Properties Calc/WkChain Improvements and Testing changes

• Large improvement/refactor of properties calculations and workchains:

  • Rename cry_ -> prop_
  • Renamed crystal17.fermi -> crystal17.newk
  • Subclass calculations from base PropAbstractCalculation;
    • all calculation take as input a wf_folder and parameter dict
    • all calculations output a result dict
    • no longer options to symlink wf_folder (it doesn't work)
    • wf_folder can now be a standard folder (or remote)
  • Add raw parsers for parsing properties stdout and gaussian cube files.
  • Parsers all use read_properties_stdout to parse standard output data, and check for errors,
    also exit codes are saved for each step, then the highest priority code is returned at the end.
  • Changed inputs/outputs of crystal17.fermi.
  • Add crystal17.ech3 calculation and parser (stores cube files as GaussianCube data objects).
  • Updated CryPropertiesWorkChain to run multiple properties calculation.
  • Add creation of VESTA file, from cube data file.
  • crystal17.doss; fix parsing of projections.
  • Update band_gap calcfunction, to use correct energy units format.
  • Add documentation: calc_doss, workflow_properties, calc_ech3.

• Improve CRYSTAL main stdout parser.

  • Extract mulliken orbital and shell populations.
  • parse 0D (MOLECULE) cartesian coordinates
  • improve regex for removing PROCESS and Fortran warning lines
  • ignore all open_hca: getaddr_netdev ERROR lines, that can occur before program start.
  • fix issues with computations that converge after the 1st cycle.

• Add fort.9 raw parser.

• Symmetry: allow for use of symbol (rather than kind) to define
  inequivalent sites.

• Improved BasisSetData.set_file and BasisSetData.upload_basisset_family,
  to accept pathlib.Path and filelike objects.

• Programatically Access Resource Files:

  Non-python files (JSON schema and raw files) are now accessed programatically,
  using the importlib_resources package.
  This means that (a) they can be accessed even if the package is zipped and,
  (b) these files can be moved to a separate package in the future.

• Replace Travis flake8/version tests with a pre-commit test:

  • Updated pre-commit and yapf versions have been updated, and
  • pre-commit run -a has been applied to the repository.
  • Added conda test, to check the conda_dev_env.yml works.

• Add pytest plugin configuration:

  • Use pytest command-line arguments to control run configuration.
  • Replace MOCK_CRY17_EXECUTABLES environmental variable with
    pytest --cry17-no-mock,
    and CRY17_TEST_WORKDIR with pytest --cry17-workdir "test_workdir".
  • Add --cry17-skip-exec, for skipping tests call executable.
  • Add pytest-notebook dependency and test function, to test and regenerate tutorial notebooks.

• GULP: improve ReaxFF parser:

  • correctly handle read/write of X symbol
  • allow reaxff tolerance value to be set, when reading file to dict.