chrisjsewell/aiida-crystal17: 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.