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BjornFJohansson/pydna

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Function assign_quantitiesB has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

def assign_quantitiesB(samples, maxdef=Q_(150, "ng")):
    """
    Assigns quantities (masses in nanograms) to the DNA fragments without
    corresponding quantity assuming a linear relationship between the DNA
    length (in basepairs) and its mass. As if the fragments originated in
Severity: Minor
Found in scripts/gel/gel_old.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

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

Gaussian = lambda x, hgt, ctr, dev: hgt * _np.exp(-((x - ctr) ** 2) / (2 * dev**2))
Severity: Major
Found in scripts/gel/gel2.py and 1 other location - About 1 hr to fix
scripts/gel/gel_old.py on lines 695..695

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 47.

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

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

    return hgt * _np.exp(-((x - ctr) ** 2) / (2 * dev**2))
Severity: Major
Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
scripts/gel/gel2.py on lines 185..185

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 47.

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 __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

    def __getitem__(self, sl):
        """docstring."""
        answer = Dseqrecord(_copy.copy(self))
        answer.seq = self.seq.__getitem__(sl)
        # answer.seq.alphabet = self.seq.alphabet
Severity: Minor
Found in src/pydna/dseqrecord.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 apply_cut has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

    def apply_cut(self, left_cut, right_cut):
        dseq = self.seq.apply_cut(left_cut, right_cut)
        # TODO: maybe remove depending on https://github.com/BjornFJohansson/pydna/issues/161

        if left_cut == right_cut:
Severity: Minor
Found in src/pydna/dseqrecord.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 toGB has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

def toGB(jseqs):
    "parses json jseq data and prints out ApE compatible genbank"

    # take first jseq from parsed list
    if type(jseqs) == type([]):
Severity: Minor
Found in scripts/BioJSON-master/genbank_writer.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 ferguson_to_mu0 has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

def ferguson_to_mu0(
    field,
    Tvals,
    DNAvals,
    dataset,
Severity: Minor
Found in scripts/gel/gel_old.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 __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

    def __getitem__(self, i):
        """Save indices of accessed items."""
        if isinstance(i, slice):
            result = self.__class__(self.data[i])
            for ind in range(i.start, i.stop, i.step or 1):
Severity: Minor
Found in src/pydna/myprimers.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 __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

    def __getitem__(self, sl):
        """Returns a subsequence. This method is used by the slice notation"""

        if not self.circular:
            x = len(self.crick) - self.ovhg - len(self.watson)
Severity: Minor
Found in src/pydna/dseq.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

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

Nbp_to_N = lambda Nbp, a, b, l: Nbp * (b / l) * (l / a) ** 2  # number of occupied pores
Severity: Major
Found in scripts/gel/gel2.py and 1 other location - About 1 hr to fix
scripts/gel/gel2.py on lines 346..346

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 44.

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

        N_to_Nbp = lambda N, a, b, l: N * (l / b) * (a / l) ** 2  # number of base pairs (bp)
Severity: Major
Found in scripts/gel/gel2.py and 1 other location - About 1 hr to fix
scripts/gel/gel2.py on lines 177..177

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 44.

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 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 11 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(
Severity: Major
Found in scripts/gel/gel2.py - About 1 hr to fix

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

    def Nbp_to_N(Nbp, a, b, l):
    return Nbp * (b / l) * (l / a) ** 2  # number of occupied pores
    Severity: Major
    Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
    scripts/gel/gel_old.py on lines 463..464

    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 42.

    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 N_to_Nbp(N, a, b, l):
    return N * (l / b) * (a / l) ** 2  # number of base pairs (bp)
    Severity: Major
    Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
    scripts/gel/gel_old.py on lines 467..468

    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 42.

    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 __init__ has 32 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def __init__(
        self,
        samples,  # list of lists of Dseqrecords
        names=None,
        percentgel=Q_(1.0, "(g/(100 mL))*100"),  # agar/buffer
    Severity: Minor
    Found in scripts/gel/gel_old.py - About 1 hr to fix

      Function __add__ has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
      Open

          def __add__(self, other):
        if hasattr(other, "seq") and hasattr(other.seq, "watson"):
            other = _copy.deepcopy(other)
            other_five_prime = other.seq.five_prime_end()
            if other_five_prime[0] == "5'":
      Severity: Minor
      Found in src/pydna/dseqrecord.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 10 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(
      Severity: Major
      Found in scripts/gel/gel_old.py - About 1 hr to fix

        Function open has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
        Open

            def open(self, seq_to_open):
        """Open a sequence for editing in an external (DNA) editor.

        Parameters
        ----------
        Severity: Minor
        Found in src/pydna/editor.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

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

            return lambda L: 1 / (beta + alpha * (1 - _np.exp(-L / gamma)))
        Severity: Major
        Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
        scripts/gel/gel2.py on lines 159..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 41.

        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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        Status
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