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

Open

    def validate_implicit_relationships_are_set(self, model, root_model):
        """ Check that there is only one instance of :obj:`root_model` and that each relationship to
        :obj:`root_model` is set. 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_from_sbml has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def import_from_sbml(self, sbml):
        """ Load from SBML compartment

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

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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):

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

Open

def create_template(path, write_schema=False, write_toc=True,

Avoid deeply nested control flow statements.

Open

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

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

Open

    def create_base_unit(cls, unit_def_id, unit_def, kind, exponent=1, scale=0, multiplier=1.0):

Avoid deeply nested control flow statements.

Open

                        if cls.call_libsbml(g_child.getName) == 'key':
                            attr_name = cls.call_libsbml(g_child.toXMLString)[12:-13]
                        elif cls.call_libsbml(g_child.getName) == 'value':
                            val = cls.call_libsbml(g_child.toXMLString)[14:-15]

Avoid deeply nested control flow statements.

Open

                        for ot_token in parsed_expr._obj_tables_tokens:
                            if (ot_token.code == ObjTablesTokenCodes.obj_id and
                                issubclass(ot_token.model_type, Reaction) and
                                ot_token.model_id == rxn.id):
                                new_obj_expr_elements.append(f'({rxn_for.id} - {rxn_bck.id})')

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

Open

    def export_relations_to_sbml(self, sbml_model, sbml_rxn):
        """ Add relationships to/from object to SBML reaction.

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

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

Open

    def run(self, path, model, models=None, get_related=True, include_all_attributes=False, validate=None,
            title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_schema=False, write_toc=True, extra_entries=0, data_repo_metadata=False, schema_package=None,
            protected=True):
        """ Write a list of model classes to an Excel file, with one worksheet for each model, or to

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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

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

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

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

Open

    def get_children(self, kind=None, __type=None, recursive=True, __include_stop_conditions=True,

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

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

Open

    def validate(self):
        """ Validate that the dFBA objective is valid

        * Check if the identifier is equal to
          `dfba-net-species-{dfba_obj_reaction.id}-{species.id}`

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Avoid deeply nested control flow statements.

Open

                        if part.species.has_attr_vals(__type=__type, **kwargs):
                            products.append(part.species)

        # products of dFBA objective reactions
        for dfba_obj_reaction in self.expression.dfba_obj_reactions:

Avoid deeply nested control flow statements.

Open

                    if hasattr(wc_lang, table_id):
                        table = getattr(wc_lang, table_id)
                        table_format = table.Meta.table_format.name
                    else:
                        table_format = 'row'

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

Open

    def get_annotations(cls, model_obj, nested_attr_paths, sbml_obj, model_objs=None):
        """ Import annotations from a model object to an SBML object

        Args:
            model_obj (:obj:`obj_tables.Model`): model object

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Avoid deeply nested control flow statements.

Open

                        if rxn:
                            assert rxn.submodel == submodel
                            assert rxn.name == name
                            assert rxn.participants == participants
                            assert rxn.reversible == reversible