly.py

Summary

Maintainability
D
2 days
Test Coverage

File assembly.py has 380 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license.  Please see the LICENSE.txt file that should have been included
Severity: Minor
Found in src/pydna/assembly.py - About 5 hrs to fix

    Function assemble_circular has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
    Open

        def assemble_circular(self, length_bound=None):
        cps = {}  # circular assembly
        cpsrc = {}
        cpaths = sorted(_nx.simple_cycles(self.G, length_bound=length_bound), key=len)
        cpaths_sorted = []
    Severity: Minor
    Found in src/pydna/assembly.py - About 5 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 assemble_linear has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
    Open

        def assemble_linear(self, start=None, end=None, max_nodes=None):
        G = _nx.MultiDiGraph(self.G)

        G.add_nodes_from(["begin", "begin_rc", "end", "end_rc"], length=0)
    Severity: Minor
    Found in src/pydna/assembly.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 __init__ has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

        def __init__(self, frags=None, limit=25, algorithm=common_sub_strings):
        # Fragments is a string subclass with some extra properties
        # The order of the fragments has significance
        fragments = []
        for f in frags:
    Severity: Minor
    Found in src/pydna/assembly.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

    Avoid deeply nested control flow statements.
    Open

                            if f.location.start > len(ct) and f.location.end > len(ct):
                            f.location += -len(ct)
                        elif f.location.end > len(ct):
                            f.location = _CompoundLocation(
                                (
    Severity: Major
    Found in src/pydna/assembly.py - About 45 mins to fix

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