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Showing 113 of 113 total issues

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

    def __call__(
Severity: Minor
Found in mdsuite/calculators/green_kubo_viscosity_flux.py - About 35 mins to fix

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

        def batch_generator(  # noqa: C901
    Severity: Minor
    Found in mdsuite/database/data_manager.py - About 35 mins to fix

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

          def __init__(
      Severity: Minor
      Found in mdsuite/file_io/lammps_flux_files.py - About 35 mins to fix

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

            def __init__(
        Severity: Minor
        Found in mdsuite/utils/report_computer_characteristics.py - About 35 mins to fix

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

              def load_matrix(
          Severity: Minor
          Found in mdsuite/experiment/experiment.py - About 35 mins to fix

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

                def __call__(
            Severity: Minor
            Found in mdsuite/calculators/green_kubo_thermal_conductivity.py - About 35 mins to fix

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

                  def __call__(
              Severity: Minor
              Found in mdsuite/calculators/green_kubo_viscosity.py - About 35 mins to fix

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

                    def __call__(
                Severity: Minor
                Found in mdsuite/calculators/coordination_number_calculation.py - About 35 mins to fix

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

                      def __call__(
                  Severity: Minor
                  Found in mdsuite/calculators/einstein_helfand_thermal_kinaci.py - About 35 mins to fix

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

                        def __call__(
                    Severity: Minor
                    Found in mdsuite/calculators/einstein_helfand_thermal_conductivity.py - About 35 mins to fix

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

                          def __init__(
        self,
        experiment: Experiment,
        molecule_input_data: Molecule,
    ):
                      Severity: Minor
                      Found in mdsuite/graph_modules/molecular_graph.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_species_information has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                      Open

                          def _get_species_information(
        self, file, header_property_names: list, n_particles: int
    ):
        """
        Get the information which species are present and which particle ids/ lines in
                      Severity: Minor
                      Found in mdsuite/file_io/lammps_trajectory_files.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 load_data has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                      Open

                          def load_data(
        self,
        path_list: list = None,
        select_slice: np.s_ = np.s_[:],
        dictionary: bool = False,
                      Severity: Minor
                      Found in mdsuite/database/simulation_database.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 _build_path_input has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                      Open

                          def _build_path_input(structure: dict) -> dict:
        """
        Build an input to a hdf5 database_path from a dictionary.

        In many cases, whilst a dict can be passed on to a method, it is not ideal for
                      Severity: Minor
                      Found in mdsuite/database/simulation_database.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 ideal_correction has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                      Open

                          def ideal_correction(self) -> float:
        """Get the correct ideal gas term.

        In the case of a cutoff value greater than half of the box size, the ideal gas
        term of the experiment must be corrected due to the lack of spherical symmetry
                      Severity: Minor
                      Found in mdsuite/calculators/radial_distribution_function.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 species has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                      Open

                          def species(self, value: dict):
        """Save the SpeciesInfo to the SQL database.

        Parameters
        ----------
                      Severity: Minor
                      Found in mdsuite/database/experiment_database.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 _run_visualization has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                      Open

                          def _run_visualization(self, plot_data: tf.Tensor, colour_map: np.ndarray):
        """
        Run the visualizer.

        Parameters
                      Severity: Minor
                      Found in mdsuite/calculators/spatial_distribution_function.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_time has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                      Open

                      def _get_time(header: str) -> float:
    """
    Retrieve the time value from a header line.
    Can be used to infer the sampling step by calling on consecutive config headers.
                      Severity: Minor
                      Found in mdsuite/file_io/extxyz_files.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_neighbour_list has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                      Open

                      def get_neighbour_list(positions: tf.Tensor, cell=None, batch_size=None) -> tf.Tensor:
    """
    Generate the neighbour list.

    Parameters
                      Severity: Minor
                      Found in mdsuite/utils/neighbour_list.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_computation_data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                      Open

                          def get_computation_data(self) -> db.Computation:
        """Query the database for computation data.

        This method used the self.args dataclass to look for matching
        calculator attributes and returns a db.Computation object if
                      Severity: Minor
                      Found in mdsuite/database/calculator_database.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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