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Function call has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def call(func):
    """
    Decorator for the calculator call method.

    This decorator provides a unified approach for handling run_computation and
Severity: Minor
Found in mdsuite/calculators/calculator.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_calculator has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def run_calculator(self):
        """
        Run analysis.

        Returns
Severity: Minor
Found in mdsuite/calculators/green_kubo_self_diffusion_coefficients.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_dimensionality has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def get_dimensionality(box: list) -> int:
    """
    Calculate the dimensionality of the experiment box.

    Parameters
Severity: Minor
Found in mdsuite/utils/meta_functions.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_calculator has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def run_calculator(self):
        """Run analysis."""
        self._run_dependency_check()
        for species in self.args.species:
            # Here for now to avoid issues. Should be moved out when calculators become
Severity: Minor
Found in mdsuite/calculators/einstein_diffusion_coefficients.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_box_l has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def _get_box_l(header: str) -> list:
    """
    Get the box lengths from the Lattice property in the header.

    Parameters
Severity: Minor
Found in mdsuite/file_io/extxyz_files.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 __call__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __call__(
Severity: Major
Found in mdsuite/calculators/green_kubo_distinct_diffusion_coefficients.py - About 1 hr to fix

    Function golden_section_search has 9 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def golden_section_search(
    Severity: Major
    Found in mdsuite/utils/meta_functions.py - About 1 hr to fix

      Function __call__ has 9 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __call__(
      Severity: Major
      Found in mdsuite/calculators/spatial_distribution_function.py - About 1 hr to fix

        Function add_experiment has 9 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def add_experiment(
        Severity: Major
        Found in mdsuite/project/project.py - About 1 hr to fix

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

          def golden_section_search(
    data: np.array,
    a: float,
    b: float,
    tol: float = 1e-5,
          Severity: Minor
          Found in mdsuite/utils/meta_functions.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 ensemble_generator has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
          Open

              def ensemble_generator(self, system: bool = False, glob_data: dict = None) -> tuple:
        """
        Build a generator for the ensemble loop.

        Parameters
          Severity: Minor
          Found in mdsuite/database/data_manager.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_property_to_column_idx_dict has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
          Open

          def _get_property_to_column_idx_dict(
    header: str, var_names: dict
) -> typing.Tuple[int, typing.Dict[str, typing.List[int]]]:
    """
    Get the property summary from the header data.
          Severity: Minor
          Found in mdsuite/file_io/extxyz_files.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 __call__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __call__(
          Severity: Major
          Found in mdsuite/calculators/einstein_diffusion_coefficients.py - About 1 hr to fix

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

                def __call__(
            Severity: Major
            Found in mdsuite/calculators/green_kubo_self_diffusion_coefficients.py - About 1 hr to fix

              Function check_input has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
              Open

                  def check_input(self):
        """
        Check the input of the call method and store defaults if needed.

        Returns
              Severity: Minor
              Found in mdsuite/calculators/radial_distribution_function.py - About 55 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 extract_properties_from_header has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
              Open

              def extract_properties_from_header(
    header_property_names: list, database_correspondence_dict: dict
) -> dict:
    """
    Takes the property names from a file header, sees if there is a corresponding
              Severity: Minor
              Found in mdsuite/file_io/lammps_trajectory_files.py - About 55 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_metadata has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
              Open

                  def _get_metadata(self) -> TrajectoryMetadata:
        """Get the necessary metadata out of chemfiles.

        Trajectory and the first chemfiles.Frame
        """
              Severity: Minor
              Found in mdsuite/file_io/chemfiles_read.py - About 55 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 7 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(
              Severity: Major
              Found in mdsuite/experiment/experiment.py - About 50 mins to fix

                Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                    def __init__(
                Severity: Major
                Found in mdsuite/memory_management/memory_manager.py - About 50 mins to fix

                  Function bin_minibatch has 7 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                      def bin_minibatch(
                  Severity: Major
                  Found in mdsuite/calculators/radial_distribution_function.py - About 50 mins to fix
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