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Function save_db_data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def save_db_data(self):
        """Save all the collected computationattributes and computation data to the
        database.

        This will be run after the computation was successful.
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

Function run_calculator has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def run_calculator(self):
        """Perform the distinct coefficient analysis analysis."""
        self.check_input()
        for combination in self.combinations:
            species_values = list(combination)
Severity: Minor
Found in mdsuite/calculators/einstein_distinct_diffusion_coefficients.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 _compute_atomwise_minibatch has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _compute_atomwise_minibatch(self, data_range: int):
        """
        Compute the number of atoms which can be loaded in at one time.

        Parameters
Severity: Minor
Found in mdsuite/memory_management/memory_manager.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 molecules has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def molecules(self, value):
        """Save the molecules dict to the database."""
        if value is None:
            return
Severity: Minor
Found in mdsuite/database/experiment_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

Function _prepare_database_entry has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _prepare_database_entry(self, species: str, system_tensor=False):
        """
        Add or extend the dataset in which the transformation result is stored.

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

def assertDeepAlmostEqual(expected, actual, *args, **kwargs):
    """
    Assert that two complex structures have almost equal contents.
    Compares lists, dicts and tuples recursively. Checks numeric values
    using test_case's :py:meth:`unittest.TestCase.assertAlmostEqual` and
Severity: Minor
Found in mdsuite/utils/testing.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 run_calculator has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def run_calculator(self):
        """Perform the distinct coefficient analysis analysis."""
        self.check_input()
        for combination in self.combinations:
            species_values = list(combination)
Severity: Minor
Found in mdsuite/calculators/green_kubo_distinct_diffusion_coefficients.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 _map_molecules has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _map_molecules(self, molecular_graph: MolecularGraph):
        """
        Map the molecules and save the data in the database.

        Returns
Severity: Minor
Found in mdsuite/transformations/map_molecules.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 _calculate_prefactor has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _calculate_prefactor(self, species: Union[str, tuple] = None):
        """
        Calculate the relevant prefactor for the analysis.

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

    def check_input(self):
        """
        Check the inputs and set defaults if necessary.

        Returns
Severity: Minor
Found in mdsuite/calculators/angular_distribution_function.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 _prepare_data_structure has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _prepare_data_structure(self):
        """
        Prepare variables and dicts for the analysis.

        Returns
Severity: Minor
Found in mdsuite/calculators/angular_distribution_function.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 _read_process_n_configurations has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _read_process_n_configurations(
        self, traj: chemfiles.Trajectory, n_configs: int
    ) -> mdsuite.database.simulation_database.TrajectoryChunkData:
        """
        Read n configurations and package them into a trajectory chunk of the
Severity: Minor
Found in mdsuite/file_io/chemfiles_read.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 run_transformation has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def run_transformation(self, molecules: List[Molecule]):
        """
        Perform the transformation.

        Parameters
Severity: Minor
Found in mdsuite/transformations/map_molecules.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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