Develop -> Master merge, release v6.0.0

[mdorf]

Overview

This PR merges develop into master for the v6.0.0 release of ncbo_annotator.

This release follows the upgrade and compatibility work introduced in:

• Infra: upgrade ncbo_annotator to Ruby 3.2 and Minitest 6 #47

It brings ncbo_annotator in line with the updated OntoPortal stack and modernizes the runtime and test infrastructure.

Prerequisites

• Sync: align ncbo/sparql-client with the AgroPortal codebase sparql-client#10
• Sync: align ncbo/goo with the AgroPortal codebase goo#176
• Sync: align ncbo/ontologies_linked_data with the AgroPortal codebase ontologies_linked_data#266

Highlights

• Ruby 3.2 upgrade
• Migration to Minitest 6
• Alignment with updated OntoPortal dependencies (goo, ontologies_linked_data, sparql-client)
• RDF 3.x compatibility fixes (including imported fix from AgroPortal)
• Test stability improvements and OntoPortal testkit integration

Notes

• AgroPortal lemmatizer support is not included in this release
• This is a major version bump from the v5.x series to v6.0.0

Post-merge

Tag master as:

• v6.0.0

[codecov-commenter]

Codecov Report

❌ Patch coverage is 85.71429% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.21%. Comparing base (6671099) to head (5243ea8).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
lib/ncbo_annotator.rb	81.81%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #48      +/-   ##
==========================================
+ Coverage   79.17%   79.21%   +0.03%     
==========================================
  Files           9        9              
  Lines         658      659       +1     
==========================================
+ Hits          521      522       +1     
  Misses        137      137              

Flag	Coverage Δ
ag	79.21% <85.71%> (?)
fs	79.21% <85.71%> (?)
gd	79.21% <85.71%> (?)
unittests	79.21% <85.71%> (+0.03%)	⬆️
vo	79.21% <85.71%> (?)

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