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BjornFJohansson/pydna

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Similar blocks of code found in 5 locations. Consider refactoring.
Open

    datasets[name]["gamma"] = temp_dset["gamma"] * ureg("kbp")
Severity: Major
Found in scripts/gel/gel_old.py and 4 other locations - About 35 mins to fix
scripts/gel/gel_old.py on lines 348..348
scripts/gel/gel_old.py on lines 349..349
scripts/gel/gel_old.py on lines 350..350
scripts/gel/gel_old.py on lines 351..351

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 33.

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 kB * T / (6 * _np.pi * eta * Rh)
Severity: Minor
Found in scripts/gel/gel_old.py and 1 other location - About 35 mins to fix
scripts/gel/gel2.py on lines 179..179

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 33.

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

                to_x = int(round(((distXmid + bandlength / 2.0) * res).magnitude))
Severity: Minor
Found in scripts/gel/gel2.py and 1 other location - About 35 mins to fix
scripts/gel/gel_old.py on lines 1000..1000

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 33.

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

    def assign_numbers(self, lst: list):
        """Find new primers in lst.

        Returns a string containing new primers with their assigned
        numbers. This string can be copied and pasted to the primer
Severity: Minor
Found in src/pydna/myprimers.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 list_parts has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

def list_parts(fusion_pcr_fragment):
    stack = [fusion_pcr_fragment]
    processed = []

    while stack:
Severity: Minor
Found in src/pydna/fusionpcr.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 __add__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def __add__(self, other):
        """Simulates ligation between two DNA fragments.

        Add other Dseq object at the end of the sequence.
        Type error is raised if any of the points below are fulfilled:
Severity: Minor
Found in src/pydna/dseq.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

Similar blocks of code found in 5 locations. Consider refactoring.
Open

    datasets[name]["muL"] = temp_dset["muL"] * ureg("1.0E-8 m**2/(V*s)")
Severity: Major
Found in scripts/gel/gel_old.py and 4 other locations - About 35 mins to fix
scripts/gel/gel_old.py on lines 348..348
scripts/gel/gel_old.py on lines 349..349
scripts/gel/gel_old.py on lines 350..350
scripts/gel/gel_old.py on lines 352..352

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 33.

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

        from_x = int(round(((distXmid - bandlength / 2.0) * res).magnitude))
Severity: Minor
Found in scripts/gel/gel_old.py and 1 other location - About 35 mins to fix
scripts/gel/gel2.py on lines 434..434

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 33.

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

def flatten(List):
    if List == []:
        return List
    flatL = []
    for elem in List:
Severity: Minor
Found in scripts/gel/gel_old.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 figure has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def figure(self, feature=0, highlight="\x1b[48;5;11m", plain="\x1b[0m"):
        """docstring."""
        if self.features:
            f = self.features[feature]
            locations = sorted(self.features[feature].location.parts, key=_SimpleLocation.start.fget)
Severity: Minor
Found in src/pydna/dseqrecord.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

Avoid too many return statements within this function.
Open

        return True
Severity: Major
Found in src/pydna/dseq.py - About 30 mins to fix

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

        def __init__(
        self,
        initlist: Iterable = None,
        path: (str, Path) = None,
        *args,
    Severity: Minor
    Found in src/pydna/myprimers.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 expose has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def expose(self, exposure=0.1, aperture=2):
        """Returns an image of the gel with the DNA highlighted"""

        c1, c2 = exposure * 100, exposure * 200
        fill_colour = (c1, c1, c2)
    Severity: Minor
    Found in scripts/experimental_gel2.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 __call__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def __call__(cls, *args):
        t = (int(time.time()) // 10000) * 10000
        h = hash(args)
        fn = "%s/%s-%i-%i.pickle" % (tempfile.gettempdir(), cls.__name__, t, h)
    Severity: Minor
    Found in scripts/memo/meta.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 __mul__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def __mul__(self, number):
        if not isinstance(number, int):
            raise TypeError("TypeError: can't multiply Dseqrecord by non-int of type {}".format(type(number)))
        if self.circular:
            raise TypeError("TypeError: can't multiply circular Dseqrecord.")
    Severity: Minor
    Found in src/pydna/dseqrecord.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 figure has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def figure(self):
        r"""Compact ascii representation of the assembled fragments.

        Each fragment is represented by:
    Severity: Minor
    Found in src/pydna/contig.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 parseGBLoc has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

    def parseGBLoc(s, l_, t):
    """retwingles parsed genbank location strings, assumes no joins of RC and FWD sequences"""
    strand = 1
    locationlist = []
    Severity: Minor
    Found in src/pydna/genbankfixer.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 expose has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def expose(self, exposure=0.1, aperture=2):
        """Returns an image of the gel with the DNA highlighted"""

        c1, c2 = exposure * 100, exposure * 200
        fill_colour = (c1, c1, c2)
    Severity: Minor
    Found in scripts/experimental_gel.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 parse has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

    def parse(data, ds=True):
    """Return *all* DNA sequences found in data.

    If no sequences are found, an empty list is returned. This is a greedy
    function, use carefully.
    Severity: Minor
    Found in src/pydna/parsers.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

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