chore: consolidated feature branch for ENVITED-X pipeline

examples/tutorial/tutorial01/data.ttl

@@ -1,7 +1,38 @@
 @prefix personinfo: <https://w3id.org/linkml/examples/personinfo> .
-
-[] a personinfo:Person ;
-    personinfo:age "32" ;
-    personinfo:full_name "Clark Kent" ;
-    personinfo:id "ORCID:1234" ;
-    personinfo:phone "555-555-5555" .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix wgs: <https://www.w3.org/2003/01/geo/wgs84_pos#> .
+@prefix geo: <http://www.opengis.net/ont/geosparql#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix brick: <https://brickschema.org/schema/Brick#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix qb: <http://purl.org/linked-data/cube#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix doap: <http://usefulinc.com/ns/doap#> .
+@prefix prof: <http://www.w3.org/ns/dx/prof/> .
+@prefix dcmitype: <http://purl.org/dc/dcmitype/> .
+@prefix odrl: <http://www.w3.org/ns/odrl/2/> .
+@prefix time: <http://www.w3.org/2006/time#> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix csvw: <http://www.w3.org/ns/csvw#> .
+@prefix shex: <http://www.w3.org/ns/shex#> .
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix sosa: <http://www.w3.org/ns/sosa/> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix org: <http://www.w3.org/ns/org#> .
+@prefix ssn: <http://www.w3.org/ns/ssn/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix dcam: <http://purl.org/dc/dcam/> .
+@prefix void: <http://rdfs.org/ns/void#> .
+@prefix linkml: <https://w3id.org/linkml/> .
+@prefix schema: <https://schema.org/> .
+@prefix schema1: <http://schema.org/> .
+_:c14n0 a personinfo:Person ;
+	personinfo:age "32" ;
+	personinfo:full_name "Clark Kent" ;
+	personinfo:id "ORCID:1234" ;
+	personinfo:phone "555-555-5555" .

examples/tutorial/tutorial04/data-semantic.ttl

@@ -1,17 +1,47 @@
-@prefix ORCID: <https://orcid.org/> .
+@prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> .
 @prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
-@prefix schema1: <http://schema.org/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix wgs: <https://www.w3.org/2003/01/geo/wgs84_pos#> .
+@prefix faldo: <http://biohackathon.org/resource/faldo#> .
+@prefix brick: <https://brickschema.org/schema/Brick#> .
+@prefix geo: <http://www.opengis.net/ont/geosparql#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix qb: <http://purl.org/linked-data/cube#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-ORCID:1234 a schema1:Person ;
-    schema1:name "Clark Kent" ;
-    schema1:telephone "555-555-5555" ;
-    personinfo:age 33 .
-
-ORCID:4567 a schema1:Person ;
-    schema1:name "Lois Lane" ;
-    personinfo:age 34 .
-
-[] a personinfo:Container ;
-    personinfo:persons ORCID:1234,
-        ORCID:4567 .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix doap: <http://usefulinc.com/ns/doap#> .
+@prefix prof: <http://www.w3.org/ns/dx/prof/> .
+@prefix dcmitype: <http://purl.org/dc/dcmitype/> .
+@prefix odrl: <http://www.w3.org/ns/odrl/2/> .
+@prefix time: <http://www.w3.org/2006/time#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix shex: <http://www.w3.org/ns/shex#> .
+@prefix sosa: <http://www.w3.org/ns/sosa/> .
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix csvw: <http://www.w3.org/ns/csvw#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix ssn: <http://www.w3.org/ns/ssn/> .
+@prefix org: <http://www.w3.org/ns/org#> .
+@prefix linkml: <https://w3id.org/linkml/> .
+@prefix oa: <http://www.w3.org/ns/oa#> .
+@prefix dcam: <http://purl.org/dc/dcam/> .
+@prefix void: <http://rdfs.org/ns/void#> .
+@prefix idot: <http://identifiers.org/> .
+@prefix schema: <https://schema.org/> .
+@prefix schema1: <http://schema.org/> .
+@prefix ORCID: <https://orcid.org/> .
+ORCID:1234 schema1:name "Clark Kent" ;
+	schema1:telephone "555-555-5555" ;
+	a schema1:Person ;
+	personinfo:age 33 .
+ORCID:4567 schema1:name "Lois Lane" ;
+	a schema1:Person ;
+	personinfo:age 34 .
+_:c14n0 a personinfo:Container ;
+	personinfo:persons ORCID:1234 , ORCID:4567 .

examples/tutorial/tutorial04/data.ttl

@@ -1,16 +1,47 @@
-@prefix ORCID: <https://orcid.org/> .
+@prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> .
 @prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix wgs: <https://www.w3.org/2003/01/geo/wgs84_pos#> .
+@prefix faldo: <http://biohackathon.org/resource/faldo#> .
+@prefix brick: <https://brickschema.org/schema/Brick#> .
+@prefix geo: <http://www.opengis.net/ont/geosparql#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix qb: <http://purl.org/linked-data/cube#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix doap: <http://usefulinc.com/ns/doap#> .
+@prefix prof: <http://www.w3.org/ns/dx/prof/> .
+@prefix dcmitype: <http://purl.org/dc/dcmitype/> .
+@prefix odrl: <http://www.w3.org/ns/odrl/2/> .
+@prefix time: <http://www.w3.org/2006/time#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix shex: <http://www.w3.org/ns/shex#> .
+@prefix sosa: <http://www.w3.org/ns/sosa/> .
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix csvw: <http://www.w3.org/ns/csvw#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix ssn: <http://www.w3.org/ns/ssn/> .
+@prefix org: <http://www.w3.org/ns/org#> .
+@prefix linkml: <https://w3id.org/linkml/> .
+@prefix oa: <http://www.w3.org/ns/oa#> .
+@prefix dcam: <http://purl.org/dc/dcam/> .
+@prefix void: <http://rdfs.org/ns/void#> .
+@prefix idot: <http://identifiers.org/> .
+@prefix schema: <https://schema.org/> .
+@prefix schema1: <http://schema.org/> .
+@prefix ORCID: <https://orcid.org/> .
 ORCID:1234 a personinfo:Person ;
-    personinfo:age 33 ;
-    personinfo:full_name "Clark Kent" ;
-    personinfo:phone "555-555-5555" .
-
+	personinfo:age 33 ;
+	personinfo:full_name "Clark Kent" ;
+	personinfo:phone "555-555-5555" .
 ORCID:4567 a personinfo:Person ;
-    personinfo:age 34 ;
-    personinfo:full_name "Lois Lane" .
-
-[] a personinfo:Container ;
-    personinfo:persons ORCID:1234,
-        ORCID:4567 .
+	personinfo:age 34 ;
+	personinfo:full_name "Lois Lane" .
+_:c14n0 a personinfo:Container ;
+	personinfo:persons ORCID:1234 , ORCID:4567 .

examples/tutorial/tutorial04/personinfo-semantic.shacl.ttl

@@ -1,39 +1,81 @@
 @prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix schema1: <http://schema.org/> .
-@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix wgs: <https://www.w3.org/2003/01/geo/wgs84_pos#> .
+@prefix brick: <https://brickschema.org/schema/Brick#> .
+@prefix geo: <http://www.opengis.net/ont/geosparql#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix qb: <http://purl.org/linked-data/cube#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-personinfo:Container a sh:NodeShape ;
-    sh:closed true ;
-    sh:ignoredProperties ( rdf:type ) ;
-    sh:property [ sh:class schema1:Person ;
-            sh:nodeKind sh:IRI ;
-            sh:order 0 ;
-            sh:path personinfo:persons ] ;
-    sh:targetClass personinfo:Container .
-
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix doap: <http://usefulinc.com/ns/doap#> .
+@prefix prof: <http://www.w3.org/ns/dx/prof/> .
+@prefix dcmitype: <http://purl.org/dc/dcmitype/> .
+@prefix odrl: <http://www.w3.org/ns/odrl/2/> .
+@prefix time: <http://www.w3.org/2006/time#> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix csvw: <http://www.w3.org/ns/csvw#> .
+@prefix sosa: <http://www.w3.org/ns/sosa/> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix org: <http://www.w3.org/ns/org#> .
+@prefix ssn: <http://www.w3.org/ns/ssn/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix linkml: <https://w3id.org/linkml/> .
+@prefix void: <http://rdfs.org/ns/void#> .
+@prefix dcam: <http://purl.org/dc/dcam/> .
+@prefix schema: <https://schema.org/> .
+@prefix schema1: <http://schema.org/> .
+@prefix ORCID: <https://orcid.org/> .
 schema1:Person a sh:NodeShape ;
-    sh:closed true ;
-    sh:ignoredProperties ( rdf:type ) ;
-    sh:property [ sh:maxCount 1 ;
-            sh:maxInclusive 200 ;
-            sh:minInclusive 0 ;
-            sh:order 4 ;
-            sh:path personinfo:age ],
-        [ sh:description "name of the person" ;
-            sh:maxCount 1 ;
-            sh:minCount 1 ;
-            sh:order 1 ;
-            sh:path schema1:name ],
-        [ sh:maxCount 1 ;
-            sh:order 0 ;
-            sh:path personinfo:id ],
-        [ sh:description "other names for the person" ;
-            sh:order 2 ;
-            sh:path personinfo:aliases ],
-        [ sh:maxCount 1 ;
-            sh:order 3 ;
-            sh:path schema1:telephone ;
-            sh:pattern "^[\\d\\(\\)\\-]+$" ] ;
-    sh:targetClass schema1:Person .
+	sh:closed true ;
+	sh:ignoredProperties _:c14n7 ;
+	sh:property _:c14n0 , _:c14n2 , _:c14n3 , _:c14n4 , _:c14n6 ;
+	sh:targetClass schema1:Person .
+personinfo:Container a sh:NodeShape ;
+	sh:closed true ;
+	sh:ignoredProperties _:c14n1 ;
+	sh:property _:c14n5 ;
+	sh:targetClass personinfo:Container .
+_:c14n0 sh:datatype xsd:string ;
+	sh:description "name of the person" ;
+	sh:maxCount 1 ;
+	sh:minCount 1 ;
+	sh:nodeKind sh:Literal ;
+	sh:order 1 ;
+	sh:path schema1:name .
+_:c14n1 rdf:first rdf:type ;
+	rdf:rest rdf:nil .
+_:c14n2 sh:datatype xsd:string ;
+	sh:maxCount 1 ;
+	sh:nodeKind sh:Literal ;
+	sh:order 0 ;
+	sh:path personinfo:id .
+_:c14n3 sh:datatype xsd:integer ;
+	sh:maxCount 1 ;
+	sh:maxInclusive 200 ;
+	sh:minInclusive 0 ;
+	sh:nodeKind sh:Literal ;
+	sh:order 4 ;
+	sh:path personinfo:age .
+_:c14n4 sh:datatype xsd:string ;
+	sh:maxCount 1 ;
+	sh:nodeKind sh:Literal ;
+	sh:order 3 ;
+	sh:path schema1:telephone ;
+	sh:pattern "^[\\d\\(\\)\\-]+$" .
+_:c14n5 sh:class schema1:Person ;
+	sh:nodeKind sh:IRI ;
+	sh:order 0 ;
+	sh:path personinfo:persons .
+_:c14n6 sh:datatype xsd:string ;
+	sh:description "other names for the person" ;
+	sh:nodeKind sh:Literal ;
+	sh:order 2 ;
+	sh:path personinfo:aliases .
+_:c14n7 rdf:first rdf:type ;
+	rdf:rest rdf:nil .

packages/linkml/pyproject.toml

@@ -49,7 +49,10 @@ dependencies = [ # Specifier syntax: https://peps.python.org/pep-0631/
     "openpyxl",
     "parse",
     "prefixcommons >= 0.1.7",
-    "prefixmaps >= 0.2.2",
+    # TODO(prefixmaps-0.2.8): Replace git pin with "prefixmaps >= 0.2.8" once released,
+    #   then remove [tool.hatch.metadata] allow-direct-references and regenerate uv.lock.
+    #   Tracked in: https://github.com/linkml/prefixmaps/issues/82
+    "prefixmaps @ git+https://github.com/linkml/prefixmaps@75435150a1b31760b9780af2b64a265943a9b263",
     "pydantic >= 2.0.0, < 3.0.0",
     "pyjsg >= 0.11.6",
     "pyshex >= 0.7.20",
@@ -78,7 +81,6 @@ tests = [
   { include-group = "lint" },
   { include-group = "typing" },
   { include-group = "shacl" },
-  "morph-kgc >= 2.9.0; python_version >= '3.10'"
 ]
 dev = [
   {include-group = "tests" },
@@ -196,6 +198,10 @@ vcs = "git"
 style = "pep440"
 fallback-version = "0.0.0"
 
+[tool.hatch.metadata]
+# TODO(prefixmaps-0.2.8): Remove this section once the git pin is replaced with >= 0.2.8
+allow-direct-references = true
+
 [tool.hatch.version]
 source = "uv-dynamic-versioning"
 

packages/linkml/src/linkml/generators/golanggen/template.py

@@ -41,8 +41,8 @@ class GolangTemplateModel(TemplateModel):
         trim_blocks=True,
         lstrip_blocks=True,
     )
-    _environment.filters["go_comment"] = lambda text, indent="": (
-        "\n".join(f"{indent}// {line}" if line.strip() else f"{indent}//" for line in text.splitlines())
+    _environment.filters["go_comment"] = lambda text, indent="": "\n".join(
+        f"{indent}// {line}" if line.strip() else f"{indent}//" for line in text.splitlines()
     )
 
     meta_exclude: ClassVar[list[str]] = None