Phase Diagram Serialization Improvement

[fadams-umd]

Summary

Addresses #3940 by modifying the serialization of pymatgen.analysis.phase_diagram.PhaseDiagram to (1) remove redundant copies of the list of all the entries and (2) serialize the subset qhull_entries as a list of indices from which the list of entries can be recreated upon deserialization.

[mkhorton]

Thanks @fadams-umd, this seems much more efficient.

For backwards compatibility, for those who have already serialized a phase diagram with the older method, could you add an appropriate from_dict() method that can handle both formats?

[fadams-umd]

Certainly! I just added a check for a dictionary key only present in the old format, and adjusted deserialization accordingly.

[mkhorton]

We're getting a test failure on analysis.test_phase_diagram.TestPhaseDiagram.test_as_from_dict that's blocking the merge. It looks like the test output just needs to be updated to reflect the changes made in this PR.

[fadams-umd]

I was inadvertently modifying the dictionary argument in the from_dict method, which was throwing off the tests. Creating a copy solved the issue.

[CompRhys]

@fadams-umd thanks for working on this! I originally noted this issue when working with patched phase diagrams which inflate this issue even more due to shared copies between patches. The only reasonable way to store them currently is as pickles which is an awful way to persist long term data.