GPR rule is not recognized by the evaluation function

[michaelpierrelee]

Hello

with Python 3.10 and cobra 0.29, the GPR rule is not recognized by the evaluation function (unsupported operation cobra.core.gene.GPR).

The solution is to reimplement it using only the AST python module:

    def __evaluate_gpr(self, node, conf_genes):

        if isinstance(node, ast.Module) or isinstance(node, ast.Expr):
            for child in ast.iter_child_nodes(node):
                return self.__evaluate_gpr(child, conf_genes)
        elif isinstance(node, ast.BoolOp):
            if isinstance(node.op, ast.Or):
                x = [self.__evaluate_gpr(child, conf_genes) for child in node.values]
                if None not in x:
                    return max(x)
            elif isinstance(node.op, ast.And):
                x = [self.__evaluate_gpr(child, conf_genes) for child in node.values]
                if None not in x:
                    return min(x)
            else:
                raise TypeError("unsupported operation " + node.op.__class__.__name__)
        elif isinstance(node, ast.Name):
            if node.id not in conf_genes:
                return 1
            return conf_genes[node.id]
        elif node is None:
            return 1
        else:
            raise TypeError("unsupported operation  " + repr(node))

and

    def __gene_set_expression(self, rule, conf_genes):

        if rule == '':
            return 1
        else:
            ast_tree = ast.parse(rule)
            return self.__evaluate_gpr(ast_tree, conf_genes)

I believe this implementation should be supported for previous versions of cobrapy, as it is only based on the property cobra.core.reaction.Reaction.gene_reaction_rule that has been set on its early versions.

Best