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BjornFJohansson/pydna

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src/pydna/amplify.py

Summary

Maintainability
C
1 day
Test Coverage

File amplify.py has 427 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/amplify.py - About 6 hrs to fix

    Function products has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
    Open

        def products(self):
        if self._products:
            return self._products

        self._products = []
    Severity: Minor
    Found in src/pydna/amplify.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 pcr has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
    Open

    def pcr(*args, **kwargs):
    """pcr is a convenience function for the Anneal class to simplify its
    usage, especially from the command line. If more than one or no PCR
    product is formed, a ValueError is raised.
    Severity: Minor
    Found in src/pydna/amplify.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 a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
    Open

        def __init__(self, primers, template, limit=13, **kwargs):
        r"""The Anneal class has to be initiated with at least an iterable of
        primers and a template.
    Severity: Minor
    Found in src/pydna/amplify.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 __str__ has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def __str__(self):
        """returns a short report describing if or where primer
        anneal on the template."""

        mystring = "Template {name} {size} bp {top} limit={limit}:\n".format(
    Severity: Minor
    Found in src/pydna/amplify.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

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