Avoid deeply nested control flow statements.

Open

                        for i_author in range(cls.call_libsbml(sbml_authors.getNumChildren, returns_int=True)):
                            sbml_au = cls.call_libsbml(sbml_authors.getChild, i_author)
                            au = model.authors.create()
                            for i_prop in range(cls.call_libsbml(sbml_au.getNumChildren, returns_int=True)):
                                sbml_prop = cls.call_libsbml(sbml_au.getChild, i_prop)

Avoid deeply nested control flow statements.

Open

                        if submodel.dfba_obj.expression.expression:
                            merged_dfba_expression.append(submodel.dfba_obj.expression.expression)
                        for rxn in list(submodel.dfba_obj.expression.reactions):

Avoid deeply nested control flow statements.

Open

                        for rxn in list(submodel.dfba_obj.expression.reactions):
                            submodel.dfba_obj.expression.reactions.remove(rxn)
                            objs_for_merged_dfba_expression[Reaction][rxn.id] = rxn
                        for dfba_obj_rxn in list(submodel.dfba_obj.expression.dfba_obj_reactions):

Function remove_metadata has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def remove_metadata(model):
        """ Remove metadata from model

        Args:
            model (:obj:`wc_utils.workbook.Workbook`): model

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Function get_errors_warnings has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def get_errors_warnings(cls, sbml_doc):
        """ Get libSBML errors and warnings

        Args:
            sbml_doc (:obj:`libsbml.SBMLDocument`): SBML document

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Avoid deeply nested control flow statements.

Open

                        if rxn.flux_bounds:
                            if not math.isnan(rxn.flux_bounds.min) and not math.isnan(rxn.flux_bounds.max):
                                # assume flux_bounds.min <= flux_bounds.max
                                assert rxn.flux_bounds.min <= rxn.flux_bounds.max, \
                                    f"min flux bound greater than max in {rxn.id}"

Function validate has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def validate(self):
        """ Determine if the model is valid

        * Network of compartments is rooted and acyclic
        * Networks of observables and functions are acyclic

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Function transform has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def transform(filename):
    # read
    wb = openpyxl.load_workbook(filename=filename)

    for ws in wb:

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Avoid deeply nested control flow statements.

Open

                    if cell.value and isinstance(cell.value, str):
                        cell.value = '!' + cell.value
        else:

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

Open

    def get_immediate_children(self, kind=None, __type=None, __include_stop_conditions=True,

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

Open

    def parse_units(cls, sbml_model):
        """ Parse SBML units to Python

        Args:
            sbml_model (:obj:`libsbml.Model`): SBML model

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

Open

    def run(cls, model):
        """ Encode a `wc_lang` model with at most 1 submodel into SBML

        * Validate model
        * Create SBML document

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

Open

    def validate_implicit_relationships(cls, root_model):
        """ Check that relationships to :obj:`root_model` do not need to be explicitly exported because
            they can be inferred by :obj:`Reader.run`. This is necessary to enable the relationships
            to :obj:`root_model` to not be exported in workbooks, and instead added by :obj:`Reader.run`.

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

Open

    def import_relations_from_sbml(self, sbml, objs):
        """ Load relationships from SBML compartment

        Args:
            sbml (:obj:`libsbml.Compartment`): SBML compartment

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

Open

    def __getitem__(cls, name):
        """ Get value by name

        Args:
            name (:obj:`str`): attribute name

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

Open

    def get_species(self, __type=None, **kwargs):
        """ Get species

        Args:
            __type (:obj:`types.TypeType` or :obj:`tuple` of :obj:`types.TypeType`): subclass(es) of :obj:`Model`

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

Open

    def validate(self):
        """ Check that the compartment is valid

        * Check that the units of density are `g l^-1`

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

Open

        def gbl_part(self, *args):
            coeff = 1.
            for arg in args:
                if arg.type == 'SPECIES_COEFFICIENT__SPECIES__SPECIES_TYPE__ID':
                    if arg.value not in self.objects.get(SpeciesType, {}):

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

Open

    def validate(self):
        """ Determine if the submodel is valid

        * dFBA submodel has an objective

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

Open

    def _serialize(species, coefficient, show_compartment=True, show_coefficient_sign=True):
        """ Serialize values

        Args:
            species (:obj:`Species`): species

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