[REF] Refactor utilities

[alyssadai]

• Closes Refactor utility modules and test_utility.py #350
• Closes Refactor the tests to be clearer and better differentiated between integration and unit #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

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For new features:

• Tests have been added

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files

@@            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

[surchs]

Thanks @alyssadai for this refactor. I think it looks very nice!
I have some very minor clarity comments, take a look.

remove test test_generate_context() (it replicates logic of function being tested and is hard to maintain)

agreed, but 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. I don't have a great idea, but let's discuss this in a follow-up issue.

🧑‍🍳

[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]

🚀 PR was released in v0.3.4 🚀