`get_xspectra_structures`: Refactor and Improve Code

[PNOGillespie]

Overview

In this PR, we have re-factored various components of get_xspectra_structures as part of ongoing improvement work. These changes are the first of two improvements intended to enable users to set symmetry data manually instead of relying on automatic symmetry analysis - ultimately enabling the same feature for the XspectraCrystalWorkChain and any others which use the same structure preparation tools.

This PR will be followed by a second one in which the logic for the XSpectra WorkChains will be added in order to properly exploit the changes in this PR. The overall changes have been separated into 2 PRs due to the number of changes made here as part of the re-factoring process.

Changes

• Moves supercell creation, processes for molecules, and generation of equivalent_sites_data to separate functions.
• Adds functionality for users to manually provide symmetry data, thus enabling the CalcFunction to be used as a means to generate structures with user control over which exact sites to mark.
• Fixes a bug discovered in the case where non-hubbard structures with custom Kind names lost their Kind names when converting the ASE supercell to StructureData type.
• Removes unnecessary usage of dict.keys() iterables where simply iterating over the dictionary directly can be used instead.
• Fixes a small oversight in the tests where spglib_settings was mistakenly named spglib_options.

[PNOGillespie]

Hi @superstar54, Thanks for the feedback. I've added a simple test for manual symmetry data input and cleaned up a few things as you suggested doing in one of your comments.

I also added an example of how the equivalent_sites_data input needs to be formatted. Was that the part which was unclear in the docstring, or do you think there's more to do on that?

[PNOGillespie]

Hi @superstar54. I fixed the issue with the docstring by formatting the example to be in-line. I also added a sentence to better explain what needs to be in the equivalent_sites_data dictionary.

Let me know if anything else is needed.