linkml 1.8.7__py3-none-any.whl → 1.9.0rc1__py3-none-any.whl

linkml/generators/docgen/class.md.jinja2

@@ -21,7 +21,7 @@
     {%- endif -%}
 {% endmacro %}
 
-# Class: {{ title }}
+# Class: {{ title }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
 
 {%- if header -%}
 {{header}}

linkml/generators/docgen/enum.md.jinja2

@@ -1,4 +1,4 @@
-# Enum: {{ gen.name(element) }}
+# Enum: {{ gen.name(element) }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
 
 {% if element.description %}
 {% set element_description_lines = element.description.split('\n') %}

linkml/generators/docgen/schema.md.jinja2

@@ -1,4 +1,4 @@
-# {{ schema.name }}
+# {{ schema.name }} {% if schema.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
 
 {{ schema.description }}
 

linkml/generators/docgen/slot.md.jinja2

@@ -21,7 +21,7 @@
     {%- endif -%}
 {% endmacro %}
 
-# Slot: {{ title }}
+# Slot: {{ title }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
 
 {%- if header -%}
 {{header}}
@@ -40,6 +40,9 @@ _{{ element_description_line }}_
 
 URI: {{ gen.uri_link(element) }}
 
+{%- if element.alias %}
+Alias: {{ element.alias }}
+{% endif -%}
 
 {% if schemaview.slot_parents(element.name) or schemaview.slot_children(element.name, mixins=False) %}
 

linkml/generators/docgen/subset.md.jinja2

@@ -1,4 +1,4 @@
-# Subset: {{ gen.name(element) }}
+# Subset: {{ gen.name(element) }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
 
 {%- if header -%}
 {{ header }}

linkml/generators/docgen/type.md.jinja2

@@ -1,4 +1,4 @@
-# Type: {{ gen.name(element) }}
+# Type: {{ gen.name(element) }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
 
 {% if element.description %}
 {% set element_description_lines = element.description.split('\n') %}

linkml/generators/linkmlgen.py

@@ -114,8 +114,16 @@ def cli(
 ):
     # You can use the `--materialize` / `--no-materialize` for control
     # over both attribute and pattern materialization.
-    materialize_attributes = bool(materialize)
-    materialize_patterns = bool(materialize)
+
+    # If the user did not explicitly specify materialize_attributes,
+    # fall back to the umbrella materialize flag.
+    if materialize_attributes is None:
+        materialize_attributes = materialize
+
+    # If the user did not explicitly specify materialize_patterns,
+    # fall back to the umbrella materialize flag.
+    if materialize_patterns is None:
+        materialize_patterns = materialize
 
     gen = LinkmlGenerator(
         yamlfile,

linkml/generators/shaclgen.py

@@ -30,6 +30,8 @@ class ShaclGenerator(Generator):
     """parameterized suffix to be appended. No suffix per default."""
     include_annotations: bool = False
     """True means include all class / slot / type annotations in generated Node or Property shapes"""
+    exclude_imports: bool = False
+    """If True, elements from imported ontologies won't be included in the generator's output"""
     generatorname = os.path.basename(__file__)
     generatorversion = "0.0.1"
     valid_formats = ["ttl"]
@@ -63,7 +65,7 @@ class ShaclGenerator(Generator):
         for pfx in self.schema.prefixes.values():
             g.bind(str(pfx.prefix_prefix), pfx.prefix_reference)
 
-        for c in sv.all_classes().values():
+        for c in sv.all_classes(imports=not self.exclude_imports).values():
 
             def shape_pv(p, v):
                 if v is not None:
@@ -364,6 +366,13 @@ def add_simple_data_type(func: Callable, r: ElementName) -> None:
     show_default=True,
     help="Use --include-annotations to include annotations of slots, types, and classes in the generated SHACL shapes.",
 )
+@click.option(
+    "--exclude-imports/--include-imports",
+    default=False,
+    show_default=True,
+    help="Use --exclude-imports to exclude imported elements from the generated SHACL shapes. This is useful when "
+    "extending a substantial ontology to avoid large output files.",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **args):
     """Generate SHACL turtle from a LinkML model"""

{linkml-1.8.7.dist-info → linkml-1.9.0rc1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.8.7
+Version: 1.9.0rc1
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink

{linkml-1.8.7.dist-info → linkml-1.9.0rc1.dist-info}/RECORD

@@ -15,16 +15,16 @@ linkml/generators/common/template.py,sha256=bjcSNiC85MYl9oGhk0ZpqwZpRxxy_NqxG8XB
 linkml/generators/common/type_designators.py,sha256=lgVcIRJJ-yCvVGeP9U_gQZpm77UmJBQo9Bh3lGJITno,1956
 linkml/generators/csvgen.py,sha256=O20K3IuDxomGJAyNFJmm1_HbPyl6xUK0l-aKY0A3KcM,3253
 linkml/generators/dbmlgen.py,sha256=IrtY65iFdXg4wHBP9vHQeV20HUOUB1XlggPtmt_YvGM,5466
-linkml/generators/docgen/class.md.jinja2,sha256=-JmjYHgYOaaBYd5r-Tr5dkk0CLM_lX0kHdocPQtRsjU,3504
+linkml/generators/docgen/class.md.jinja2,sha256=LqQSKfH-wWR1ELTbhuEK5QFypU__uqwLmbGvS9rZsKo,3602
 linkml/generators/docgen/class_diagram.md.jinja2,sha256=gzskx4hOpU_s6BqOXdYZ9DwKxuClnsEgDzPurm30PeY,3469
 linkml/generators/docgen/common_metadata.md.jinja2,sha256=gy9J8rghBfKDKimwtHj_XuHY4PJRRYHLXVlBHqWrUzU,1604
-linkml/generators/docgen/enum.md.jinja2,sha256=mXnUrRkleY2bOTEyAZ5c4pcUnqhs6BNa8a-4LVve-eo,1014
+linkml/generators/docgen/enum.md.jinja2,sha256=BCi4PUamCjszM17yrg2KNltR_JfrBjNdH87S5uz9DtY,1112
 linkml/generators/docgen/index.md.jinja2,sha256=suXRgJydHrxcMm3quXukaKkThtdzYA9i7BTuMAVKOP0,1502
 linkml/generators/docgen/index.tex.jinja2,sha256=Go_EA-_N4JUpbOYbk3OY11mz5yV70VF2l2sMtgIPWw4,501
-linkml/generators/docgen/schema.md.jinja2,sha256=xlENfnzNRYgPT_0tdqNFxgklVM4Qf5BuzhFVvSMDuxs,70
-linkml/generators/docgen/slot.md.jinja2,sha256=dJHugIv9OPTi3FIn8Iez7CzjQizdXrcn0hcmCmXSgV4,3339
-linkml/generators/docgen/subset.md.jinja2,sha256=EPln_fjlhlkmwEGEp2iPX-9Xm2vVodPZLlRBlYCB_sA,2705
-linkml/generators/docgen/type.md.jinja2,sha256=QmCMJZrFwP33eHkggBVtypbyrxTb-XZn9vHOYojVaYk,635
+linkml/generators/docgen/schema.md.jinja2,sha256=b52xmnlTheigxKgP_2Sq1nnQUEW6XNi_ScPnqxptjps,167
+linkml/generators/docgen/slot.md.jinja2,sha256=_0xgRUlSYJMpxwGcboFoCAcELFDEzzXSTwBduPvwY-Q,3501
+linkml/generators/docgen/subset.md.jinja2,sha256=ttcsDa2fLYOU1_tDzHOyEsplhc1UHY_cy1_apQZyk6A,2803
+linkml/generators/docgen/type.md.jinja2,sha256=K0f7x5b3Nfjm1W-rDI4OHj2sU-RNm9hP1nuRJjHHJMU,733
 linkml/generators/docgen.py,sha256=iDSu2LsZ7MStrzXdxFwK-oBlVevq2MwBc1n5WzHzTyw,38996
 linkml/generators/dotgen.py,sha256=vjHveFtKBItHRkowi1I4FHffcn4u4wLpBydYgVxB-vE,5028
 linkml/generators/erdiagramgen.py,sha256=BteqzyVgKeUXfdCq3VHiiJMbuMrsn_D08IoNq8QMBcY,11462
@@ -39,7 +39,7 @@ linkml/generators/jsonldcontextgen.py,sha256=LpuTtzU4H6BH_615E4Fbt0QBCEopvqRMVOM
 linkml/generators/jsonldgen.py,sha256=d94TEPu9zeHDZqPU6cSaiQiJnv0kc_AXkXahi1xOBZ8,7789
 linkml/generators/jsonschemagen.py,sha256=8luthDkItlZ5bU4Lxt9b7tZx0HTIP4FZEZ5C2nwMMqA,30867
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/generators/linkmlgen.py,sha256=7GbD-ZErCblapbl_CukfHvFYOTbhgWiTIyg6O5BJSO0,3915
+linkml/generators/linkmlgen.py,sha256=xYgS4i-Xo5Z3t9gqEdqxHKv5KGUxOerpy8M9kX6WeuI,4225
 linkml/generators/markdowngen.py,sha256=0gjMPJ0Ycm9se4Y4cyqjbTntGYqRRZu4RL-9Qf5n4lk,34464
 linkml/generators/mermaidclassdiagramgen.py,sha256=NzRDXmy2qMOUHmvrcd7LrKZiVR1J___pLRhQpGstGyA,4946
 linkml/generators/namespacegen.py,sha256=C4p9LSwsnDqf6sv-wG5l0VQniWFJ1HA1hRXJBDOg3pM,6467
@@ -72,7 +72,7 @@ linkml/generators/rdfgen.py,sha256=OT8oS8MPUVf5UK3OKvRWgAh9iQiWwdyWJSA69PncOw4,2
 linkml/generators/shacl/__init__.py,sha256=KgMOyESGTdKk2Vhx9uuUYgEJPuJQ-iT1vDQVIMoiXCM,58
 linkml/generators/shacl/shacl_data_type.py,sha256=gX3Y2KyTVPwMyef0cJMTEpU9h0oH-H0ThVDORdNW170,1828
 linkml/generators/shacl/shacl_ifabsent_processor.py,sha256=usmqdCvAPiivHzXWkNzW0G_KOaAG8bHdTCkEH2pI0b4,4364
-linkml/generators/shaclgen.py,sha256=RcGoo4j-NJUavbdUo1gnYo4mXTivaYb8o-oIfaUrA_g,14833
+linkml/generators/shaclgen.py,sha256=Gvg6Tm7S1FMQxPZ7fJErMrJ3mUbi5rj1yYPTiuuDf-Y,15283
 linkml/generators/shexgen.py,sha256=cr4x4ORZlre6XlToWKho5F4XjFwOlzR1SpOpbeOvRA4,9939
 linkml/generators/sparqlgen.py,sha256=2DaFrFIeMI7QQfiPn79J8ERILlkJALrabDnKK7usDJQ,6188
 linkml/generators/sqlalchemy/__init__.py,sha256=mb9AC1rIFkSiNZhhG0TAk45ol9PjS1XvsrvCjgfVUpQ,249
@@ -155,8 +155,8 @@ linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 linkml/workspaces/datamodel/workspaces.py,sha256=4HdkqweGNfMPqnB1_Onc9DcTfkhoagTRcqruh08nRoI,14905
 linkml/workspaces/datamodel/workspaces.yaml,sha256=EjVrwPpeRZqJRjuGyyDRxxFzuv55SiLIXPBRUG6HStU,4233
 linkml/workspaces/example_runner.py,sha256=oViQ5gT8NkFTZbg0dW5LAOSAOAfJK8_QmKdYwzzGhgQ,12919
-linkml-1.8.7.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.8.7.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.8.7.dist-info/METADATA,sha256=hubj7dcgTrPQ2ZHmC9Es38FRabdXlkYzrYOqHNp_PS0,3874
-linkml-1.8.7.dist-info/entry_points.txt,sha256=CtvrM-5f3NuMEBTXONEnIo5UUJegBRWJvXUmrYfdIfM,2194
-linkml-1.8.7.dist-info/RECORD,,
+linkml-1.9.0rc1.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.9.0rc1.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
+linkml-1.9.0rc1.dist-info/entry_points.txt,sha256=CtvrM-5f3NuMEBTXONEnIo5UUJegBRWJvXUmrYfdIfM,2194
+linkml-1.9.0rc1.dist-info/METADATA,sha256=U1wGvCcI0OTj9vrh7K-P_Avet2QMD1jGe1IA_jKCuuA,3877
+linkml-1.9.0rc1.dist-info/RECORD,,