Superupgrade

[ardunn]

Summary of upgrades

• Update all requirements. Closes New release #623
• Fix all tests and CI to run on GH actions and removing running of CircleCI WFs - include running of full datasets tests on package releases. Test coverage is shown in CI stdout, not connected to coveralls or any coverage reporting tools yet. Linting has thresholds for failing (e.g., pylint rating below 9, black having any errors) but will not cause dev headaches by failing constantly or requiring insane configuration not to fail. Closes aflow test no longer passing #587 , closes Fix MDFDataRetrieval and MPDSDataRetrieval #227.
• Add citations function for all data_retrieval classes (closes data retrieval classes should also have citations() function (just like featurizers) #390 )
• Enable running of expensive dataset download CI on new releases only
• Enforce logical structure of featurizers (fix Restructure repo for increased readability #564 , fix External Libraries and Matminer #378)
• Update documentation comprehensively (fix Docs need to be updated for readability/links #629)
• Tune up some featurizers (SOAP fixes with newest dscribe, add sitestatsfingerprint preset for SOAP, make ERDF flat + make clear if oxi states not passed, make MinimumRelativeDistances with option for flat, improve GlobalSymmetryFeatures with n_symm_ops, improve usability of RDF for flat output, add prechecking to P/ERDFs, vastly expand testing of all of these featurizers and upgrades). Closes it's not clear ElectronicRadialDistributionFunction needs oxidation states due to uninformative error #262, closes Add presets to soap featurizer and include structure featurizer #479, closes SOAP implementation details need to be checked #420, closes A structure descriptor that is the number of symmetry operations in the spacegroup #253, closes Provide Flat Outputs for All Structure Featurizers #300.
• Move figrecipes to its own repo complete with its own doc page - Closes figrecipes should use palettable colors #232 , closes Move figrecipes to a different repo, or delete it #453, closes PlotlyFig heatmap, triangle, violin, and bar don't work with hover* options #255
• Add progress bars to store_dataframe_as_json and load_dataframe_from_json. pbar argument is optional. Also create pbar for downloading datasets from repositories like Figshare and MPContribs. Fixes Progress bar option for load_dataframe_from_json and store_dataframe_as_json #622 and fixes add progress bar for loading/dowloading datasets #588. Example of reading the matbench_log_kvrh from disk, then writing it to disk:
  
• Clean up, add tests for, and add prechecking for new WenAlloys composition featurizer
• Removal of CGCNN code: rationale being it is almost impossible to use in its current state. if we are going to include things like CGCNN, we can do it much more cleanly and reliably (I will make a separate issue for this)
• Remove CrystalSiteFingerprint featurizer which has been deprecated for years. Remove utils.conversions as they have been deprecated since mid 2018.
• Add PymatgenFunctionApplicator as a conversion featurizer, fixes Add conversions for arbitrary pymatgen composition/structure/etc #455 . Add ASEAtomsToStructure converter, fixes tutorials / examples should make it clear how to use ASE structures #388.
• Random fixes (fix move has_oxidation_states function to pymatgen? #142 )