Update save recursive and layout

[francescalb]

Description

Update layout and fix recursive saving of ontology

* save now returns the path to the saved ontology.
  This change does not change the previous usage.
  This is practical when the filename is generated and not given.

* generated layout is updated so that the root is (protocol+domain)
  if there are more of these. Otherwise the generated layout is as before.

* updated test_save to check emmo-structure, recursive saving, also for
  emmo based domain ontologies that import ontologies with various starts of iris

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

[codecov]

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (d59e983) 71.52% compared to head (577931d) 71.74%.

Files	Patch %	Lines
ontopy/ontology.py	94.73%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #710      +/-   ##
==========================================
+ Coverage   71.52%   71.74%   +0.22%     
==========================================
  Files          16       16              
  Lines        3407     3423      +16     
==========================================
+ Hits         2437     2456      +19     
+ Misses        970      967       -3     

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[jesper-friis]

Very nice PR 👍

Added a few comments and suggestions.

[jesper-friis]

Followed up on two comments