This PR switches JPhyloRef to being able to test model 2.0 ontologies, i.e. by expecting Phyloreferences to be classes instead of instances. This updates the testing files so that they are in model 2.0 as well. It also adds support for the Elk reasoner, which is now the default reasoner.
Note that JPhyloRef still uses the old system for deciding whether a phyloreference has resolved correctly, i.e. by comparing a phylogeny node's label and its testcase:expected_phyloreference_named property to the label of the resolved phyloreference. I'll add that in a separate PR once phyx.js supports that.
This PR switches JPhyloRef to being able to test model 2.0 ontologies, i.e. by expecting Phyloreferences to be classes instead of instances. This updates the testing files so that they are in model 2.0 as well. It also adds support for the Elk reasoner, which is now the default reasoner.
Note that JPhyloRef still uses the old system for deciding whether a phyloreference has resolved correctly, i.e. by comparing a phylogeny node's label and its
testcase:expected_phyloreference_namedproperty to the label of the resolved phyloreference. I'll add that in a separate PR once phyx.js supports that.