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Showing 107 of 113 total issues

File scheme.py has 280 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
MDSuite: A Zincwarecode package.

License
-------
Severity: Minor
Found in mdsuite/database/scheme.py - About 2 hrs to fix

    File green_kubo_self_diffusion_coefficients.py has 275 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """
MDSuite: A Zincwarecode package.

License
-------
    Severity: Minor
    Found in mdsuite/calculators/green_kubo_self_diffusion_coefficients.py - About 2 hrs to fix

      File project.py has 273 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      """
MDSuite: A Zincwarecode package.

License
-------
      Severity: Minor
      Found in mdsuite/project/project.py - About 2 hrs to fix

        File spatial_distribution_function.py has 267 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        """
MDSuite: A Zincwarecode package.

License
-------
        Severity: Minor
        Found in mdsuite/calculators/spatial_distribution_function.py - About 2 hrs to fix

          File einstein_diffusion_coefficients.py has 265 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          """
MDSuite: A Zincwarecode package.

License
-------
          Severity: Minor
          Found in mdsuite/calculators/einstein_diffusion_coefficients.py - About 2 hrs to fix

            File test_project_add_experiment.py has 260 lines of code (exceeds 250 allowed). Consider refactoring.
            Open

            """
MDSuite: A Zincwarecode package.

License
-------
            Severity: Minor
            Found in CI/unit_tests/project/test_project_add_experiment.py - About 2 hrs to fix

              ExperimentDatabase has 21 functions (exceeds 20 allowed). Consider refactoring.
              Open

              class ExperimentDatabase:
    """Experiment Database helper class for lazy access."""

    temperature = LazyProperty()
    time_step = LazyProperty()
              Severity: Minor
              Found in mdsuite/database/experiment_database.py - About 2 hrs to fix

                File green_kubo_ionic_conductivity.py has 253 lines of code (exceeds 250 allowed). Consider refactoring.
                Open

                """
MDSuite: A Zincwarecode package.

License
-------
                Severity: Minor
                Found in mdsuite/calculators/green_kubo_ionic_conductivity.py - About 2 hrs to fix

                  Function get_prop_through_transformation has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def get_prop_through_transformation(self, sp_name, prop):
        # todo prevent infinite recursion
        # (e.g. unwrap_pos calls wrap_pos calls unwrap_pos calls ...)
        from mdsuite.transformations.transformation_dict import (
            property_to_transformation_dict,
                  Severity: Minor
                  Found in mdsuite/transformations/transformations.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 14 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

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

                    Function __init__ has 14 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                        def __init__(
                    Severity: Major
                    Found in mdsuite/database/data_manager.py - About 1 hr to fix

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

                          def add_data(self, chunk: TrajectoryChunkData):
        """
        Add new data to the dataset.

        Parameters
                      Severity: Minor
                      Found in mdsuite/database/simulation_database.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 12 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

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

                        Function __call__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

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

                          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
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