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obj_tables/math/numeric.py

Summary

Maintainability
D
2 days
Test Coverage
A
100%

File numeric.py has 317 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Math attributes

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2017-05-10
:Copyright: 2017, Karr Lab
Severity: Minor
Found in obj_tables/math/numeric.py - About 3 hrs to fix

    Function validate has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
    Open

        def validate(self, obj, value):
        """ Determine if :obj:`value` is a valid value

        Args:
            obj (:obj:`Model`): class being validated
    Severity: Minor
    Found in obj_tables/math/numeric.py - About 2 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 validate has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
    Open

        def validate(self, obj, value):
        """ Determine if :obj:`value` is a valid value

        Args:
            obj (:obj:`Model`): class being validated
    Severity: Minor
    Found in obj_tables/math/numeric.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 deserialize has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
    Open

        def deserialize(self, value):
        """ Deserialize value

        Args:
            value (:obj:`str`): semantically equivalent representation
    Severity: Minor
    Found in obj_tables/math/numeric.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 deserialize has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

        def deserialize(self, value):
        """ Deserialize value

        Args:
            value (:obj:`str`): semantically equivalent representation
    Severity: Minor
    Found in obj_tables/math/numeric.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 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
    Severity: Major
    Found in obj_tables/math/numeric.py - About 1 hr to fix

      Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, default=None, none_value=None, verbose_name='', description='',
      Severity: Minor
      Found in obj_tables/math/numeric.py - About 45 mins to fix

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

            def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
                 primary=False, unique=False):
        """
        Args:
            min_length (:obj:`int`, optional): minimum length
        Severity: Minor
        Found in obj_tables/math/numeric.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 8 locations. Consider refactoring.
        Open

            def validate_unique(self, objects, values):
        """ Determine if the attribute values are unique

        Args:
            objects (:obj:`list` of :obj:`Model`): list of :obj:`Model` objects
        Severity: Major
        Found in obj_tables/math/numeric.py and 7 other locations - About 2 hrs to fix
        obj_tables/bio/seq.py on lines 113..127
        obj_tables/bio/seq.py on lines 275..289
        obj_tables/chem/core.py on lines 102..116
        obj_tables/chem/core.py on lines 466..480
        obj_tables/chem/core.py on lines 976..990
        obj_tables/math/numeric.py on lines 309..323
        obj_tables/math/symbolic.py on lines 93..107

        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 52.

        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 8 locations. Consider refactoring.
        Open

            def validate_unique(self, objects, values):
        """ Determine if the attribute values are unique

        Args:
            objects (:obj:`list` of :obj:`Model`): list of :obj:`Model` objects
        Severity: Major
        Found in obj_tables/math/numeric.py and 7 other locations - About 2 hrs to fix
        obj_tables/bio/seq.py on lines 113..127
        obj_tables/bio/seq.py on lines 275..289
        obj_tables/chem/core.py on lines 102..116
        obj_tables/chem/core.py on lines 466..480
        obj_tables/chem/core.py on lines 976..990
        obj_tables/math/numeric.py on lines 135..149
        obj_tables/math/symbolic.py on lines 93..107

        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 52.

        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

                if not isinstance(min_length, (int, float)) or min_length < 0:
            raise ValueError('`min_length` must be a non-negative integer')
        Severity: Minor
        Found in obj_tables/math/numeric.py and 1 other location - About 40 mins to fix
        obj_tables/bio/seq.py on lines 199..200

        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 34.

        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

                if not isinstance(max_length, (int, float)) or max_length < min_length:
            raise ValueError('`max_length` must be an integer greater than or equal to `min_length`')
        Severity: Minor
        Found in obj_tables/math/numeric.py and 1 other location - About 40 mins to fix
        obj_tables/bio/seq.py on lines 201..202

        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 34.

        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

                if default is not None and not isinstance(default, pandas.DataFrame):
            raise ValueError('`default` must be a `pandas.DataFrame` or `None`')
        Severity: Minor
        Found in obj_tables/math/numeric.py and 1 other location - About 35 mins to fix
        obj_tables/math/numeric.py on lines 42..43

        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

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

                if default is not None and not isinstance(default, numpy.ndarray):
            raise ValueError('`default` must be a `numpy.array` or `None`')
        Severity: Minor
        Found in obj_tables/math/numeric.py and 1 other location - About 35 mins to fix
        obj_tables/math/numeric.py on lines 217..218

        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

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