Method run has 18 arguments (exceeds 4 allowed). Consider refactoring.

Open

     public static java.lang.Object run(String inStructure, String inStructureFormat, String outImageFormat,
        int[] atomsToLabel, String[] atomElements, String[] atomLabels, int[] atomLabelColors, double atomLabelFontSize,
        int[][] atomSets, String[][] atomSetElements, int[] atomSetColors, 
        int[][][] bondSets, String[][][] bondSetElements, int[] bondSetColors, 
        boolean showAtomNums,

Function copytree_to_existing_destination has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

def copytree_to_existing_destination(src, dst):
    """ Copy files from :obj:`src` to :obj:`dst`, overwriting existing files with the same paths
    and keeping all other existing directories and files

    Args:

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

Open

    def apply(self, ws, first_row, first_col, last_row, last_col, include_help_comments=False):
        """ Apply validation to worksheet

        Args:
            ws (:obj:`xlsxwriter.Worksheet`): worksheet

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

Open

    def validate_dataclass_type(self, attr_name):
        """ Validate the type of an attribute in a dataclass instance

        Args:
            attr_name (:obj:`str`): the name of the attribute to validate

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Function __init__ has 15 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self, input_title='', input_message='', show_input=True,

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

Open

    def expand_dict(d, separator='.'):
        """ Expand a dict, converting string or tuple keys into nested keys

        Args:
            d (:obj:`dict`): dictionary to expand

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

Open

def default_mutable_params(mutable_args):
    """A function or method decorator that handles mutable optional parameters.

    Optional parameters with mutable default values like d and l in "def f( d={}, l=[])" have
    the awkward behavior that a global mutable data strcture is created when the function (or

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Function draw_molecule has 11 arguments (exceeds 4 allowed). Consider refactoring.

Open

def draw_molecule(structure, format, image_format='svg', atom_labels=None, atom_label_font_size=0.4,

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

Open

def validate_random_state(random_state):
    """ Validates a random state

    Args:
        random_state (:obj:`obj`): random state

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

Open

    def difference(self, other):
        """ Get difference with another workbook

        Args:
            other (:obj:`Workbook`): other workbook

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

Open

    def flatten_dict(d, root_flat_key=None):
        """ Flatten a dict, converting nested keys into tuples

        Args:
            d (:obj:`dict`): dictionary to flatten

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

Open

def write(path, workbook,

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

Open

    def __init__(self, path=None, namespace=None, package=None, hash=None,

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

Open

    def __init__(self, sources, config):
        """
        Args:
            sources (:obj:`list` of :obj:`str`): list of sources of configuration values
            config (:obj:`configobj.ConfigObj`): configuration

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

Open

    def write_cell(self, xls_worksheet, sheet_name, i_row, i_col, value, format):
        """ Write a value to a cell

        Args:
            xls_worksheet (:obj:`xlsxwriter.Worksheet`): Excel worksheet

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

Open

def draw_molecule(structure, format, image_format='svg', atom_labels=None, atom_label_font_size=0.4,
                  atom_sets=None, bond_sets=None,
                  show_atom_nums=False, width=200, height=200, include_xml_header=True):
    """ Draw an image of a molecule

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

Open

def partition_nth(s, sep, n):
    """ Partition a string on the nth occurrence of a substring

    Args:
        s (:obj:`str`): string to partition

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

Open

def rpartition_nth(s, sep, n):
    """ Partition a string on the nth-last occurrence of a substring

    Args:
        s (:obj:`str`): string to partition

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

Open

    def __str__(self):
        """ Return string representation of this `DebugLogsManager`'s logs

        Returns:
            :obj:`str`: the name, level, template and filename (if used) for each log

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

Open

        def get_format(i_row, i_col, style=style,