Refactor Pathway class

[stefsmeets]

This PR refactors the Pathway class. I endend up tackling a bunch of cascading issues. It changes the following:

• Add .dims attribute to Pathway. This simplifies a bunch of site transformations that before depended on passing a volume
• Add method to calculate Pathway total length
• Move frac_sites / wrap to methods that return sites instead of in-place updates
• Pathway.path_over_structure returns list of PeriodicSite which simplifies return statement and gives more options to user
• Move some plots to methods of Pathway
• Streamlines creation of Pathways object from Volume
• Path plots no longer needs Volume because Pathway now has dims
• Rename path functions to hopefully make them a bit more consistent

Todo

• Update notebook with Volume/Pathway api gemdat-notebooks#11

[stefsmeets]

Hi @SCiarella could you review this pr please? It may seem like a bit much, but I think it is easiest to start with the Pathway refactor, most of the other changes follow from there. And then Volume next. Changes to both classes enabled a bunch of other small changes and corrections that I included (e.g. plots).

I'm happy to talk you through it offline.

[SCiarella]

Looks excellent! 🚀

My only comment is that I am not convinced that wrapped_sites should be optional. I would make it mandatory, or at least default on True.

[stefsmeets]

Good point on the wrapping! I'll go through that part again with this in mind.