BooleanNetwork.instantiate - infer_valid_graph by default

[smijeva]

Currently, when an instantiate method is called upon BooleanNetwork (in any version), the Boolean network is still referencing the original regulatory network. This is a counter-intuitive behavior, since the former regulatory network might contain numerous extra (unobservable) regulations. An extra call of infer_valid_graph is going to be needed in the majority of the use cases of this method.

An improved behavior would be to introduce an extra optional parameter to the instantiate method (e.g. infer_regularizatin=True), which will make the method call the infer_valid_graph right upon instantiation. If a former regulatory network is desired to be preserved, this parameter then can be set to False.