linkml 1.9.1rc3__py3-none-any.whl → 1.9.2__py3-none-any.whl

linkml/transformers/rollup_transformer.py

@@ -0,0 +1,115 @@
+"""
+flatten_transformer.py
+
+This module provides a FlattenTransformer that transforms a LinkML schema into a flattened version.
+The transformer takes a target class name and rolls up all slots from its descendants into that class.
+This is useful for implementing single table inheritance or simplifying inheritance for systems like KGX.
+"""
+
+import copy
+from dataclasses import dataclass
+from typing import Optional
+
+from linkml_runtime.linkml_model.meta import (
+    ClassDefinitionName,
+    SchemaDefinition,
+)
+from linkml_runtime.utils.schemaview import SchemaView
+
+from linkml.transformers.model_transformer import ModelTransformer
+
+
+@dataclass
+class FlattenTransformerConfiguration:
+    """
+    Configuration options for the FlattenTransformer.
+
+    Attributes:
+        preserve_class_designator: If True, preserves the original class name in the specified
+            class designator slot (e.g., 'category').
+        class_designator_slot: The name of the slot that designates the original class (e.g., 'category').
+        include_all_classes: If True, keeps all classes in the schema; otherwise, only the target class
+            and non-descendants are kept.
+        include_mixins: If True, includes properties from mixins in the flattened class.
+    """
+
+    preserve_class_designator: bool = True
+    class_designator_slot: Optional[str] = "category"
+    include_all_classes: bool = False
+    include_mixins: bool = True
+
+
+class RollupTransformer(ModelTransformer):
+    """
+    Transforms a LinkML schema by flattening an inheritance hierarchy into a single class.
+
+    This transformer takes a schema and a target class name, and produces a new schema where
+    all descendant classes of the target class are removed and their slots are rolled up into the
+    target class.
+    """
+
+    def __init__(
+        self,
+        target_class: str,
+        config: Optional[FlattenTransformerConfiguration] = None,
+    ):
+        super().__init__()
+        self.target_class = target_class
+        self.config = config or FlattenTransformerConfiguration()
+        self._descendant_classes: set[str] = set()
+        self._class_to_slot_map: dict[str, set[str]] = {}
+
+    def transform(self, tgt_schema_name: str = None, top_class: ClassDefinitionName = None) -> SchemaDefinition:
+        """
+        Transform the schema by flattening the inheritance hierarchy.
+
+        Args:
+            tgt_schema_name: Optional target schema name (not used in this transformer)
+            top_class: Optional top class name (not used in this transformer)
+
+        Returns:
+            A transformed SchemaDefinition with the target class having all slots from its descendants.
+        """
+        if not self.schemaview:
+            raise ValueError("SchemaView not set. Ensure schema is set by calling set_schema().")
+
+        schema_copy = copy.deepcopy(self.source_schema)
+        view = SchemaView(schema_copy)
+        descendants = view.class_descendants(self.target_class, imports=True, mixins=True, reflexive=False, is_a=True)
+        self._descendant_classes = set(descendants)
+
+        # Collect all slots from the target class and its descendant classes, and
+        # populate a mapping of class name to the set of its slot names.
+        for descendant in self._descendant_classes:
+            slots = view.class_induced_slots(descendant)
+            self._class_to_slot_map[descendant] = {s.name for s in slots}
+
+        # flatten the schema
+        return self._create_flattened_schema(schema_copy)
+
+    def _create_flattened_schema(self, schema: SchemaDefinition) -> SchemaDefinition:
+        """
+        Create a new flattened version of the schema based on collected slots.
+        """
+        target_class_def = schema.classes[self.target_class]
+        existing_slot_names = set(target_class_def.slots or [])
+        all_slots = set()
+
+        for descendant in self._descendant_classes:
+            if descendant in schema.classes:
+                for slot_name in self._class_to_slot_map.get(descendant, set()):
+                    if slot_name not in existing_slot_names:
+                        all_slots.add(slot_name)
+
+        if not target_class_def.slots:
+            target_class_def.slots = []
+
+        target_class_def.slots.extend(list(all_slots))
+
+        # Optionally remove descendant classes.
+        if not self.config.include_all_classes:
+            for descendant in self._descendant_classes:
+                if descendant in schema.classes:
+                    del schema.classes[descendant]
+
+        return schema

linkml/utils/deprecation.py

@@ -232,6 +232,32 @@ DEPRECATIONS = (
         ),
         recommendation="Update to use linkml.validator",
     ),
+    Deprecation(
+        name="gen-markdown",
+        # the last update to any code in markdowngen.py was in v1.9.1
+        # we can start considering it as deprecated from this version
+        deprecated_in=SemVer.from_str("1.9.1"),
+        removed_in=SemVer.from_str("1.10.0"),
+        message=(
+            "gen-markdown has been deprecated in favor of gen-doc, which is the new "
+            "de-facto generator for generating markdown documentation files (with "
+            "embedded mermaid class diagrams) from a LinkML schema"
+        ),
+        recommendation="Update to use `gen-doc`",
+    ),
+    Deprecation(
+        name="gen-yuml",
+        # the last update to any code in yumlgen.py was in v1.8.7
+        # we can start considering it as deprecated from this version
+        deprecated_in=SemVer.from_str("1.8.7"),
+        removed_in=SemVer.from_str("1.10.0"),
+        message=(
+            "gen-yuml has been deprecated and is no longer supported. "
+            "It has been replaced by more feature-rich diagram generators such as "
+            "gen-doc (embedded mermaid diagrams), gen-plantuml, gen-mermaid-class-diagram, and gen-erdiagram."
+        ),
+        recommendation="Update to use `gen-doc`, `gen-plantuml`, `gen-mermaid-class-diagram`, or `gen-erdiagram`",
+    ),
 )  # type: tuple[Deprecation, ...]
 
 EMITTED = set()  # type: set[str]

linkml/utils/execute_tutorial.py

@@ -1,3 +1,22 @@
+"""
+This module executes and evaluates code blocks in tutorial markdown files.
+Command line usage example: `python -m linkml.utils.execute_tutorial -d /tmp/tutorial/ docs/intro/tutorial01.md`
+
+It requires that the code blocks have the following format:
+- A code block containing file contents that should be written to a file for testing should be preceded by a line
+whose text is the file name (no spaces) and a colon.
+- A code block containing expected output should be preceded by a line whose text is a single word containing the
+text "output" (case insensitive) and a colon.
+- A code block containing a command that is expected to fail should be preceded by a line that starts with
+"<!-- fail" (case insensitive).
+- A code block containing commands that should not be executed should be preceded by a line that starts with
+"<!-- no_execute" (case insensitive).
+- The code block starts with a line containing three backticks. It can then contain either the language name
+(e.g., `bash`, `python`, etc.) or `{literalinclude}` followed by a file path. If using `{literalinclude}`,
+the next line should contain the language tag (e.g., `:language: python`).
+- The code block ends with a line containing three backticks.
+"""
+
 import logging
 import re
 import subprocess
@@ -12,8 +31,9 @@ from linkml._version import __version__
 logger = logging.getLogger(__name__)
 
 re_decl = re.compile(r"^(\S+):$")
-re_start_yaml = re.compile(r"^```(\w+)$")
-re_end_yaml = re.compile(r"^```$")
+re_start_code_block = re.compile(r"^```(\w+)$")  # does not include literalinclude blocks
+re_literalinclude = re.compile(r"^```\{literalinclude\} (.+)$")
+re_end_code_block = re.compile(r"^```$")
 re_html_comment = re.compile(r"^<!-- (.+) -->")
 
 
@@ -58,8 +78,9 @@ def execute_blocks(directory: str, blocks: list[Block]) -> list[str]:
     for block in blocks:
         write_lines(block.prior_lines)
         logger.info(f"# Block: {block.category} {block.title}")
-        if block.is_file_block():
+        if block.is_file_block() and not block.is_bash():
             path = PurePath(directory, block.title)
+            logger.info(f"Writing to: {path}")
             with open(path, "w", encoding="UTF-8") as stream:
                 stream.write(block.content)
         elif block.is_bash():
@@ -82,7 +103,7 @@ def execute_blocks(directory: str, blocks: list[Block]) -> list[str]:
             block.output = r.stdout.decode("utf-8")
             if outpath:
                 with open(outpath, "w", encoding="UTF-8") as stream:
-                    logger.info(f"WRITING {len(block.output)} TO = {outpath}")
+                    logger.info(f"WRITING {len(block.output)} CHARS TO = {outpath}")
                     stream.write(block.output)
             block.error = r.stderr.decode("utf-8")
             logger.info(f"OUT [sample] = {block.output[0:30]}")
@@ -123,7 +144,7 @@ def write_lines(lines: list[str]) -> None:
 
 def parse_file_to_blocks(input) -> list[Block]:
     """
-    Parses a markdown tutorial file to code blacks to be executed
+    Parses a markdown tutorial file to code blocks to be executed
 
     :param input:
     :return:
@@ -150,9 +171,9 @@ def parse_file_to_blocks(input) -> list[Block]:
             m = re_decl.match(line)
             if m:
                 fn = m.group(1)
-                print(f"FILE={fn}")
+                print(f"TITLE={fn}")
             else:
-                m = re_start_yaml.match(line)
+                m = re_start_code_block.match(line)
                 if m:
                     curr_block = Block(
                         category=m.group(1),
@@ -165,12 +186,53 @@ def parse_file_to_blocks(input) -> list[Block]:
                     prior_lines = []
                     anns = []
                 else:
-                    prior_lines += [line]
+                    m = re_literalinclude.match(line)
+                    if m and fn:
+                        # Handle literalinclude directive
+                        file_path = m.group(1).strip()
+                        # Look ahead and extract language from the language tag
+                        language = "yaml"  # Default to yaml if no language tag is found
+                        if lines and lines[0].strip().startswith(":language:"):
+                            language_line = lines[0].strip()
+                            language = language_line.split(":language:")[1].strip()
+                            lines = lines[1:]
+                        # Skip end of code block
+                        if lines and lines[0].strip() == "```":
+                            lines = lines[1:]
+                        else:
+                            logger.warning(
+                                f"Expected end of code block after literalinclude, but found: {lines[0].strip()}"
+                            )
+
+                        # Convert relative path to absolute path
+                        input_dir = Path(input).parent
+                        abs_path = input_dir / file_path
+
+                        try:
+                            with open(abs_path) as f:
+                                file_content = f.read()
+
+                            # Create a block for this file
+                            file_block = Block(
+                                category=language,  # Use the extracted language
+                                title=fn,
+                                expected_fail=expected_fail,
+                                content=file_content,
+                                annotations=anns,
+                                prior_lines=prior_lines,
+                            )
+                            blocks.append(file_block)
+                            prior_lines = []
+                            anns = []
+                        except Exception as e:
+                            logger.error(f"Failed to read included file {abs_path}: {e}")
+                    else:
+                        prior_lines += [line]
         else:
             # in block
             fn = None
             expected_fail = False
-            m = re_end_yaml.match(line)
+            m = re_end_code_block.match(line)
             if m:
                 blocks.append(curr_block)
                 curr_block = None

linkml/validator/plugins/recommended_slots_plugin.py

@@ -30,15 +30,15 @@ class RecommendedSlotsPlugin(ValidationPlugin):
                     )
                 slot_range_class = context.schema_view.get_class(slot_def.range)
                 if slot_range_class is not None and slot_value is not None:
-                    location += [slot_def.name]
+                    slot_location = location + [slot_def.name]
                     if slot_def.multivalued:
                         if slot_def.inlined and isinstance(slot_value, dict):
                             for k, v in slot_value.items():
-                                yield from _do_process(v, slot_range_class.name, location + [k])
+                                yield from _do_process(v, slot_range_class.name, slot_location + [k])
                         elif slot_def.inlined_as_list and isinstance(slot_value, list):
                             for i, v in enumerate(slot_value):
-                                yield from _do_process(v, slot_range_class.name, location + [str(i)])
+                                yield from _do_process(v, slot_range_class.name, slot_location + [str(i)])
                     else:
-                        yield from _do_process(instance[slot_def.name], slot_range_class.name, location)
+                        yield from _do_process(instance[slot_def.name], slot_range_class.name, slot_location)
 
         yield from _do_process(instance, context.target_class)

{linkml-1.9.1rc3.dist-info → linkml-1.9.2.dist-info}/METADATA

@@ -1,59 +1,62 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: linkml
-Version: 1.9.1rc3
+Version: 1.9.2
 Summary: Linked Open Data Modeling Language
-Home-page: https://linkml.io/linkml/
+License: Apache-2.0
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
 Author: Chris Mungall
 Author-email: cjmungall@lbl.gov
-Requires-Python: >=3.9.0,<4.0.0
+Requires-Python: >=3.9
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Healthcare Industry
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Provides-Extra: black
 Provides-Extra: numpydantic
+Provides-Extra: pandera
+Provides-Extra: polars-lts-cpu
 Provides-Extra: shacl
 Provides-Extra: tests
 Requires-Dist: antlr4-python3-runtime (>=4.9.0,<4.10)
-Requires-Dist: black (>=24.0.0) ; extra == "black" or extra == "tests"
+Requires-Dist: black (>=24.0.0) ; extra == "black"
+Requires-Dist: black (>=24.0.0) ; extra == "tests"
 Requires-Dist: click (>=7.0)
 Requires-Dist: graphviz (>=0.10.1)
 Requires-Dist: hbreader
 Requires-Dist: isodate (>=0.6.0)
 Requires-Dist: jinja2 (>=3.1.0)
-Requires-Dist: jsonasobj2 (>=1.0.3,<2.dev0)
+Requires-Dist: jsonasobj2 (>=1.0.3,<2.0.0)
 Requires-Dist: jsonschema[format] (>=4.0.0)
-Requires-Dist: linkml-runtime (>=1.9.1,<2.0.0)
-Requires-Dist: numpydantic (>=1.6.1) ; extra == "numpydantic" or extra == "tests"
+Requires-Dist: linkml-runtime (>=1.9.2,<2.0.0)
+Requires-Dist: numpydantic (>=1.6.1) ; extra == "numpydantic"
+Requires-Dist: numpydantic (>=1.6.1) ; extra == "tests"
 Requires-Dist: openpyxl
+Requires-Dist: pandera (>=0.19.0) ; extra == "pandera"
 Requires-Dist: parse
+Requires-Dist: polars-lts-cpu (>=1.0.0) ; extra == "polars-lts-cpu"
 Requires-Dist: prefixcommons (>=0.1.7)
 Requires-Dist: prefixmaps (>=0.2.2)
 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: pyshacl (>=0.25.0) ; extra == "shacl"
+Requires-Dist: pyshacl (>=0.25.0) ; extra == "tests"
 Requires-Dist: pyshex (>=0.7.20)
 Requires-Dist: pyshexc (>=0.8.3)
 Requires-Dist: python-dateutil
 Requires-Dist: pyyaml
 Requires-Dist: rdflib (>=6.0.0)
 Requires-Dist: requests (>=2.22)
+Requires-Dist: sphinx-click (>=6.0.0)
 Requires-Dist: sqlalchemy (>=1.4.31)
 Requires-Dist: typing-extensions (>=4.6.0) ; python_version < "3.12"
 Requires-Dist: watchdog (>=0.9.0)
-Project-URL: Documentation, https://linkml.io/linkml/
-Project-URL: Repository, https://github.com/linkml/linkml
 Description-Content-Type: text/markdown
 
 [![Pyversions](https://img.shields.io/pypi/pyversions/linkml.svg)](https://pypi.python.org/pypi/linkml)

{linkml-1.9.1rc3.dist-info → linkml-1.9.2.dist-info}/RECORD

@@ -2,10 +2,10 @@ linkml/__init__.py,sha256=0REu65rXiOk3F1CYLzq60HiSZ2DfFySfGS6QFljZ01s,3663
 linkml/_version.py,sha256=udxv6OEqcE89DTVMYPtetXYg8IA8Sgc6yW26-6f8C3M,310
 linkml/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/cli/__main__.py,sha256=oPa7Fl2DQP40UivpIWNRr1CgwT2SQM0rhE478155zBY,80
-linkml/cli/main.py,sha256=4X0OXU53nqkS18ViOIRLH8bx2eDVzgisWixhx9bhgPQ,5484
+linkml/cli/main.py,sha256=EncEEYMqaSlXj3pOEi8_xqZe12BYPW9IdEMJilGqIkI,5594
 linkml/generators/PythonGenNotes.md,sha256=wb9BPLLhF6378OKLbwSBAwmniLpwrcT5_bbfCHfLme8,51006
 linkml/generators/README.md,sha256=RMzT8EblC_GEdPy5WyfXHDBXlFI6k6mz3Cx2sdpcyWI,4438
-linkml/generators/__init__.py,sha256=2qSOnibL6KtzBW3KNqVX1gx1LQttrXlOPbbVDLLV2go,1587
+linkml/generators/__init__.py,sha256=AxTltouJeNayg3sJmVM7h4JkCx8NxGa4AV-_awtvfmo,1669
 linkml/generators/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/common/build.py,sha256=X2QDnybdr5GwDIaXWfwAzIqduqk7_rDReU-7CvcJ2OI,2835
 linkml/generators/common/ifabsent_processor.py,sha256=qefNF_rd24DxF4IGAynR9J7zWGH-oMfDULNbFMvZalA,13527
@@ -16,16 +16,16 @@ linkml/generators/common/type_designators.py,sha256=ORA9siVxHUXqn3TMuun81m_whqZc
 linkml/generators/csvgen.py,sha256=gPwX5GuwToD2KQF7SrINatqwMYY-54ZsgDTgYH1EM1Y,3242
 linkml/generators/dbmlgen.py,sha256=IrtY65iFdXg4wHBP9vHQeV20HUOUB1XlggPtmt_YvGM,5466
 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/class_diagram.md.jinja2,sha256=hCBPUyhvZWFow5eWVyzCtZ-_nMbq5fHFLxz7d6hpdNI,3633
+linkml/generators/docgen/common_metadata.md.jinja2,sha256=Gj2JltvwCvVHBloYkXFtudFsu407pibfgmKRw4NFY4k,1603
 linkml/generators/docgen/enum.md.jinja2,sha256=BCi4PUamCjszM17yrg2KNltR_JfrBjNdH87S5uz9DtY,1112
-linkml/generators/docgen/index.md.jinja2,sha256=suXRgJydHrxcMm3quXukaKkThtdzYA9i7BTuMAVKOP0,1502
+linkml/generators/docgen/index.md.jinja2,sha256=jP_sx7b96bf1WDmtsS7XtdsNoRuHrOI2Wbl8VE223pQ,1512
 linkml/generators/docgen/index.tex.jinja2,sha256=Go_EA-_N4JUpbOYbk3OY11mz5yV70VF2l2sMtgIPWw4,501
 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=st4g-1QucP0HIVAWSK_Eahv9pPKBz-lOzf06j2yy-Qc,38890
+linkml/generators/docgen.py,sha256=wkcg62Dkx2ksx7m3M_0wEK3F6NfGTemVSkD8HhWMFzk,39929
 linkml/generators/dotgen.py,sha256=DR1tC-vZ7Vj-NxEkE-zOPGrwPUIk5Bo2LISsJpS0rUk,5022
 linkml/generators/erdiagramgen.py,sha256=_NVBq7RzJNDZPjMtb0NYE_mbYrOyZVG-8uqGy5J5KC0,11451
 linkml/generators/excelgen.py,sha256=81x0Ib13ZjLC5WBWsH0aePn8swv_pjZnwV4X-T4q4Jc,7684
@@ -36,15 +36,26 @@ linkml/generators/javagen/example_template.java.jinja2,sha256=ec4CVTv_0zS7V5Y-1E
 linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMltvrYyVeut7l2Q-tzK7AOiVmWs,1729
 linkml/generators/javagen.py,sha256=BTAXgvOOvRa3AOfaaiVFyuyaqg4XFR_JbO6_7tT_AnQ,5335
 linkml/generators/jsonldcontextgen.py,sha256=3bu4OY4t5eyiCghXJZ1m9mGPrLpHcJ2ap21Cov_IWpM,8947
-linkml/generators/jsonldgen.py,sha256=d94TEPu9zeHDZqPU6cSaiQiJnv0kc_AXkXahi1xOBZ8,7789
+linkml/generators/jsonldgen.py,sha256=titjvZz7pMozT0kR1UJh4H57RTPBKKYQ35t0g5Ofj_Q,7794
 linkml/generators/jsonschemagen.py,sha256=F2lJCS-8cSYRgljh-6OM395aCeL2Fb3Qx6gB2X2mXXw,30848
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/linkmlgen.py,sha256=xYgS4i-Xo5Z3t9gqEdqxHKv5KGUxOerpy8M9kX6WeuI,4225
-linkml/generators/markdowngen.py,sha256=QkZ-LDT_Vm9gmHDFhVPFFR2oqPA-xATYgEYZS8bbVAE,34403
-linkml/generators/mermaidclassdiagramgen.py,sha256=S-fsMKZrR4BxDD1eK7TZBEaF4JuDzhBdzx3z7SBT2ds,4940
+linkml/generators/markdowngen.py,sha256=23fYWzVfufbzQxrRLKvYLEDDlBBKqVfJCguelIiW2Fs,35214
+linkml/generators/mermaidclassdiagramgen.py,sha256=yllg4l8psxdeti1kYOgiseB0fGeFQK_4FAealjFZ5bE,5011
 linkml/generators/namespacegen.py,sha256=C4p9LSwsnDqf6sv-wG5l0VQniWFJ1HA1hRXJBDOg3pM,6467
 linkml/generators/oocodegen.py,sha256=dgcHhpO81qC2Tx-kG_VhZVaoRjOwrcrulIXV8gEU1bY,7808
 linkml/generators/owlgen.py,sha256=HcW5EIohi9YMd6pXH62bAesZrrbBt5H8-4eQ3Eab6ow,58095
+linkml/generators/panderagen/__init__.py,sha256=Bcthn0rKU6xzQoBU--hfTUJwyOvKjASGICYamEglzcQ,109
+linkml/generators/panderagen/class_generator_mixin.py,sha256=LKdpKb1_pyBN3iyhzsQE_Q9A3S9CnXj0RQUDQw0_Ly4,826
+linkml/generators/panderagen/enum_generator_mixin.py,sha256=CMILBMjP35L8HHdp7WuO0dAHe9zEVBvN5CBSQlq41_g,708
+linkml/generators/panderagen/panderagen.py,sha256=OxLZrVLzUD5PrmomsC0MYaUM8v0R4djKHDtVr6UjPjQ,6445
+linkml/generators/panderagen/panderagen_class_based/class.jinja2,sha256=56Pb-6iiGgyfcCT1oE7mD4Rbs637SLgn2wsqH3Eyzwc,686
+linkml/generators/panderagen/panderagen_class_based/enums.jinja2,sha256=7eXfmoz7F6Tb2aYumTwW6UrwrQvqD73oYTi-LbmNCVw,295
+linkml/generators/panderagen/panderagen_class_based/header.jinja2,sha256=shLPwNAjIPMgR7uoqZWUxo4a_OtV15ywSjYh0m9dIKo,396
+linkml/generators/panderagen/panderagen_class_based/mixins.jinja2,sha256=JCgwGre4FuoEUSbPrg5MRJXZbcx5_3uCt-JuBsG3LRY,955
+linkml/generators/panderagen/panderagen_class_based/pandera.jinja2,sha256=Vlh5tdp7T9gbPst1RR72PdFeboE4Ha0yX5wILXHeZyE,506
+linkml/generators/panderagen/panderagen_class_based/slots.jinja2,sha256=cy8LKkGNDkNZBoECVOwkvN0MKLj0U_KrgkiOaY317Rc,1416
+linkml/generators/panderagen/slot_generator_mixin.py,sha256=mDoyptHXiR4TehDmSe3cYX4Mpa1oJUH8apPiJEKycLo,2586
 linkml/generators/plantumlgen.py,sha256=S05S13kxDLeKJihZ7BZesuj_8-tQUzsWjL6S478dzQg,15603
 linkml/generators/prefixmapgen.py,sha256=X-3K1q5WcSS8TL7rHBOL4qBGBk2Szr7l1_UzRQVvFGA,4246
 linkml/generators/projectgen.py,sha256=vPaCv8Qf3rwi2aPlEpFc2-Q27ed9WwZiJfseZvflIXU,9764
@@ -60,11 +71,11 @@ linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=4s4eUZEqiTxHV2
 linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=6KRQ1ZVHh1uwZnYL3qxBnyit8_DNE7D-4l2-1wsRsG0,406
 linkml/generators/pydanticgen/templates/class.py.jinja,sha256=GqR2t5y0vLmvUpT2vyP5VX42PO9AkAnGE-U2RZPa9AI,690
 linkml/generators/pydanticgen/templates/conditional_import.py.jinja,sha256=YheknDrxvepiJUzeItSL5aSbAkCdR1k0a6m6aTA4qNM,240
-linkml/generators/pydanticgen/templates/enum.py.jinja,sha256=572XFQyEMZfL-G_Cj68T-NI_mUnDoFOAVJOGIKu2Hb8,338
+linkml/generators/pydanticgen/templates/enum.py.jinja,sha256=d2j0FbQ4HT-TjspaUkfSHWaHJ50didUBTE8RV9Cj7bo,372
 linkml/generators/pydanticgen/templates/footer.py.jinja,sha256=t_24p1xmqdbfxGqz_XCXSTvkkWt26_2w_RcQjGIAWlY,155
 linkml/generators/pydanticgen/templates/imports.py.jinja,sha256=vwAOWV98rM4reAUXUYQXihukTPoVDcs8D9HWsVZmTiQ,1249
 linkml/generators/pydanticgen/templates/module.py.jinja,sha256=hqZKsJ72yUioBkZAunscVgLSe58OFHf0z6-so_b43U4,526
-linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=5vDpqdfxLpie4BzcyjE82agO6NsThIZjNlcz6gq_kFg,465
+linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=oz8XWh4Mt7DRHH0KObKGZWl_WUoR0KzoGMkLOh-NXFU,525
 linkml/generators/python/__init__.py,sha256=NS9fPEuAo0punDplD91F9mcViXMJJv04Q5NkFcKPNvY,40
 linkml/generators/python/python_ifabsent_processor.py,sha256=io-bLevkdy2xgKl0kqGB3o5iR7O7P1uE4qWEhKt-GcM,3838
 linkml/generators/pythongen.py,sha256=LDYQxtl4PEDmzX4e9mR9DQ2X9ANcE3vIOI4JMwnl8R8,55769
@@ -79,14 +90,14 @@ linkml/generators/sqlalchemy/__init__.py,sha256=mb9AC1rIFkSiNZhhG0TAk45ol9PjS1Xv
 linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBikMI5HuNgEhl_PIeWM-B-c2B0W9KUBH4QTg,2542
 linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py,sha256=u4ZpponG1h6XROrOHGOf_0H2e6xL1_s8twAOA-gx94A,1622
 linkml/generators/sqlalchemygen.py,sha256=fl8twO36TkC8mWu6pJjgGzrKEGpAinRdGJYOK5ck5wI,9326
-linkml/generators/sqltablegen.py,sha256=BaWAuvwVHsXVt85GYxzH5_UL3ZeqRI9SojlvMmh4KkE,12395
+linkml/generators/sqltablegen.py,sha256=9HMFs0JE9HKzdJgUwgvCpHoPE0Mm8ByW9o64y9lrLG4,14785
 linkml/generators/sssomgen.py,sha256=zrZy0WL9fF5bk-XAcB-MZYZkhHhqVRHt2rGBUtfqnLY,6891
 linkml/generators/string_template.md,sha256=kRcfic6entgIaJdpSg6GF3jcjC9wbKsCVM6wVT2qipc,1788
 linkml/generators/summarygen.py,sha256=abNd39Z-Kn3FX2fjXLeCqvXvFunpqM7UFPimtiCB2p0,3081
 linkml/generators/terminusdbgen.py,sha256=om2pHIIMmL2mh3DkzCO_J20ni7qr43L4ptl3jqSsZN4,4689
 linkml/generators/typescriptgen.py,sha256=wRnZpZ3LEepJRFYHVNP06PX5rPFzIDPglDRxi0Z6Zro,8870
 linkml/generators/yamlgen.py,sha256=PWexYoR3wHRoAUk6zK67fRYjBF6sAmX_iGlOAT0PJq0,1623
-linkml/generators/yumlgen.py,sha256=vaXOQtweJjpKEqa2D-IsjWGLsijxjF9AKj98ycECOeQ,12197
+linkml/generators/yumlgen.py,sha256=ZK42N3hJPvvOdztOWCwysARrGVWjg5V4Qx2XcS2Vvgc,13277
 linkml/linter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/linter/cli.py,sha256=N6MRbRU2bE9ee4xVtgWoqBRh_IZ_SSt15S6RJDP1m1I,4514
 linkml/linter/config/datamodel/.linkmllint.yaml,sha256=40rNhcL35FXQSjlVBMWnyPgplwEUqFT_sJmeZqUzxMw,292
@@ -109,15 +120,16 @@ linkml/transformers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSu
 linkml/transformers/logical_model_transformer.py,sha256=g_o23EDfFnEdKD71Td1m8ZZ1hYuHrqOyvx9sBuX8_LE,29938
 linkml/transformers/model_transformer.py,sha256=tK_MpRDI-q2qfe8KHT6qJHP8ZruKjYx1FcM-Fnjse-E,678
 linkml/transformers/relmodel_transformer.py,sha256=9_r4bNJ6HDjaqZZTOE6nmjXjLgmRm-i96NbgBma8iR4,19663
+linkml/transformers/rollup_transformer.py,sha256=YP3RyYa0TzfkTrPZ4LnTIedmQWCnneFk3wAT77E1Amc,4549
 linkml/transformers/schema_renamer.py,sha256=DvXsAsxAb8p8RAxR_c74zbn_VRFN1JHCLHcjH9z7qr0,5263
 linkml/utils/__init__.py,sha256=Pkyv-Gfb8QoJdInRdJuuUz1Igfe0sT9t8Gv3V_fyTXc,92
 linkml/utils/cli_utils.py,sha256=MdVbox1qr6kDUHUCWAmFhV-D6ebs_nn8vVwB8KDQfew,742
 linkml/utils/converter.py,sha256=0xcUXdVPUXZvVuHivUibfVMoCd24oPsjYU1M17H173U,7121
 linkml/utils/datautils.py,sha256=QlbzwXykh5Fphfe5KxPo6_ekXfniLbHiEGJtLWjUrvY,3742
 linkml/utils/datavalidator.py,sha256=kBdWaVi8IZT1bOwEJgJYx-wZAb_PTBObB9nHpYORfKA,472
-linkml/utils/deprecation.py,sha256=jSU93Xi9pdg1rTokb3IY9I3N2V0uzb_YA_5MgJjs-Wg,8487
+linkml/utils/deprecation.py,sha256=fFd_rUmTJInovuhuHVZf_44fQRve6FyJ43DY2-0XLmA,9781
 linkml/utils/exceptions.py,sha256=3S6lf5WAUgVvjPRaES597_YjUjbbJ5KqjKjpjcaRLoU,217
-linkml/utils/execute_tutorial.py,sha256=CFMDSbCU66jCmIkvWPchqvdsXj1Ol3ujEQnchy4688Q,7033
+linkml/utils/execute_tutorial.py,sha256=gGgkuTjP8Tsb-4imsNAa_1ESlrsl3qCz02skFvhI5dE,10587
 linkml/utils/generator.py,sha256=TWif2M7LHv6pAW5uRHJKBzNmEkasAen1W3uMjO1VPIA,39576
 linkml/utils/helpers.py,sha256=MomYM4Oof-c1SgyMpjoG0Aob-eaVeF8kXvuzdJiKo_g,3351
 linkml/utils/logictools.py,sha256=pV66YWCWhQyCjra77k2H_hygaIq3Dy6vAb9N67rrAdc,23649
@@ -141,7 +153,7 @@ linkml/validator/loaders/yaml_loader.py,sha256=JqTWBV1V4Imk-uktQugjaxl88sqWS0X5Q
 linkml/validator/plugins/__init__.py,sha256=0ifiDqpcXVy4X7OJFm7FMYi1-6E06avNIIk9R0c6nD8,693
 linkml/validator/plugins/jsonschema_validation_plugin.py,sha256=F40Ml5Qs71mXmcMqoIsZsNJEhrkmNHMgnl33EuPF7HQ,2696
 linkml/validator/plugins/pydantic_validation_plugin.py,sha256=dJ-LDUtbD8Y6tH1RE-eGRkhu1XTjxGXIzL4bflW5T4M,2017
-linkml/validator/plugins/recommended_slots_plugin.py,sha256=6xJBJ5g0LQvwZVn_Eld_ydmrJNovFPSzj63weK6-Oaw,2329
+linkml/validator/plugins/recommended_slots_plugin.py,sha256=6P2WYNgA_UPSJja_0jhh4hlLD6P8HXIkefnD9IxH4Hc,2359
 linkml/validator/plugins/shacl_validation_plugin.py,sha256=4QxFAhuMKKkKTl8VDtD-FTBqnXsQEoG_d3osDKggcQk,3915
 linkml/validator/plugins/validation_plugin.py,sha256=Gx4S5nFZ7DPoYIGlFe_o2vQJyCX0vBB3Qk2t606IfFs,1557
 linkml/validator/report.py,sha256=fhXGkm1Yxdy1fmxJD08Kn_yZ7FikJMW0LVPmZiF4lHw,1055
@@ -155,8 +167,8 @@ linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 linkml/workspaces/datamodel/workspaces.py,sha256=YIGzErECZuMER03h3DcuY3psMb0lDF1Pia_8hreKoTE,14667
 linkml/workspaces/datamodel/workspaces.yaml,sha256=EjVrwPpeRZqJRjuGyyDRxxFzuv55SiLIXPBRUG6HStU,4233
 linkml/workspaces/example_runner.py,sha256=EjaAn6vaAKZnFcW5hRopkYBguiaR05aqKbuaM-o_7IE,12940
-linkml-1.9.1rc3.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.9.1rc3.dist-info/METADATA,sha256=kbd_uaAi7FJqc02QSUHVdUselPurehDdtdOZeaw3iq8,3715
-linkml-1.9.1rc3.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-linkml-1.9.1rc3.dist-info/entry_points.txt,sha256=CtvrM-5f3NuMEBTXONEnIo5UUJegBRWJvXUmrYfdIfM,2194
-linkml-1.9.1rc3.dist-info/RECORD,,
+linkml-1.9.2.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.9.2.dist-info/METADATA,sha256=Dxc9EJ467qTcNWS63GOUMyDGwRsskLvCpe87XY0NSQM,3720
+linkml-1.9.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+linkml-1.9.2.dist-info/entry_points.txt,sha256=AgYAJBnCIEYZsOidFnZKRbTJRxMRtmapbXbtx5imB0E,2239
+linkml-1.9.2.dist-info/RECORD,,

{linkml-1.9.1rc3.dist-info → linkml-1.9.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.1
+Generator: poetry-core 2.1.3
 Root-Is-Purelib: true
 Tag: py3-none-any

{linkml-1.9.1rc3.dist-info → linkml-1.9.2.dist-info}/entry_points.txt

@@ -17,6 +17,7 @@ gen-markdown=linkml.generators.markdowngen:cli
 gen-mermaid-class-diagram=linkml.generators.mermaidclassdiagramgen:cli
 gen-namespaces=linkml.generators.namespacegen:cli
 gen-owl=linkml.generators.owlgen:cli
+gen-pandera=linkml.generators.panderagen:cli
 gen-plantuml=linkml.generators.plantumlgen:cli
 gen-prefix-map=linkml.generators.prefixmapgen:cli
 gen-project=linkml.generators.projectgen:cli