linkml 1.7.4__tar.gz → 1.7.6__tar.gz

{linkml-1.7.4 → linkml-1.7.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.7.4
+Version: 1.7.6
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -22,6 +22,8 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Provides-Extra: shacl
+Provides-Extra: tests
 Requires-Dist: antlr4-python3-runtime (>=4.9.0,<4.10)
 Requires-Dist: click (>=7.0)
 Requires-Dist: graphviz (>=0.10.1)
@@ -38,6 +40,7 @@ Requires-Dist: prefixcommons (>=0.1.7)
 Requires-Dist: prefixmaps (>=0.1.3)
 Requires-Dist: pydantic (>=1.0.0,<3.0.0)
 Requires-Dist: pyjsg (>=0.11.6)
+Requires-Dist: pyshacl (>=0.25.0,<0.26.0) ; extra == "shacl" or extra == "tests"
 Requires-Dist: pyshex (>=0.7.20)
 Requires-Dist: pyshexc (>=0.8.3)
 Requires-Dist: python-dateutil

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/__init__.py

@@ -5,6 +5,7 @@ representation such as JsonSchema
 
 from linkml.generators.javagen import JavaGenerator
 from linkml.generators.jsonldcontextgen import ContextGenerator
+from linkml.generators.jsonldgen import JSONLDGenerator
 from linkml.generators.jsonschemagen import JsonSchemaGenerator
 from linkml.generators.owlgen import OwlSchemaGenerator
 from linkml.generators.pydanticgen import PydanticGenerator
@@ -43,6 +44,7 @@ __all__ = [
     "PythonGenerator",
     "JavaGenerator",
     "ContextGenerator",
+    "JSONLDGenerator",
     "JsonSchemaGenerator",
     "ShaclGenerator",
     "ShExGenerator",

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/docgen/class.md.jinja2

@@ -8,6 +8,19 @@
     {%- endif -%}
 {%- endif -%}
 
+{% macro compute_range(slot) -%}
+    {%- if slot.any_of or slot.exactly_one_of -%}
+        {%- for subslot_range in schemaview.slot_range_as_union(slot) -%}
+            {{ gen.link(subslot_range) }}
+            {%- if not loop.last -%}
+                &nbsp;or&nbsp;<br />
+            {%- endif -%}
+        {%- endfor -%}
+    {%- else -%}
+        {{ gen.link(slot.range) }}
+    {%- endif -%}
+{% endmacro %}
+
 # Class: {{ title }}
 
 {%- if header -%}
@@ -55,12 +68,12 @@ URI: {{ gen.uri_link(element) }}
 | ---  | --- | --- | --- |
 {% if gen.get_direct_slots(element)|length > 0 %}
 {%- for slot in gen.get_direct_slots(element) -%}
-| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | direct |
+| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ compute_range(slot) }} | {{ slot.description|enshorten }} | direct |
 {% endfor -%}
 {% endif -%}
 {% if gen.get_indirect_slots(element)|length > 0 %}
 {%- for slot in gen.get_indirect_slots(element) -%}
-| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | {{ gen.links(gen.get_slot_inherited_from(element.name, slot.name))|join(', ') }} |
+| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ compute_range(slot) }} | {{ slot.description|enshorten }} | {{ gen.links(gen.get_slot_inherited_from(element.name, slot.name))|join(', ') }} |
 {% endfor -%}
 {% endif %}
 

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/docgen/slot.md.jinja2

@@ -8,6 +8,19 @@
     {%- endif -%}
 {%- endif -%}
 
+{% macro compute_range(slot) -%}
+    {%- if slot.any_of or slot.exactly_one_of -%}
+        {%- for subslot_range in schemaview.slot_range_as_union(slot) -%}
+            {{ gen.link(subslot_range) }}
+            {%- if not loop.last -%}
+                &nbsp;or&nbsp;<br />
+            {%- endif -%}
+        {%- endfor -%}
+    {%- else -%}
+        {{ gen.link(slot.range) }}
+    {%- endif -%}
+{% endmacro %}
+
 # Slot: {{ title }}
 
 {%- if header -%}
@@ -58,7 +71,7 @@ URI: {{ gen.uri_link(element) }}
 
 ## Properties
 
-* Range: {{gen.link(element.range)}}
+* Range: {{ compute_range(element) }}
 {% if element.multivalued %}
 * Multivalued: {{ element.multivalued }}
 {% endif -%}

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/docgen.py

@@ -192,52 +192,65 @@ class DocGenerator(Generator):
             "diagram_type": self.diagram_type.value if self.diagram_type else None,
             "include_top_level_diagram": self.include_top_level_diagram,
         }
+        self.logger.debug("Processing Index")
         template = self._get_template("index")
         out_str = template.render(gen=self, schema=sv.schema, schemaview=sv, **template_vars)
         self._write(out_str, directory, self.index_name)
         if self._is_single_file_format(self.format):
-            logging.info(f"{self.format} is a single-page format, skipping non-index elements")
+            self.logger.info(f"{self.format} is a single-page format, skipping non-index elements")
             return
+        self.logger.debug("Processing Schemas...")
         template = self._get_template("schema")
         for schema_name in sv.imports_closure():
+            self.logger.debug(f"  Generating doc for {schema_name}")
             imported_schema = sv.schema_map.get(schema_name)
             out_str = template.render(gen=self, schema=imported_schema, schemaview=sv, **template_vars)
             self._write(out_str, directory, imported_schema.name)
+        self.logger.debug("Processing Classes...")
         template = self._get_template("class")
         for cn, c in sv.all_classes().items():
             if self._is_external(c):
                 continue
             n = self.name(c)
+            self.logger.debug(f"  Generating doc for {n}")
             out_str = template.render(gen=self, element=c, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Slots...")
         template = self._get_template("slot")
         for sn, s in sv.all_slots().items():
             if self._is_external(s):
                 continue
             n = self.name(s)
+            self.logger.debug(f"  Generating doc for {n}")
             s = sv.induced_slot(sn)
             out_str = template.render(gen=self, element=s, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Enums...")
         template = self._get_template("enum")
         for en, e in sv.all_enums().items():
             if self._is_external(e):
                 continue
             n = self.name(e)
+            self.logger.debug(f"  Generating doc for {n}")
             out_str = template.render(gen=self, element=e, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Types...")
         template = self._get_template("type")
         for tn, t in sv.all_types().items():
             if self._exclude_type(t):
                 continue
             n = self.name(t)
+            self.logger.debug(f"  Generating doc for {n}")
             t = sv.induced_type(tn)
             out_str = template.render(gen=self, element=t, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
+        self.logger.debug("Processing Subsets...")
         template = self._get_template("subset")
         for _, s in sv.all_subsets().items():
             if self._is_external(c):
                 continue
             n = self.name(s)
+            self.logger.debug(f"  Generating doc for {n}")
             out_str = template.render(gen=self, element=s, schemaview=sv, **template_vars)
             self._write(out_str, directory, n)
 
@@ -253,6 +266,7 @@ class DocGenerator(Generator):
         path = Path(directory)
         path.mkdir(parents=True, exist_ok=True)
         file_name = f"{name}.{self._file_suffix()}"
+        self.logger.debug(f"  Writing file: {file_name}")
         with open(path / file_name, "w", encoding="UTF-8") as stream:
             stream.write(out_str)
 
@@ -294,7 +308,7 @@ class DocGenerator(Generator):
                 if p.is_file():
                     folder = self.template_directory
                 else:
-                    logging.info(
+                    self.logger.info(
                         f"Could not find {base_file_name} in {self.template_directory} - falling back to default"
                     )
             if not folder:
@@ -325,7 +339,7 @@ class DocGenerator(Generator):
 
         :param element: SchemaView element definition
         :return: slot name or numeric portion of CURIE prefixed
-        slot_uri
+            slot_uri
         """
         if type(element).class_name == "slot_definition":
             if self.use_slot_uris:
@@ -422,7 +436,8 @@ class DocGenerator(Generator):
         else:
             return False
 
-    def _markdown_link(self, n: str, name: str = None, subfolder: str = None) -> str:
+    @staticmethod
+    def _markdown_link(n: str, name: str = None, subfolder: str = None) -> str:
         if subfolder:
             rel_path = f"{subfolder}/{n}"
         else:
@@ -507,7 +522,8 @@ class DocGenerator(Generator):
         s += "\n"
         return s
 
-    def bullet(self, e: Element, meta_slot: SlotDefinitionName, backquote=False) -> str:
+    @staticmethod
+    def bullet(e: Element, meta_slot: SlotDefinitionName, backquote=False) -> str:
         """
         Render tag-value for an element as a bullet
 
@@ -526,7 +542,8 @@ class DocGenerator(Generator):
         else:
             return ""
 
-    def number_value_range(self, e: Union[SlotDefinition, TypeDefinition]) -> str:
+    @staticmethod
+    def number_value_range(e: Union[SlotDefinition, TypeDefinition]) -> str:
         """
         Render the minimum and maximum values for a slot or type as a range, e.g 5-100
 
@@ -547,7 +564,8 @@ class DocGenerator(Generator):
                 r = f"<= {e.maximum_value}"
         return r
 
-    def cardinality(self, slot: SlotDefinition) -> str:
+    @staticmethod
+    def cardinality(slot: SlotDefinition) -> str:
         """
         Render combination of required, multivalued, and recommended as a range, e.g. 0..*
         :param slot:
@@ -605,7 +623,8 @@ class DocGenerator(Generator):
         else:
             raise NotImplementedError(f"Diagram type {self.diagram_type} not implemented")
 
-    def latex(self, text: Optional[str]) -> str:
+    @staticmethod
+    def latex(text: Optional[str]) -> str:
         """
         Makes text safe for latex
 
@@ -757,7 +776,8 @@ class DocGenerator(Generator):
                 # depth first - place at end of stack (to be processed next)
                 stack.append((depth + 1, child))
 
-    def _is_single_file_format(self, format: str):
+    @staticmethod
+    def _is_single_file_format(format: str):
         if format == "latex":
             return True
         else:
@@ -778,7 +798,8 @@ class DocGenerator(Generator):
             slot.range = "string"
         return slot
 
-    def get_direct_slot_names(self, cls: ClassDefinition) -> List[SlotDefinitionName]:
+    @staticmethod
+    def get_direct_slot_names(cls: ClassDefinition) -> List[SlotDefinitionName]:
         """Fetch list of all own attributes of a class, i.e.,
         all slot names of slots that belong to the domain of a class.
 
@@ -845,7 +866,7 @@ class DocGenerator(Generator):
     def example_object_blobs(self, class_name: str) -> List[Tuple[str, str]]:
         """Fetch list of all examples of a class.
 
-        :param cls: class for which we want to determine the examples
+        :param class_name: class for which we want to determine the examples
         :return: list of all examples of a class
         """
         if not self.example_runner:

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/excelgen.py

@@ -30,7 +30,8 @@ class ExcelGenerator(Generator):
         self.logger = logging.getLogger(__name__)
         self.schemaview = SchemaView(self.schema)
 
-    def create_workbook(self, workbook_path: Path) -> Workbook:
+    @staticmethod
+    def create_workbook(workbook_path: Path) -> Workbook:
         """
         Creates an Excel workbook using the openpyxl library and returns it.
 
@@ -87,7 +88,8 @@ class ExcelGenerator(Generator):
         if self.split_workbook_by_class:
             self.logger.info(f"The Excel workbooks have been written to {output_path}")
 
-    def add_columns_to_worksheet(self, workbook: Workbook, worksheet_name: str, sheet_headings: List[str]) -> None:
+    @staticmethod
+    def add_columns_to_worksheet(workbook: Workbook, worksheet_name: str, sheet_headings: List[str]) -> None:
         """
         Get a worksheet by name and add a column to it in an existing workbook.
 
@@ -102,8 +104,8 @@ class ExcelGenerator(Generator):
         for i, heading in enumerate(sheet_headings):
             worksheet.cell(row=1, column=i + 1, value=heading)
 
+    @staticmethod
     def column_enum_validation(
-        self,
         workbook: Workbook,
         worksheet_name: str,
         column_name: str,

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/golanggen.py

@@ -100,7 +100,8 @@ class GolangGenerator(Generator):
         out_str = template_obj.render(gen=self, schema=self.schemaview.schema, view=self.schemaview)
         return out_str
 
-    def name(self, element: Element) -> str:
+    @staticmethod
+    def name(element: Element) -> str:
         """
         Returns the name of the element in its canonical form
 
@@ -112,7 +113,8 @@ class GolangGenerator(Generator):
             alias = element.alias
         return camelcase(alias)
 
-    def json_name(self, element: Element) -> str:
+    @staticmethod
+    def json_name(element: Element) -> str:
         """
         Returns the name of the element in its JSON (snake-case) form
 
@@ -181,7 +183,8 @@ class GolangGenerator(Generator):
                     logging.warning(f"Unknown type.base: {t.name}")
             return "string"
 
-    def parents(self, cls: ClassDefinition) -> List[ClassDefinitionName]:
+    @staticmethod
+    def parents(cls: ClassDefinition) -> List[ClassDefinitionName]:
         if cls.is_a:
             parents = [cls.is_a]
         else:

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/jsonldcontextgen.py

@@ -6,14 +6,14 @@ Generate JSON-LD contexts
 import os
 import re
 from dataclasses import dataclass, field
-from typing import Dict, Optional, Set
+from typing import Dict, Optional, Set, Union
 
 import click
 from jsonasobj2 import JsonObj, as_json
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
 from linkml_runtime.linkml_model.types import SHEX
 from linkml_runtime.utils.formatutils import camelcase, underscore
-from rdflib import SKOS, XSD
+from rdflib import SKOS, XSD, Namespace
 
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
@@ -47,7 +47,7 @@ class ContextGenerator(Generator):
     slot_class_maps: Dict = field(default_factory=lambda: dict())
     emit_metadata: bool = False
     model: Optional[bool] = True
-    base: Optional[str] = None
+    base: Optional[Union[str, Namespace]] = None
     output: Optional[str] = None
     prefixes: Optional[bool] = True
     flatprefixes: Optional[bool] = False
@@ -57,7 +57,7 @@ class ContextGenerator(Generator):
         if self.namespaces is None:
             raise TypeError("Schema text must be supplied to context generator.  Preparsed schema will not work")
 
-    def visit_schema(self, base: Optional[str] = None, output: Optional[str] = None, **_):
+    def visit_schema(self, base: Optional[Union[str, Namespace]] = None, output: Optional[str] = None, **_):
         # Add any explicitly declared prefixes
         for prefix in self.schema.prefixes.values():
             self.emit_prefixes.add(prefix.prefix_prefix)
@@ -80,11 +80,10 @@ class ContextGenerator(Generator):
                     self.namespaces[self.schema.name] = default_uri
                     self.emit_prefixes.add(self.schema.name)
             self.context_body["@vocab"] = default_uri
-            # self.context_body['@base'] = self.base_dir
 
     def end_schema(
         self,
-        base: Optional[str] = None,
+        base: Optional[Union[str, Namespace]] = None,
         output: Optional[str] = None,
         prefixes: Optional[bool] = True,
         flatprefixes: Optional[bool] = False,
@@ -102,6 +101,7 @@ class ContextGenerator(Generator):
             context.comments = comments
         context_content = {}
         if base:
+            base = str(base)
             if "://" not in base:
                 self.context_body["@base"] = os.path.relpath(base, os.path.dirname(self.schema.source_file))
             else:
@@ -178,6 +178,9 @@ class ContextGenerator(Generator):
         if slot_def:
             self.context_body[underscore(aliased_slot_name)] = slot_def
 
+    def serialize(self, base: Optional[Union[str, Namespace]] = None, **kwargs) -> str:
+        return super().serialize(base=base, **kwargs)
+
 
 @shared_arguments(ContextGenerator)
 @click.command()

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/jsonldgen.py

@@ -37,7 +37,8 @@ class JSONLDGenerator(Generator):
 
     Status: incompletely implemented
 
-    Note: this is distinct from :ref:`ContextGenerator`, which generates a JSON-LD context
+    Note: this is distinct from
+    :class:`~linkml.generators.jsonldcontextgen.ContextGenerator`, which generates a JSON-LD context
     """
 
     # ClassVars
@@ -49,6 +50,7 @@ class JSONLDGenerator(Generator):
     ]  # jsonld includes @type and @context.  json is pure JSON
     uses_schemaloader = True
     requires_metamodel = True
+    file_extension = "jsonld"
 
     # ObjectVars
     original_schema: SchemaDefinition = None

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/oocodegen.py

@@ -95,7 +95,8 @@ class OOCodeGenerator(Generator):
     def default_value_for_type(self, typ: str) -> str:
         raise NotImplementedError
 
-    def get_class_name(self, cn):
+    @staticmethod
+    def get_class_name(cn):
         return camelcase(cn)
 
     def get_slot_name(self, sn):
@@ -108,10 +109,12 @@ class OOCodeGenerator(Generator):
     def map_type(self, t: TypeDefinition, required: bool = False) -> str:
         return t.base
 
-    def make_multivalued(self, range: str) -> str:
+    @staticmethod
+    def make_multivalued(range: str) -> str:
         return f"List<{range}>"
 
-    def replace_invalid_identifier_character(self, char: str) -> str:
+    @staticmethod
+    def replace_invalid_identifier_character(char: str) -> str:
         if char.isalpha() or char.isnumeric() or char == "_":
             return char
         else:

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/owlgen.py

@@ -22,6 +22,7 @@ from linkml_runtime.linkml_model.meta import (
     EnumDefinition,
     EnumDefinitionName,
     PermissibleValue,
+    SchemaDefinitionName,
     SlotDefinition,
     SlotDefinitionName,
     TypeDefinition,
@@ -199,6 +200,12 @@ class OwlSchemaGenerator(Generator):
         for enm in sv.all_enums(imports=mergeimports).values():
             self.add_enum(enm)
 
+        if not mergeimports:
+            for imp in schema.imports:
+                if imp == "linkml:types":
+                    continue
+                graph.add((base, OWL.imports, self._schema_uri(imp)))
+
         # Add metadata as annotation properties
         self.add_metadata(schema, base)
         return graph
@@ -459,6 +466,7 @@ class OwlSchemaGenerator(Generator):
         an anonymous expression)
 
         :param cls: LinkML class expression (anonymous if called recursively)
+        :param quantifier_predicate:
         :return: blank node representing the OWL expression
         """
         if cls is None:
@@ -569,6 +577,7 @@ class OwlSchemaGenerator(Generator):
         :param cls:
         :param slot:
         :param main_slot:
+        :param owl_types:
         :return:
         """
         sv = self.schemaview
@@ -687,6 +696,14 @@ class OwlSchemaGenerator(Generator):
                 eq_uris = [URIRef(self.schemaview.expand_curie(s)) for s in equals_string_in]
                 owl_exprs.append(self._union_of(eq_uris))
         for constraint_prop, constraint_val in constraints.items():
+            if is_literal is not None and not is_literal:
+                # In LinkML, it is permissible to have a literal constraints on slots that refer to
+                # other objects. E.g. a pattern on a in_organization slot which refers to an Organization
+                # will be applied to the id of that Organization.
+                # To support this in OWL we would need to change this to a complex expression - for
+                # now we will skip this.
+                # See: https://github.com/linkml/linkml/issues/1841
+                continue
             if constraint_val is not None:
                 owl_types.add(RDFS.Literal)
                 dr = BNode()
@@ -958,7 +975,8 @@ class OwlSchemaGenerator(Generator):
         self.graph.add((node, OWL.hasValue, filler))
         return node
 
-    def _swrl_var(self, var: str) -> URIRef:
+    @staticmethod
+    def _swrl_var(var: str) -> URIRef:
         return URIRef(var)
 
     def _swrl_class_atom(self, cls_ref: Union[BNode, URIRef], var: str) -> BNode:
@@ -983,7 +1001,8 @@ class OwlSchemaGenerator(Generator):
         self.graph.add((node, SWRL.head, head))
         return node
 
-    def _metaslot_uri(self, name: str) -> URIRef:
+    @staticmethod
+    def _metaslot_uri(name: str) -> URIRef:
         return URIRef("https://w3id.org/linkml/" + name)
 
     def _complement_of_union_of(
@@ -1086,7 +1105,8 @@ class OwlSchemaGenerator(Generator):
         else:
             return self._class_uri(ClassDefinitionName(slot.range))
 
-    def _mixin_grouping_class_uri(self):
+    @staticmethod
+    def _mixin_grouping_class_uri():
         return URIRef(ClassDefinition.class_class_uri + "#Mixin")
 
     def _class_uri(self, cn: Union[str, ClassDefinitionName]) -> URIRef:
@@ -1116,6 +1136,13 @@ class OwlSchemaGenerator(Generator):
             default_prefix = self.schemaview.schema.default_prefix or ""
             return URIRef(self.schemaview.expand_curie(f"{default_prefix}:{underscore(p.name)}"))
 
+    def _schema_uri(self, scn: Union[str, SchemaDefinitionName]) -> URIRef:
+        if ":" in scn:
+            return URIRef(self.schemaview.expand_curie(scn))
+        else:
+            default_prefix = self.schemaview.schema.default_prefix or ""
+            return URIRef(self.schemaview.expand_curie(f"{default_prefix}:{scn}"))
+
     def _type_uri(self, tn: TypeDefinitionName, native: bool = None) -> URIRef:
         if native is None:
             # never use native unless type shadowing with objects is enabled

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/prefixmapgen.py

@@ -6,14 +6,14 @@ Generate JSON-LD contexts
 import csv
 import os
 from dataclasses import dataclass, field
-from typing import Dict, Optional, Set
+from typing import Dict, Optional, Set, Union
 
 import click
 from jsonasobj2 import JsonObj, as_json
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
 from linkml_runtime.linkml_model.types import SHEX
 from linkml_runtime.utils.formatutils import camelcase
-from rdflib import XSD
+from rdflib import XSD, Namespace
 
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
@@ -35,7 +35,7 @@ class PrefixGenerator(Generator):
     default_ns: str = None
     context_body: Dict = field(default_factory=lambda: dict())
     slot_class_maps: Dict = field(default_factory=lambda: dict())
-    base: str = None
+    base: Optional[Union[str, Namespace]] = None
 
     def __post_init__(self):
         super().__post_init__()
@@ -59,9 +59,10 @@ class PrefixGenerator(Generator):
             if self.default_ns:
                 self.emit_prefixes.add(self.default_ns)
 
-    def end_schema(self, base: Optional[str] = None, output: Optional[str] = None, **_) -> None:
+    def end_schema(self, base: Optional[Union[str, Namespace]] = None, output: Optional[str] = None, **_) -> None:
         context = JsonObj()
         if base:
+            base = str(base)
             if "://" not in base:
                 self.context_body["@base"] = os.path.relpath(base, os.path.dirname(self.schema.source_file))
             else:

{linkml-1.7.4 → linkml-1.7.6}/linkml/generators/projectgen.py

@@ -22,7 +22,7 @@ from linkml.generators.protogen import ProtoGenerator
 from linkml.generators.pythongen import PythonGenerator
 from linkml.generators.shaclgen import ShaclGenerator
 from linkml.generators.shexgen import ShExGenerator
-from linkml.generators.sqlddlgen import SQLDDLGenerator
+from linkml.generators.sqltablegen import SQLTableGenerator
 from linkml.utils.cli_utils import log_level_option
 from linkml.utils.generator import Generator
 
@@ -53,7 +53,7 @@ GEN_MAP = {
     #    'rdf': (RDFGenerator, 'rdf/{name}.ttl', {'context': '{parent}/../jsonld/{name}.context.jsonld'}),
     "shex": (ShExGenerator, "shex/{name}.shex", {}),
     "shacl": (ShaclGenerator, "shacl/{name}.shacl.ttl", {}),
-    "sqlddl": (SQLDDLGenerator, "sqlschema/{name}.sql", {}),
+    "sqltable": (SQLTableGenerator, "sqlschema/{name}.sql", {}),
     # # linkml/generators/javagen.py uses different architecture from most of the other generators
     # # also linkml/generators/excelgen.py, which has a different mechanism for determining the output path
     # 'java': (JavaGenerator, 'java/{name}.java', {'directory': '{parent}'}),
@@ -96,7 +96,8 @@ class ProjectGenerator:
     Note this doesn't conform to overall generator framework, as it is a meta-generator
     """
 
-    def generate(self, schema_path: str, config: ProjectConfiguration = ProjectConfiguration()):
+    @staticmethod
+    def generate(schema_path: str, config: ProjectConfiguration = ProjectConfiguration()):
         if config.directory is None:
             raise Exception("Must pass directory")
         Path(config.directory).mkdir(parents=True, exist_ok=True)
@@ -197,26 +198,38 @@ def cli(
 
     Generate all downstream artefacts using default configuration:
 
-       gen-project -d . personinfo.yaml
+    .. code-block: bash
+
+        gen-project -d . personinfo.yaml
 
     Exclusion lists: all except ShEx:
 
-       gen-project --exclude shex -d . personinfo.yaml
+    .. code-block: bash
+
+        gen-project --exclude shex -d . personinfo.yaml
 
     Inclusion lists: only jsonschema and python:
 
+    .. code-block: bash
+
        gen-project -I python -I jsonschema -d . personinfo.yaml
 
     Configuration, on command line:
 
+    .. code-block: bash
+
         gen-project -A 'jsonschema: {top_class: Container}' -d . personinfo.yaml
 
     Configuration, via yaml file:
 
+    .. code-block: bash
+
         gen-project --config config.yaml personinfo.yaml
 
     config.yaml:
 
+    .. code-block: yaml
+
         directory: .
         generator_args:
           json_schema:

linkml-1.7.6/linkml/generators/pydanticgen/__init__.py

@@ -0,0 +1,29 @@
+from linkml.generators.pydanticgen.pydanticgen import DEFAULT_IMPORTS, PydanticGenerator, cli
+from linkml.generators.pydanticgen.template import (
+    ConditionalImport,
+    Import,
+    Imports,
+    PydanticAttribute,
+    PydanticBaseModel,
+    PydanticClass,
+    PydanticEnum,
+    PydanticModule,
+    PydanticValidator,
+    TemplateModel,
+)
+
+__all__ = [
+    "cli",
+    "ConditionalImport",
+    "DEFAULT_IMPORTS",
+    "Import",
+    "Imports",
+    "PydanticAttribute",
+    "PydanticBaseModel",
+    "PydanticClass",
+    "PydanticEnum",
+    "PydanticGenerator",
+    "PydanticModule",
+    "PydanticValidator",
+    "TemplateModel",
+]