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

                        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):

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}"

Avoid deeply nested control flow statements.

Open

                        if species.species_type.structure and species.species_type.structure.has_carbon():
                            flux_bounds = carbon_flux_bounds
                        else:
                            flux_bounds = no_carbon_flux_bounds

Avoid deeply nested control flow statements.

Open

                        for cls_obj in cls_objects:
                            setattr(cls_obj, attr.name, model)

        # validate
        config = wc_lang.config.core.get_config()['wc_lang']['io']

Avoid deeply nested control flow statements.

Open

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

Avoid deeply nested control flow statements.

Open

                        if part_back:
                            rxn_bck.participants.append(part_back)
                        else:
                            rxn_bck.participants.create(species=part.species, coefficient=-1 * part.coefficient)

Function create_parameter has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def create_parameter(cls, sbml_model, id, value, units, name=None, constant=True):

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 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_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 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 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 __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 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 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 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 _default has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def _default(self):
        args = self.app.pargs

        if args.compare_files:
            model1 = read_workbook(args.path_1)

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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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