Reasoner-validator

Enforce kgx upgrade to >=1.6.0 (to accommodated recent linkml dependencies)

Inject more graph validation context into codes; leverage this context in message management and generation. Unit tests all fixed.

Fix python dependencies in setup.py.

This release has the full commitment to the Biolink Model Toolkit 0.8.12 release, which also defaults the Biolink Model validation to the latest release 3.0.* of the schema.

This doesn't mean that the 2.4.8 and lower Biolink Models won't be substantially validated correctly, but simply that one will expect a few spurious validation errors against such releases. One known spurious error is in the incorrect validation of 'non_canonical' predicates (i.e. canonical will be reported as `non_canonical`...).

This major release of the reasoner-validator centers around a **ValidationReporter** (Python) class wrapping all validation messages and supporting detection calls. This particular latest iteration also injects more context into the validation message codes (as a [master YAML file with hierarchically-indexed Python string templates](reasoner_validator/codes.yaml)).

The underlying code validates TRAPI responses (using _jsonschema_) against the TRAPI _ReasonerAPI.yaml_ data model and orthogonally validates Biolink Model compliance of the internal content of such responses.

A given validation targets TRAPI and Biolink Model releases as specified by user parameter or by default (generally, with default versions TRAPI 1.3 and Biolink Model (default assumed by Biolink Model Toolkit).

Various iterations of refinement of Biolink validation