nlesc-nano/data-CAT: Data-CAT 0.4.0

See https://github.com/nlesc-nano/data-CAT/milestone/3:

• Updated the hdf5 logging system.
• Moved all dtype-related functions and data to dataCAT.dtype.
• Cleaned up the global namespace.
• Added the PDBContainer.index attribute.
• Create the index Dataset when calling PDBContainer.create_hdf5_group(). Aforementioned Dataset is used as dimensional scale.
• Provide users more control over the keyword arguments used for creating datasets.
• Fixed an issue wherePDBContainer.to_molecules() would set values as numpy scalars rather than using its builtin counterparts.
• Added an API for creating and managing datasets for containing quantum-mechanical properties in hdf5 format.
• Cleaned up the backwards-compatibility checks in dataCAT.create_database.