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BjornFJohansson/pydna

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src/pydna/design.py

Summary

Maintainability
D
2 days
Test Coverage

File design.py has 536 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: Major
Found in src/pydna/design.py - About 1 day to fix

    Function primer_design has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
    Open

    def primer_design(template, fp=None, rp=None, limit=13, target_tm=55.0, tm_func=_tm_default, **kwargs):
    """This function designs a forward primer and a reverse primer for PCR amplification
    of a given template sequence.

    The template argument is a Dseqrecord object or equivalent containing the template sequence.
    Severity: Minor
    Found in src/pydna/design.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 assembly_fragments has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
    Open

    def assembly_fragments(f, overlap=35, maxlink=40):
    """This function return a list of :mod:`pydna.amplicon.Amplicon` objects where
    primers have been modified with tails so that the fragments can be fused in
    the order they appear in the list by for example Gibson assembly or homologous
    recombination.
    Severity: Minor
    Found in src/pydna/design.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 primer_design has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def primer_design(template, fp=None, rp=None, limit=13, target_tm=55.0, tm_func=_tm_default, **kwargs):
    Severity: Major
    Found in src/pydna/design.py - About 50 mins to fix

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

      if __name__ == "__main__":
    cached = _os.getenv("pydna_cached_funcs", "")
    _os.environ["pydna_cached_funcs"] = ""
    import doctest
      Severity: Major
      Found in src/pydna/design.py and 1 other location - About 3 hrs to fix
      src/pydna/download.py on lines 34..40

      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 67.

      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

              try:
            fp = _Anneal((fp,), template).forward_primers.pop()
        except IndexError:
            raise ValueError("Forward primer does not anneal")
        except Exception:  # pragma: no cover
      Severity: Major
      Found in src/pydna/design.py and 1 other location - About 1 hr to fix
      src/pydna/design.py on lines 155..161

      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 40.

      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

              try:
            rp = _Anneal((rp,), template).reverse_primers.pop()
        except IndexError:
            raise ValueError("Reverse primer does not anneal")
        except Exception:  # pragma: no cover
      Severity: Major
      Found in src/pydna/design.py and 1 other location - About 1 hr to fix
      src/pydna/design.py on lines 144..150

      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 40.

      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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