Raise error when disordered structure is passed to Transitions

[stefsmeets]

This PR changes how disordered species are handled by Transitions. It now raises an error, because the analysis does not work with disordered species. I also added this Transitions.from_trajectory), so it now breaks at the earliest possible stage. I added a function gemdat.utils.remove_disorder_from_species to help 'fix' the structure.

This fixes 2 issues with the current code:

1. The current code updates sites in-place. This can give unintended side effects
2. There is better separation of concerns. This changes allows the user to inspect the sites before using the Transitions code. This prevents unwanted changes to the structure and places control for making sure the structure is what they wanted with the users.

Usage:

from gemdat.utils import remove_disorder_from_structure

new_structure = remove_disorder_from_structure(structure)

Closes #343

[AstyLavrinenko]

Hi @stefsmeets this function still doesn't address the problem with duplicated sites after setting the occupancies to 1. Could you please fix this.

Also for the error could please change the text from "disorder" to "partial occupancy" as disorder implies ordered and disordered phases while we state here only the existence of all possible for occupation sites which is not necessarily ordered phase.