Add functionality for setting name part of IRI to prefLabel

[jesper-friis]

fix #398

Description:

Added --rename-iris and --annotate-source options of ontoconvert.
In order to allow combining these options with with the --squash, --recursive and --reasoner options, the --squash and --recursive functionality had to be moved into Ontology.save(), which made this PR ending up being quite large... It didn't became better, when I realised that the Owlready2 currently completely messes up the ontology when adding new relations from the reasoner...

Changes:

• implemented ontopy.utils.rename_iris()
• implemented ontopy.utils.annotate_sources()
• improved writing of catalog files
• added recursive, squash and write_catalog_file keyword arguments to Ontology.save()
• cleaned up Ontology.sync_reasoner()
• added new options to the ontoconvert tool
• added a workaround to ontoconvert for correct reasoning using rdflib - if the related bug in Owlready2 is not fixed soon, we should consider to add a correct implementation of owlready2.reasoning._apply_reasoning_results() to EMMOntoPy.

Type of change:

• Bug fix.
• [ x] New feature.
• Documentation update.

Checklist:

This checklist can be used as a help for the reviewer.

• Is the code easy to read and understand?
• Are comments for humans to read, not computers to disregard?
• Does a new feature has an accompanying new test (in the CI or unit testing schemes)?
• Has the documentation been updated as necessary?
• Does this close the issue?
• Is the change limited to the issue?
• Are errors handled for all outcomes?
• Does the new feature provide new restrictions on dependencies, and if so is this documented?

Comments:

[francescalb]

Remove uneccesary functions that remain in utils so that we do not do the same things wtice in two different places.

[francescalb]

Also a test is needed

[francescalb]

Looks good. I think the has_triple and get_triples can be made as general utility functions. I suggest adding an Issue on that referring to the code here.