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File diffusion.py has 787 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
The modules is focused on tools for the evaluation of the mean squared displacement and resulting
diffusion coefficient from a material.
"""
Severity: Major
Found in kinisi/diffusion.py - About 1 day to fix

    File parser.py has 640 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """
Parser functions, including implementation for :py:mod:`pymatgen` compatible VASP files and :py:mod:`MDAnalysis`
compatible trajectories.

This parser borrows heavily from the :py:class:`pymatgen.analysis.diffusion_analyzer.DiffusionAnalyzer` class,
    Severity: Major
    Found in kinisi/parser.py - About 1 day to fix

      Function _group_to_dict has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.
      Open

      def _group_to_dict(h5file: 'h5py._hl.files.File', path: str) -> dict:
    """
    A recursive function to load data from hdf5 files.

    :param h5file: Open hdf5 file.
      Severity: Minor
      Found in kinisi/analyzer.py - About 6 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

      File analyzer.py has 371 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      """
This module contains the base class for the different :py:class:`Analyzer` objects used by :py:mod:`kinisi`.
"""

# Copyright (c) Andrew R. McCluskey and Benjamin J. Morgan
      Severity: Minor
      Found in kinisi/analyzer.py - About 4 hrs to fix

        Bootstrap has 24 functions (exceeds 20 allowed). Consider refactoring.
        Open

        class Bootstrap:
    """
    The top-level class for bootstrapping.

    :param delta_t: An array of the timestep values.
        Severity: Minor
        Found in kinisi/diffusion.py - About 2 hrs to fix

          Function _dict_to_group has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
          Open

          def _dict_to_group(h5file: 'h5py._hl.files.File', path: str, my_dict: dict):
    """
    A recursive function to help with saving to hdf5 file formats.

    :param h5file: Open hdf5 file.
          Severity: Minor
          Found in kinisi/analyzer.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 __init__ has 17 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(self,
          Severity: Major
          Found in kinisi/parser.py - About 2 hrs to fix

            Function __init__ has 16 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def __init__(self,
            Severity: Major
            Found in kinisi/parser.py - About 2 hrs to fix

              Function __init__ has 16 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(self,
              Severity: Major
              Found in kinisi/parser.py - About 2 hrs to fix

                Function __init__ has 13 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                    def __init__(self,
                Severity: Major
                Found in kinisi/diffusion.py - About 1 hr to fix

                  Function __init__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def __init__(self,
                 delta_t: np.ndarray,
                 disp_3d: List[np.ndarray],
                 ionic_charge: Union[np.ndarray, int],
                 n_o: np.ndarray,
                  Severity: Minor
                  Found in kinisi/diffusion.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 12 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                      def __init__(self,
                  Severity: Major
                  Found in kinisi/parser.py - About 1 hr to fix

                    Function __init__ has 12 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                        def __init__(self,
                    Severity: Major
                    Found in kinisi/diffusion.py - About 1 hr to fix

                      Function __init__ has 12 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                          def __init__(self,
                      Severity: Major
                      Found in kinisi/diffusion.py - About 1 hr to fix

                        Function __init__ has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
                        Open

                            def __init__(self,
                 delta_t: np.ndarray,
                 disp_3d: List[np.ndarray],
                 n_o: np.ndarray,
                 sub_sample_dt: int = 1,
                        Severity: Minor
                        Found in kinisi/diffusion.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 a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
                        Open

                            def __init__(self,
                 delta_t: np.ndarray,
                 disp_3d: List[np.ndarray],
                 n_o: np.ndarray,
                 sub_sample_dt: int = 1,
                        Severity: Minor
                        Found in kinisi/diffusion.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 bootstrap_GLS has 10 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                            def bootstrap_GLS(self,
                        Severity: Major
                        Found in kinisi/diffusion.py - About 1 hr to fix

                          Function __init__ has 28 lines of code (exceeds 25 allowed). Consider refactoring.
                          Open

                              def __init__(self,
                 delta_t: np.ndarray,
                 disp_3d: List[np.ndarray],
                 n_o: np.ndarray,
                 sub_sample_dt: int = 1,
                          Severity: Minor
                          Found in kinisi/diffusion.py - About 1 hr to fix

                            Function from_dict has 27 lines of code (exceeds 25 allowed). Consider refactoring.
                            Open

                                def from_dict(cls, my_dict: dict) -> 'Bootstrap':
        """
        Generate a :py:class:`Bootstrap` object from a dictionary.

        :param my_dict: The input dictionary.
                            Severity: Minor
                            Found in kinisi/diffusion.py - About 1 hr to fix

                              Function __init__ has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
                              Open

                                  def __init__(self,
                 universe: "MDAnalysis.core.universe.Universe",
                 specie: str,
                 time_step: float,
                 step_skip: int,
                              Severity: Minor
                              Found in kinisi/parser.py - About 45 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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