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Resolve "plotly config dictionary can't be fed in from normalize function"

Dinga Wonanke requested to merge 1888-parsing-structure-files-to-results-material into develop

We created a new function create_topology_porosity, which will enable users to easily populate the topology. In addition, we moved most of the global functions from mof_deconstructor into atomutils, which will facilitate the implementation of the wrapping function in the future.

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