Merge pull request #41 from linkml/bump-linkml-version

bumped version
linkml · Feb 27, 2024 · 8e2b8c6 · 8e2b8c6
2 parents 3ea977a + a6f2a5e
commit 8e2b8c6
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Showing 8 changed files with 1,399 additions and 1,183 deletions.
diff --git a/Makefile b/Makefile
@@ -4,8 +4,7 @@ RUN = poetry run
 all: docs/examples.md test
 
 test:
-	$(RUN) python -m unittest discover
-#	$(RUN) pytest
+	$(RUN) pytest tests
 
 tests/model/%.py: tests/model/%.yaml
 	$(RUN) gen-python $< > $@.tmp && mv $@.tmp $@

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -34,13 +34,13 @@ style = "pep440"
 linkml-data2owl = "linkml_owl.dumpers.owl_dumper:cli"
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.8.1"
 
 click = "*"
 funowl = ">=0.2.3"
 Jinja2 = ">=3.0.3"
-linkml = ">=1.3.0"
-linkml-runtime = ">=1.3.4"
+linkml = ">=1.7.4"
+linkml-runtime = ">=1.7.0"
 
 [tool.poetry.dev-dependencies]
 tox = ">=3.24.5"

diff --git a/tests/inputs/expected_ro.ofn b/tests/inputs/expected_ro.ofn
@@ -29,6 +29,7 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/RO_0002131> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000051> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/BFO_0000051> "has part" )
+    AnnotationAssertion( dcterms:conformsTo BFO:0000051 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000051> )
     TransitiveObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000050> )
     SubObjectPropertyOf(     ObjectPropertyChain(
@@ -59,6 +60,7 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/BFO_0000004> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002203> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002203> "develops into" )
+    AnnotationAssertion( dcterms:conformsTo RO:0002203 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/RO_0002203> )
     TransitiveObjectProperty( <http://purl.obolibrary.org/obo/RO_0002202> )
     AnnotationAssertion( IAO:0000115 RO:9999998 "Inverse of RO:0002012 occurrent part of" )
@@ -70,6 +72,7 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000003> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_9999998> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_9999998> "has occurrent part" )
+    AnnotationAssertion( dcterms:conformsTo RO:9999998 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/RO_9999998> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002104> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002104> "has plasma membrane part" )
@@ -93,10 +96,12 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002447> <http://purl.obolibrary.org/obo/RO_0002436> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_9999999> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_9999999> "phosphorylated by" )
+    AnnotationAssertion( dcterms:conformsTo RO:9999999 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002447> <http://purl.obolibrary.org/obo/RO_9999999> )
     SubClassOf( GO:0016301     ObjectHasSelf( RO:0002481 ) )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002481> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002481> "is kinase activity" )
+    AnnotationAssertion( dcterms:conformsTo RO:0002481 rometa:RolifiedObjectProperty )
     AnnotationAssertion( IAO:0000115 RO:0018003 "Inverse of RO:0018002 myristoylates" )
     SubObjectPropertyOf( RO:0018001 RO:0002564 )
     AnnotationAssertion( IAO:0000115 RO:0018001 "Helper relation for OWL definition of RO:0018002 myristoylates" )
@@ -112,8 +117,10 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0018002> <http://purl.obolibrary.org/obo/RO_0002436> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018003> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018003> "myristoylated by" )
+    AnnotationAssertion( dcterms:conformsTo RO:0018003 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0018002> <http://purl.obolibrary.org/obo/RO_0018003> )
     SubClassOf( GO:0019107     ObjectHasSelf( RO:0018001 ) )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018001> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018001> "is myristoyltransferase activity" )
+    AnnotationAssertion( dcterms:conformsTo RO:0018001 rometa:RolifiedObjectProperty )
 )
diff --git a/tests/inputs/monsters_and_magic.yaml b/tests/inputs/monsters_and_magic.yaml
@@ -404,7 +404,7 @@ slots:
       owl: AnnotationProperty
 
   type:
-    designates_type: true
+    #designates_type: true
     #range: Grouping
     description: >-
       The type of a thing