Merged changes

[jesper-friis]

Description

Merged changes from PRs #739, #740 and #742.

The aim of this PR is to have one place to fix failing tests. Real bugs to be addressed:

• test_save.py: Sub-directories for catalogue files are not created even though the argument mkdir=True is provided to Ontology.save().
• ontopy_tests/test_iri.py: Ontology.save() does now save turtle file.
• tools/test_ontoconvert.py: The annotation comment is not available for copy_annotations().

Type of change

• Bug fix.
• New feature.
• Documentation update.
• Test 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

[jesper-friis]

Closing. most changes should have been taken care of by now...