Commit re-generated Makefile.

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for cl
 # Generated using ontology-development-kit
-# ODK Version: v1.5.2
+# ODK Version: v1.5.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use cl.Makefile instead
 
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                9b733c5ec38a935d574d153b99b0d69d2e8f730b562d33d8ece39a3917e022b7
+CONFIG_HASH=                54146b660b46ab72c0abd98ae67a46d194ff618c90da889ded7ed1b99fd74ae2
 
 
 # ----------------------------------------
@@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy illegal-date def-not-only-xref 
 SPARQL_EXPORTS =            cl_terms cl-edges cl-synonyms cl-xrefs cl-def-xrefs 
-ODK_VERSION_MAKEFILE =      v1.5.2
+ODK_VERSION_MAKEFILE =      v1.5.3
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -102,7 +102,7 @@ release_diff: $(REPORTDIR)/release-diff.md
 
 .PHONY: reason_test
 reason_test: $(EDIT_PREPROCESSED)
-	$(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed asserted-only \
+	$(ROBOT) reason --input $< --reasoner WHELK --equivalent-classes-allowed asserted-only \
 		--exclude-tautologies structural --output test.owl && rm test.owl
 
 .PHONY: odkversion
@@ -854,9 +854,9 @@ ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --tri
 # base: A version of the ontology that does not include any externally imported axioms.
 $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \
-	reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
+	reason --reasoner WHELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
 	relax \
-	reduce -r ELK \
+	reduce -r WHELK \
 	remove --base-iri http://purl.obolibrary.org/obo/CP_ --base-iri http://purl.obolibrary.org/obo/CL_ --base-iri http://purl.obolibrary.org/obo/cl# --axioms external --preserve-structure false --trim false \
 	$(SHARED_ROBOT_COMMANDS) \
 	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
@@ -865,9 +865,9 @@ $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 # Full: The full artefacts with imports merged, reasoned.
 $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \
-		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
+		reason --reasoner WHELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
 		relax \
-		reduce -r ELK \
+		reduce -r WHELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
 # foo-non-classified: (edit->imports-merged)
 $(ONT)-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
@@ -878,12 +878,12 @@ $(ONT)-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 #	remove --select imports --trim false
 $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \
-		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
+		reason --reasoner WHELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
 		relax \
 		remove --axioms equivalent \
 		relax \
 		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
-		reduce -r ELK \
+		reduce -r WHELK \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
 
@@ -892,14 +892,14 @@ $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILE
 # removes any axioms that contains one of the ops that not in the whitelist file
 $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATIONS) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \
-		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
+		reason --reasoner WHELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
 		relax \
 		remove --axioms equivalent \
 		remove --axioms disjoint \
 		remove --term-file $(KEEPRELATIONS) --select complement --select object-properties --trim true \
 		relax \
 		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
-		reduce -r ELK \
+		reduce -r WHELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
 
 cl-plus.owl: