linkml 1.8.7__tar.gz → 1.9.0rc1__tar.gz

{linkml-1.8.7 → linkml-1.9.0rc1}/PKG-INFO

@@ -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 → linkml-1.9.0rc1}/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-1.8.7 → linkml-1.9.0rc1}/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-1.9.0rc1/linkml/generators/docgen/schema.md.jinja2

@@ -0,0 +1,7 @@
+# {{ schema.name }} {% if schema.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
+
+{{ schema.description }}
+
+URI: {{ schema.id }}
+
+

{linkml-1.8.7 → linkml-1.9.0rc1}/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-1.8.7 → linkml-1.9.0rc1}/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-1.8.7 → linkml-1.9.0rc1}/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-1.8.7 → linkml-1.9.0rc1}/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-1.8.7 → linkml-1.9.0rc1}/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 → linkml-1.9.0rc1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "linkml"
-version = "1.8.7"
+version = "1.9.0rc1"
 description = "Linked Open Data Modeling Language"
 authors = [
     "Chris Mungall <cjmungall@lbl.gov>",

{linkml-1.8.7 → linkml-1.9.0rc1}/setup.py

@@ -121,7 +121,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'linkml',
-    'version': '1.8.7',
+    'version': '1.9.0rc1',
     'description': 'Linked Open Data Modeling Language',
     'long_description': '[![Pyversions](https://img.shields.io/pypi/pyversions/linkml.svg)](https://pypi.python.org/pypi/linkml)\n![](https://github.com/linkml/linkml/workflows/Build/badge.svg)\n[![PyPi](https://img.shields.io/pypi/v/linkml.svg)](https://pypi.python.org/pypi/linkml)\n[![badge](https://img.shields.io/badge/launch-binder-579ACA.svg)](https://mybinder.org/v2/gh/linkml/linkml/main?filepath=notebooks)\n[![DOI](https://zenodo.org/badge/13996/linkml/linkml.svg)](https://zenodo.org/badge/latestdoi/13996/linkml/linkml)\n[![PyPIDownloadsTotal](https://pepy.tech/badge/linkml)](https://pepy.tech/project/linkml)\n[![PyPIDownloadsMonth](https://img.shields.io/pypi/dm/linkml?logo=PyPI&color=blue)](https://pypi.org/project/linkml)\n[![codecov](https://codecov.io/gh/linkml/linkml/branch/main/graph/badge.svg?token=WNQNG986UN)](https://codecov.io/gh/linkml/linkml)\n\n\n# LinkML - Linked Data Modeling Language\n\nLinkML is a linked data modeling language following object-oriented and ontological principles. LinkML models are typically authored in YAML, and can be converted to other schema representation formats such as JSON or RDF.\n\nThis repo holds the tools for generating and working with LinkML. For the LinkML schema (metamodel), please see https://github.com/linkml/linkml-model\n\nThe complete documentation for LinkML can be found here:\n\n - [linkml.io/linkml](https://linkml.io/linkml)\n',
     'author': 'Chris Mungall',

linkml-1.8.7/linkml/generators/docgen/schema.md.jinja2

@@ -1,7 +0,0 @@
-# {{ schema.name }}
-
-{{ schema.description }}
-
-URI: {{ schema.id }}
-
-