[REF] Refactor utilities

[alyssadai]

• Closes #350
• Closes #164

Changes proposed in this pull request:

• move all utility files into a utilities module
• rename utility.py to model_utils.py (includes utility functions related to generating + extracting entities from graph dataset instances, etc.)
• split test_utility.py into:
  • test_putil.py
  • test_butil.py
  • test_dutil.py
  • test_futil.py
  • test_mutil.py
  • and organized them into integration/ and unit/ subdirs
• remove test test_generate_context() (it replicates logic of function being tested and is hard to maintain)
• refactor out into utility functions:
  • merging context + final dataset instance for output to JSONLD
  • saving final JSONLD

Checklist

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• [x] PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• [x] PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• [x] PR links to GitHub issue with mention Closes #XXXX
• [x] Tests pass
• [x] Checks pass

For new features:

• [x] Tests have been added

For bug fixes:

• [ ] There is at least one test that would fail under the original bug conditions.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 98.36%. Comparing base (e93423d) to head (e387f06). Report is 11 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #385 +/- ## ========================================== - Coverage 98.37% 98.36% -0.01% ========================================== Files 16 21 +5 Lines 982 980 -2 ========================================== - Hits 966 964 -2 Misses 16 16 ```

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[coveralls]

Pull Request Test Coverage Report for Build 11784441718

Details

• 229 of 229 (100.0%) changed or added relevant lines in 9 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-0.004%) to 98.367%

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Totals
Change from base Build 11716298122:	-0.004%
Covered Lines:	964
Relevant Lines:	980

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💛 - Coveralls

[alyssadai]

Hey @surchs, just to reply to your concern regarding the removed test:

I think we already had the case that we didn't include a class in the context and that then breaks things in confusing ways. So I don't think removing the test completely is a solution either

To clarify, we added two new tests in PR #349, test_all_used_namespaces_have_urls and test_used_namespaces_in_context, that should catch these issues without requiring us to remember to update the test parameters whenever we update the data model! :) The removed test was just leftover from a #TODO in that PR.

[neurobagel-bot[bot]]

:rocket: PR was released in v0.3.4 :rocket: