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Mapping should default to None in Protocol methods #643

@IAlibay

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@IAlibay

As of 1.7, mappings are not used in the majority of our Protocols. I realise that the intent is that Transformations just deal with the user facing parts of the API, but we also often have examples that just have users call Protocol.create directly. In those cases, it doesn't make a ton of sense to have to pass mapping=None when it is only necessary for a few Protocols.

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