Added directory_layout() function

[jesper-friis]

Description

It can suggest a directory layout from the IRIs of all the imported ontologies.

The generation of catalog files has been updated and some bugs in write_catalog() has been fixed. Including:

• irimap dict is now not modified as a side-effect when relative_paths is true
• relative paths in irimap are not modified
• absolute paths written to the catalog file are now relative to the directory or the catalog file when relative_path=True

The read_catalog() has gotten a new argument relative_to which is needed when asking for relative paths. Using this argument ensures that the catalog test is now not dependent on the current working directory when invoking the test.

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: 3 lines in your changes are missing coverage. Please review.

Comparison is base (b6594d1) 71.02% compared to head (5b10822) 71.49%.
Report is 1 commits behind head on master.

Files	Patch %	Lines
ontopy/utils.py	92.30%	2 Missing ⚠️
ontopy/ontology.py	95.23%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #696      +/-   ##
==========================================
+ Coverage   71.02%   71.49%   +0.46%     
==========================================
  Files          16       16              
  Lines        3369     3385      +16     
==========================================
+ Hits         2393     2420      +27     
+ Misses        976      965      -11     

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[francescalb]

This looks good, but please describe system for how the layout is generated.

[francescalb]

PLease explain the heurestics more in detail. This is documentation so that people understand what to expect.

[jesper-friis]

Har lagt til et eksempel i docstring.