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Showing 542 of 542 total issues

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

def set_git_repo_metadata_from_path(model, repo_type, path='.', url_attr='url', branch_attr='branch',
Severity: Minor
Found in obj_tables/utils.py - About 45 mins to fix

    Avoid deeply nested control flow statements.
    Open

                        if isinstance(val, list) and len(val) > 1:
                        # randomize children
                        objs_to_randomize.extend(val)

                        # shuffle related manager
    Severity: Major
    Found in obj_tables/utils.py - About 45 mins to fix

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

              if default is not None and not isinstance(default, Bio.SeqFeature.FeatureLocation):
            raise ValueError('`default` must be a `Bio.SeqFeature.FeatureLocation` or `None`')
      Severity: Major
      Found in obj_tables/bio/seq.py and 3 other locations - About 45 mins to fix
      obj_tables/bio/seq.py on lines 197..198
      obj_tables/sci/uncertainty.py on lines 41..42
      obj_tables/sci/uncertainty.py on lines 43..44

      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 35.

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

          def link_model(self, model, attributes, data, objects, objects_by_primary_attribute, decoded=None):
      Severity: Minor
      Found in obj_tables/io.py - About 45 mins to fix

        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/bio/seq.py and 1 other location - About 40 mins to fix
        obj_tables/math/numeric.py on lines 46..47

        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

        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/bio/seq.py and 1 other location - About 40 mins to fix
        obj_tables/math/numeric.py on lines 44..45

        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(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

        Function import_module_for_migration has 5 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def import_module_for_migration(self, validate=True, required_attrs=None, debug=False,
        Severity: Minor
        Found in obj_tables/migrate.py - About 35 mins to fix

          Function get_attrs_by_val has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def get_attrs_by_val(self, type=None, reverse=True,
          Severity: Minor
          Found in obj_tables/core.py - About 35 mins to fix

            Function get_children has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def get_children(self, kind=None, __type=None, recursive=True, **kwargs):
            Severity: Minor
            Found in obj_tables/core.py - About 35 mins to fix

              Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(self, attribute, messages, related=False, location=None, value=None):
              Severity: Minor
              Found in obj_tables/core.py - About 35 mins to fix

                Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                    def __init__(self, default=False, default_cleaned_value=None, none_value=None, verbose_name='', description='Enter a Boolean value'):
                Severity: Minor
                Found in obj_tables/core.py - About 35 mins to fix

                  Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                      def __init__(self, path_name, sheet_name, attribute_seq, row, table_id=None):
                  Severity: Minor
                  Found in obj_tables/core.py - About 35 mins to fix

                    Function add_to_decoding_queue has 5 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                            def add_to_decoding_queue(json, models_by_name=models_by_name, decoded=decoded, to_decode=to_decode,
                    Severity: Minor
                    Found in obj_tables/core.py - About 35 mins to fix

                      Function get_attribute_by_name has 5 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                      def get_attribute_by_name(cls, group_name, attr_name, verbose_name=False, case_insensitive=False):
                      Severity: Minor
                      Found in obj_tables/utils.py - About 35 mins to fix

                        Function to_pandas has 5 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                        def to_pandas(objs, models=None, get_related=True,
                        Severity: Minor
                        Found in obj_tables/utils.py - About 35 mins to fix

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

                              def __init__(self, repo_location=None, repo_url=None, branch='master', search_parent_directories=False):
        """ Initialize a :obj:`GitRepo` from an existing Git repo

        If :obj:`repo_location` is a directory then use the Git repo in the directory. Otherwise it must
        be an URL and the repo is cloned into a temporary directory.
                          Severity: Minor
                          Found in obj_tables/migrate.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 _get_disambiguated_id has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                          Open

                              def _get_disambiguated_id(self, idx, case_fold_match=False):
        """ Try to parse a disambiguated `ObjTables` id from :obj:`self._py_tokens` at :obj:`idx`

        Look for a disambugated id (a Model written as :obj:`ModelType.model_id`). If tokens do not match,
        return :obj:`None`. If tokens match, but their values are wrong, return an error :obj:`str`.
                          Severity: Minor
                          Found in obj_tables/math/expression.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 clean has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                          Open

                              def clean(self, value):
        """ Convert attribute value into the appropriate type

        Args:
            value (:obj:`object`): value of attribute to clean
                          Severity: Minor
                          Found in obj_tables/sci/uncertainty.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

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