Slightly more informative 'skipped.test' validation message

• 'skipped.test' validation message given more metadata to clarify circumstances of event.

predicate mixin patch (reverted)

• postpone full mixin predicate validation until (putative) 4.2.1 release of Biolink fixing biolink:treats predicate hierarchy

mixin predicate validation; more granular one hop validation of input test case S-P-O against TRAPI Response Message

• cleaned up predicate related mixin handling distinguishing between Biolink Model 4.2.0 versus pre-4.2.0 validation.
• Added more fine-grained validation reporting inside case_input_found_in_response() TRAPI Response validation method, also extracted "missing edge" validation message from graph-validation-tests module and embedded it into the method; added/refactored validation codes accordingly
• Full TRAPI 1.5.0 unit tests still skipped (need rework); some other unit test temporarily skipped (due to TRAPI master branch schema bugs).
• git action updates

Treats mixin permitted predicate in graphs; fixed some trapi logic

• Generalize trapi_1.4 testing predicate to trapi_1.4 or later
• biolink:treats as a mixin is tagged as permitted in TRAPI graphs (further code review for this use case is recommended)

"knowledge_level" and "agent_type" conditionally ignored for all Biolink Model releases lower than 4.2.0

Add back ATTRIBUTE_TYPE_ID_INCLUSIONS filtering for "knowledge_level" and "agent_type" such that the presence of these 'attribute_type_id' values are (blissfully) ignored, conditionally for all Biolink Model releases lower than 4.2.0

TRAPI 1.5 + some Biolink 4.2 validation, with added back support of Python 3.9

• Reasoner-validator is TRAPI 1.5 aware but nothing more than basic schema validation provided; unit tests which are incompletely refactored are skipped.
• Biolink Model 4.2.0 validation starting to be added : validate presence and values of "knowledge_level" and "agent_type", with compliant values, on all knowledge graph edges (removed previous ATTRIBUTE_TYPE_ID_INCLUSIONS for these fields, since no longer surprising to see them...)
• Update BiolinkValidator.get_result() to properly return Tuple[str, MESSAGES_BY_TARGET]
• Cleaned up some technical debt
• Some environments (i.e. ARAX) still work with Python 3.9, so add back support for this

General build refactor and upgrade workflows

• Refactored pyproject.toml specified poetry dependencies into groups rather than extras, updating README accordingly.
• Updated Git action workflows

Upgrade BMT and add BioRegistry

• Bioregistry "^0.11.1" added as a possible cure for some downstream LinkML issues.
• BMT upgraded to "^1.4.0"

Pydantic V2 upgrade

Upgrading Pydantic to "^2"; fixed associated conflicts (mainly with fastapi)

Major release 4 with new hierarchical validation message indexing

The major release changes relate to adapting the reasoner-validator to the new (2023-24) Translator testing infrastructure:

• Two higher levels of indexing are added to the message catalogue of the ValidationReporter: indexing by target (endpoint url) and indexing by test identifier.
• Support for "Skipped Tests" added to the codes.yaml and code base
• The ValidationReporter 'prefix' field converted into a 'default_target' field and accessor methods provided, with a new basic unit test
• OpenTelemetry features in API disabled for the time being, pending future update
• Validation still mainly done in TRAPI 1.4.2 but runs tests with a recent Biolink Model release 4.1.4