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KarrLab/obj_tables

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Function get_obj_units has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def get_obj_units(obj):
    """ Get units used in a model object and related objects

    Args:
        obj (:obj:`core.Model`): model object
Severity: Minor
Found in obj_tables/sci/units.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 lcl has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

        def lcl(self, *args):
            parts = []
            for arg in args:
                if isinstance(arg, lark.tree.Tree):
                    if arg.data == 'lcl_reactants':
Severity: Minor
Found in obj_tables/chem/core.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 is_equal has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def is_equal(self, other):
        """ Determine if two reaction equations are semantically equivalent

        Args:
            other (:obj:`ReactionEquation`): other reaction equation
Severity: Minor
Found in obj_tables/chem/core.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 from_dict has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def from_dict(self, dict_value):
        """ Set value from a dictionary representation

        Args:
            dict_value (:obj:`dict`): dictionary representation
Severity: Minor
Found in obj_tables/chem/core.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 serialized_format has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def serialized_format(self, value):
        if value in [ChemicalStructureFormat.inchi, ChemicalStructureFormat.smiles]:
            if self._serialized_format in [ChemicalStructureFormat.inchi, ChemicalStructureFormat.smiles]:
                if value != self._serialized_format:
                    self._serialized_format = value
Severity: Minor
Found in obj_tables/chem/core.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 test_eval has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def test_eval(self, values=1., with_units=False):
        """ Test evaluate this :obj:`ParsedExpression` with the value of all models given by :obj:`values`

        This is used to validate this :obj:`ParsedExpression`, as well as for testing.
Severity: Minor
Found in obj_tables/math/expression.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 get_str has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def get_str(self, obj_tables_token_to_str, with_units=False, number_units=' * __dimensionless__'):
        """ Generate string representation of expression, e.g. for evaluation by :obj:`eval`

        Args:
            obj_tables_token_to_str (:obj:`callable`): method to get string representation of a token
Severity: Minor
Found in obj_tables/math/expression.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 validate has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def validate(self):
        """ Determine if the object is valid

        Returns:
            :obj:`InvalidObject` or None: :obj:`None` if the object is valid,
Severity: Minor
Found in obj_tables/core.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 save_out_workbook has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def save_out_workbook(format, objs, schema_name, doc_metadata, model_metadata, models,
                      write_toc=False, write_schema=False, write_empty_models=True, write_empty_cols=True,
                      protected=True):
    """
    Args:
Severity: Minor
Found in obj_tables/web_service.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 has_attr_vals has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def has_attr_vals(self, __type=None, __check_attr_defined=True, **kwargs):
        """ Check if the type and values of the attributes of an object match a set of conditions

        Args:
            __type (:obj:`types.TypeType` or :obj:`tuple` of :obj:`types.TypeType`): subclass(es) of :obj:`Model`
Severity: Minor
Found in obj_tables/core.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 validate has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

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

        Args:
            obj (:obj:`Model`): object being validated
Severity: Minor
Found in obj_tables/core.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 get_all_related has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def get_all_related(objs, forward=True, reverse=True):
        """ Optimally obtain all objects related to objects in :obj:`objs`

        The set of all :obj:`Model`\ s can be viewed as a graph whose nodes are :obj:`Model` instances
        and whose edges are related connections. Because related edges are bi-directional, this graph
Severity: Minor
Found in obj_tables/core.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 run has 26 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,
            models=None, get_related=True, include_all_attributes=True, validate=True,
            title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_toc=True, write_schema=False, write_empty_models=True, write_empty_cols=True,
            extra_entries=0, group_objects_by_model=True, data_repo_metadata=False, schema_package=None,
Severity: Minor
Found in obj_tables/io.py - About 1 hr to fix

    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 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/bio/seq.py - About 1 hr to fix

        Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def __init__(self, verbose_name='', description='Enter a path to a local file or directory',
        Severity: Major
        Found in obj_tables/core.py - About 1 hr to fix

          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/bio/seq.py - About 1 hr to fix

            Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def __init__(self, none=True, default=None, default_cleaned_value=None, none_value=None,
            Severity: Major
            Found in obj_tables/core.py - About 1 hr to fix

              Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(self, none=True, default=None, default_cleaned_value=None, none_value=None,
              Severity: Major
              Found in obj_tables/core.py - About 1 hr to fix
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