Adding occupancy to py4DSTEM diffraction

[cophus]

PR adds occupancy to crystal, plotting of structures, kinematical SF calcs.

Still needs to be done:
-add occupancy to dynamical SFs
-read occupancy from cif files

[cophus]

Comparing 2 structures with minor occupancy differences:

Notebook: (unfinished)
diffraction_05_occupancy.zip

[alex-rakowski]

Just to check so I can make sure I make #534 compatible, occupancy can either be None or 1D list or array with the same len as positions?

[sezelt]

Next steps:

• @sezelt add occupancy to dynamical structure factor calculations
• @sezelt add occupancy to pymatgen CIF reader
• @alex-rakowski add ASE importer to this PR

[alex-rakowski]

• changed self.occupancy to store as ones and updated the structure calcs to expect this. Crystal can still have None passed to init, and it will check that the occupancy and positions shapes match.
• added from_prismatic and from_ase loads from the objects and attempts to scrape the occupancy from the files

I have tests set up from the other PR; I'll add them when @sezelt has updated the CIF reader func

[sezelt]

I've added occupancy to the CIF reader and the structure factor calculations but I haven't tested it thoroughly