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KarrLab/obj_tables

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

    def verify_schemas(self):
        """ Verify that each schema can be independently imported

        It can be difficult to import a schema via `importlib.import_module()` in
        `import_module_for_migration()`. This method tests that proactively.
Severity: Minor
Found in obj_tables/migrate.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 __str__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __str__(self):
        """ Get string representation

        Returns:
            :obj:`str`: string representation of a :obj:`Migrator`; collections attributes are rendered
Severity: Minor
Found in obj_tables/migrate.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 load has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def load(schema_changes_file):
        """ Read a schema changes file

        Args:
            schema_changes_file (:obj:`str`): path to the schema changes file
Severity: Minor
Found in obj_tables/migrate.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 get_xlsx_validation has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def get_xlsx_validation(self, sheet_models=None, doc_metadata_model=None):
        """ Get XLSX validation

        Args:
            sheet_models (:obj:`list` of :obj:`Model`, optional): models encoded as separate sheets
Severity: Minor
Found in obj_tables/sci/units.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 plot_data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def plot_data(data_filename=DATA_FILENAME, plot_filename=PLOT_FILENAME):
    data = wc_utils.workbook.io.read(data_filename)['!!Data']
    data = data[3:]

    rxn_ids = []
Severity: Minor
Found in examples/merged_metabolic_model/run.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 get_xlsx_validation has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def get_xlsx_validation(self, sheet_models=None, doc_metadata_model=None):
        """ Get XLSX validation

        Args:
            sheet_models (:obj:`list` of :obj:`Model`, optional): models encoded as separate sheets
Severity: Minor
Found in obj_tables/sci/uncertainty.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 commits_as_graph has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def commits_as_graph(self):
        """ Make a DAG for this repo's commit dependencies - edges point from dependent commit to parent commit

        The DAG contains all commits in the repo on which the latest commit depends. Also creates
        `git_hash_map`, a map from all git hashes to their commits.
Severity: Minor
Found in obj_tables/migrate.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 _decode_instance has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def _decode_instance(encoded_data, decoded_objects, data_to_decode):
    """ Decode a data structure

    Args:
        encoded_data (:obj:`dict`, :obj:`list`, or scalar): data structure with
Severity: Minor
Found in examples/decode_json_data.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 validate has a Cognitive Complexity of 6 (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/sci/refs.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 validate has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def validate(self):
        """ Validate files to migrate, and load all schema changes files

        Raises:
            :obj:`MigratorError`: if any files to migrate do not exist,
Severity: Minor
Found in obj_tables/migrate.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 _get_mapped_attribute has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _get_mapped_attribute(self, existing_class, existing_attribute):
        """ Get the corresponding migrated class and attribute for the existing class and attribute

        Args:
            existing_class (:obj:`obj_tables.core.ModelMeta` or :obj:`str`): an existing class
Severity: Minor
Found in obj_tables/migrate.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 deserialize has a Cognitive Complexity of 6 (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/bio/seq.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 _dump_index_dicts has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _dump_index_dicts(self, file=None):
        """ Dump the index dictionaries for debugging

        Args:
            file (:obj:`object`, optitonal): an object with a :obj:`write(string)` method
Severity: Minor
Found in obj_tables/core.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 clean has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

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

        Args:
            value (:obj:`str`): semantically equivalent representation
Severity: Minor
Found in obj_tables/core.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 validate has a Cognitive Complexity of 6 (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 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 _gc_weaksets has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _gc_weaksets(self):
        """ Garbage collect empty WeakSets formed by deletion of weak refs to :obj:`Model` instances with no strong refs

        Returns:
            :obj:`int`: number of empty WeakSets deleted
Severity: Minor
Found in obj_tables/core.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 __init__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, min=float('nan'), max=float('nan'), nan=True,
                 default=float('nan'), default_cleaned_value=float('nan'), none_value=float('nan'), verbose_name='', description='',
                 primary=False, unique=False):
        """
        Args:
Severity: Minor
Found in obj_tables/core.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 value_equal has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def value_equal(self, val1, val2, tol=0.):
        """ Determine if attribute values are equal, optionally,
        up to a tolerance

        Args:
Severity: Minor
Found in obj_tables/core.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 __init__ has a Cognitive Complexity of 6 (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/bio/seq.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_attr_path_el has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _parse_attr_path_el(cls, attr):
        """ Parse an element of a path to a nested attribute

        Args:
            attr (:obj:`list` of :obj:`dict`): an element of a path to a nested attribute
Severity: Minor
Found in obj_tables/core.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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