From bec9644cb767f73bca7d8a6553ee06175777f61d Mon Sep 17 00:00:00 2001
From: Chris Mungall <cjm@berkeleybop.org>
Date: Sun, 30 Mar 2025 13:09:32 -0700
Subject: [PATCH 01/16] restore dataclass_extensions. See #345

---
 .../utils/dataclass_extensions_376.py         | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 linkml_runtime/utils/dataclass_extensions_376.py

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
new file mode 100644
index 00000000..d90b542f
--- /dev/null
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -0,0 +1,30 @@
+import dataclasses
+#
+# The dataclass library builds a rigid `__init__` function that doesn't allow any unrecognized named parameters
+#
+# The purpose of this extension is to enhance the library to allow additional keyword arguments to passed in
+# and then on to the __post_init__ function that can deal with them accordingly
+
+# Beware that there is no promise that signature of the create function will remain consistent
+loc_fn = dataclasses._create_fn
+
+
+def dc_create_fn(name, args, body, *_posargs, **_kwargs):
+    # If overriding the initializer and using a post init
+    if name == '__init__' and dataclasses._POST_INIT_NAME in body[-1]:
+        # Then insert the kwargs into the both the call and the post init
+        pi_parms = body[-1].rsplit(')', 1)[0]
+        body[-1] = pi_parms + ('' if pi_parms[-1] == '(' else ',') + ' **_kwargs)'
+        return loc_fn(name, list(args) + ["**_kwargs"], body, *_posargs, **_kwargs)
+    else:
+        return loc_fn(name, args, body, *_posargs, **_kwargs)
+
+
+dataclasses._create_fn = dc_create_fn
+
+# The following line is here solely to be backwards compatible.
+dataclasses_init_fn_with_kwargs = dataclasses._init_fn
+
+# The following line can be used to make certain that the import of the new create function doesn't get
+# discarded as being potentially unused
+DC_CREATE_FN = True

From fdf3302b18be4868ba6186da8a254e87b858ce11 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Sun, 30 Mar 2025 16:17:16 -0700
Subject: [PATCH 02/16] restore test to go along with dataclass_extensions_376

---
 tests/test_issues/test_issue_718a.py | 51 ++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 tests/test_issues/test_issue_718a.py

diff --git a/tests/test_issues/test_issue_718a.py b/tests/test_issues/test_issue_718a.py
new file mode 100644
index 00000000..b5710e20
--- /dev/null
+++ b/tests/test_issues/test_issue_718a.py
@@ -0,0 +1,51 @@
+import dataclasses
+import unittest
+from dataclasses import dataclass
+from typing import Optional, ClassVar
+
+import yaml
+
+import linkml_runtime.utils.dataclass_extensions_376 as dc_tweak
+# This line makes certain that the import remains
+DC_IN = dc_tweak.DC_CREATE_FN
+
+from linkml_runtime.utils.yamlutils import YAMLRoot, DupCheckYamlLoader
+
+
+class Issue83TestCase(unittest.TestCase):
+    # The goal is to provide line numbers on error messages.   We've tweaked the parser so that it returns augmented
+    # str's and int's with the line numbers on them.  The problem we are trying to address now is that the dataclass
+    # constructor doesn't support **argv out of the box.  We can certainly tweak the generator to emit the __init__
+    # method to do this, but it would be really handy
+
+    @dataclass
+    class FesterBesterTester(YAMLRoot):
+        cv: ClassVar[int] = 42
+
+        a: Optional[int] = 0
+        b: Optional[str] = None
+
+    def test_initvar(self):
+        with self.assertRaises(ValueError) as e:
+            Issue83TestCase.FesterBesterTester(a=12, b="Sell", c="buy")
+        self.assertEqual("Unknown argument: c = 'buy'", str(e.exception).strip())
+        yaml_str = """base:
+        a: 17
+        b: Ice Cream
+        c: sell
+"""
+        parsed_yaml = yaml.load(yaml_str, DupCheckYamlLoader)
+        with self.assertRaises(ValueError) as e:
+            Issue83TestCase.FesterBesterTester(**parsed_yaml['base'])
+        self.assertEqual('File "<unicode string>", line 4, col 9:  Unknown argument: c = \'sell\'',
+                         str(e.exception).strip())
+
+        parsed_yaml['base'].pop('c', None)
+        try:
+            Issue83TestCase.FesterBesterTester(**parsed_yaml['base'])
+        except Exception as e:
+            self.fail(f'Raised exception unexpectedly: {str(e.exception)}')
+
+
+if __name__ == '__main__':
+    unittest.main()

From 638d87374498b2a2823b24104e84a984c3b5f031 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Sun, 30 Mar 2025 16:37:49 -0700
Subject: [PATCH 03/16] remove tests again - dataclass fn rm'd

---
 tests/test_issues/test_issue_718a.py | 51 ----------------------------
 1 file changed, 51 deletions(-)
 delete mode 100644 tests/test_issues/test_issue_718a.py

diff --git a/tests/test_issues/test_issue_718a.py b/tests/test_issues/test_issue_718a.py
deleted file mode 100644
index b5710e20..00000000
--- a/tests/test_issues/test_issue_718a.py
+++ /dev/null
@@ -1,51 +0,0 @@
-import dataclasses
-import unittest
-from dataclasses import dataclass
-from typing import Optional, ClassVar
-
-import yaml
-
-import linkml_runtime.utils.dataclass_extensions_376 as dc_tweak
-# This line makes certain that the import remains
-DC_IN = dc_tweak.DC_CREATE_FN
-
-from linkml_runtime.utils.yamlutils import YAMLRoot, DupCheckYamlLoader
-
-
-class Issue83TestCase(unittest.TestCase):
-    # The goal is to provide line numbers on error messages.   We've tweaked the parser so that it returns augmented
-    # str's and int's with the line numbers on them.  The problem we are trying to address now is that the dataclass
-    # constructor doesn't support **argv out of the box.  We can certainly tweak the generator to emit the __init__
-    # method to do this, but it would be really handy
-
-    @dataclass
-    class FesterBesterTester(YAMLRoot):
-        cv: ClassVar[int] = 42
-
-        a: Optional[int] = 0
-        b: Optional[str] = None
-
-    def test_initvar(self):
-        with self.assertRaises(ValueError) as e:
-            Issue83TestCase.FesterBesterTester(a=12, b="Sell", c="buy")
-        self.assertEqual("Unknown argument: c = 'buy'", str(e.exception).strip())
-        yaml_str = """base:
-        a: 17
-        b: Ice Cream
-        c: sell
-"""
-        parsed_yaml = yaml.load(yaml_str, DupCheckYamlLoader)
-        with self.assertRaises(ValueError) as e:
-            Issue83TestCase.FesterBesterTester(**parsed_yaml['base'])
-        self.assertEqual('File "<unicode string>", line 4, col 9:  Unknown argument: c = \'sell\'',
-                         str(e.exception).strip())
-
-        parsed_yaml['base'].pop('c', None)
-        try:
-            Issue83TestCase.FesterBesterTester(**parsed_yaml['base'])
-        except Exception as e:
-            self.fail(f'Raised exception unexpectedly: {str(e.exception)}')
-
-
-if __name__ == '__main__':
-    unittest.main()

From 15baee31d6018af1058463040096cdbed527d0f2 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Sun, 30 Mar 2025 20:50:20 -0700
Subject: [PATCH 04/16] DO NOT MERGE - testing a reimplementation of a previous
 version of code

---
 .../utils/dataclass_extensions_376.py         | 29 ++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
index d90b542f..0f1af1d3 100644
--- a/linkml_runtime/utils/dataclass_extensions_376.py
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -6,7 +6,34 @@
 # and then on to the __post_init__ function that can deal with them accordingly
 
 # Beware that there is no promise that signature of the create function will remain consistent
-loc_fn = dataclasses._create_fn
+
+def _create_fn(name, args, body, *, globals=None, locals=None,
+               return_type=MISSING):
+    # Note that we mutate locals when exec() is called.  Caller
+    # beware!  The only callers are internal to this module, so no
+    # worries about external callers.
+    if locals is None:
+        locals = {}
+    if 'BUILTINS' not in locals:
+        locals['BUILTINS'] = builtins
+    return_annotation = ''
+    if return_type is not MISSING:
+        locals['_return_type'] = return_type
+        return_annotation = '->_return_type'
+    args = ','.join(args)
+    body = '\n'.join(f'  {b}' for b in body)
+
+    # Compute the text of the entire function.
+    txt = f' def {name}({args}){return_annotation}:\n{body}'
+
+    local_vars = ', '.join(locals.keys())
+    txt = f"def __create_fn__({local_vars}):\n{txt}\n return {name}"
+    ns = {}
+    exec(txt, globals, ns)
+    return ns['__create_fn__'](**locals)
+
+
+loc_fn = _create_fn()
 
 
 def dc_create_fn(name, args, body, *_posargs, **_kwargs):

From 9666efd639b9ad9375eb3efd61db64cb4f9e6523 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 31 Mar 2025 11:06:27 -0700
Subject: [PATCH 05/16] add warning and patch tests to skip if > 3.13.0

---
 .../utils/dataclass_extensions_376.py         | 91 ++++++++-----------
 .../test_dataclass_extensions_376.py          | 46 ++++++++++
 2 files changed, 82 insertions(+), 55 deletions(-)
 create mode 100644 tests/test_issues/test_dataclass_extensions_376.py

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
index 0f1af1d3..d61dffa1 100644
--- a/linkml_runtime/utils/dataclass_extensions_376.py
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -1,57 +1,38 @@
+import sys
 import dataclasses
-#
-# The dataclass library builds a rigid `__init__` function that doesn't allow any unrecognized named parameters
-#
-# The purpose of this extension is to enhance the library to allow additional keyword arguments to passed in
-# and then on to the __post_init__ function that can deal with them accordingly
+import warnings
+
+# Raise helpful error in unsupported Python versions
+if sys.version_info >= (3, 13):
+    raise RuntimeError(
+        "The LinkML dataclass_extensions_376 is no longer compatible with Python 3.13 or newer.\n\n"
+        "Python 3.13 removed _create_fn), which this extension relies on.\n\n"
+        "To resolve this:\n"
+        "  • Upgrade your LinkML schema and code to use LinkML >= 1.9.0, which no longer requires this patch\n"
+        "  • Or migrate to Pydantic models for runtime dataclass behavior\n\n"
+    )
+
+# Emit deprecation warning in all other Python versions
+warnings.warn(
+    "The LinkML dataclass extension monkeypatch is deprecated and will be removed in a future release.\n"
+    "Consider upgrading to LinkML >=1.9.0 or switching to Pydantic.",
+    DeprecationWarning,
+    stacklevel=2
+)
+
+# Patch _create_fn if it still exists
+if hasattr(dataclasses, "_create_fn"):
+    loc_fn = dataclasses._create_fn
+
+    def dc_create_fn(name, args, body, *_posargs, **_kwargs):
+        if name == '__init__' and dataclasses._POST_INIT_NAME in body[-1]:
+            pi_parms = body[-1].rsplit(')', 1)[0]
+            body[-1] = pi_parms + ('' if pi_parms[-1] == '(' else ',') + ' **_kwargs)'
+            return loc_fn(name, list(args) + ["**_kwargs"], body, *_posargs, **_kwargs)
+        else:
+            return loc_fn(name, args, body, *_posargs, **_kwargs)
+
+    dataclasses._create_fn = dc_create_fn
+    dataclasses_init_fn_with_kwargs = dataclasses._init_fn
+    DC_CREATE_FN = True
 
-# Beware that there is no promise that signature of the create function will remain consistent
-
-def _create_fn(name, args, body, *, globals=None, locals=None,
-               return_type=MISSING):
-    # Note that we mutate locals when exec() is called.  Caller
-    # beware!  The only callers are internal to this module, so no
-    # worries about external callers.
-    if locals is None:
-        locals = {}
-    if 'BUILTINS' not in locals:
-        locals['BUILTINS'] = builtins
-    return_annotation = ''
-    if return_type is not MISSING:
-        locals['_return_type'] = return_type
-        return_annotation = '->_return_type'
-    args = ','.join(args)
-    body = '\n'.join(f'  {b}' for b in body)
-
-    # Compute the text of the entire function.
-    txt = f' def {name}({args}){return_annotation}:\n{body}'
-
-    local_vars = ', '.join(locals.keys())
-    txt = f"def __create_fn__({local_vars}):\n{txt}\n return {name}"
-    ns = {}
-    exec(txt, globals, ns)
-    return ns['__create_fn__'](**locals)
-
-
-loc_fn = _create_fn()
-
-
-def dc_create_fn(name, args, body, *_posargs, **_kwargs):
-    # If overriding the initializer and using a post init
-    if name == '__init__' and dataclasses._POST_INIT_NAME in body[-1]:
-        # Then insert the kwargs into the both the call and the post init
-        pi_parms = body[-1].rsplit(')', 1)[0]
-        body[-1] = pi_parms + ('' if pi_parms[-1] == '(' else ',') + ' **_kwargs)'
-        return loc_fn(name, list(args) + ["**_kwargs"], body, *_posargs, **_kwargs)
-    else:
-        return loc_fn(name, args, body, *_posargs, **_kwargs)
-
-
-dataclasses._create_fn = dc_create_fn
-
-# The following line is here solely to be backwards compatible.
-dataclasses_init_fn_with_kwargs = dataclasses._init_fn
-
-# The following line can be used to make certain that the import of the new create function doesn't get
-# discarded as being potentially unused
-DC_CREATE_FN = True
diff --git a/tests/test_issues/test_dataclass_extensions_376.py b/tests/test_issues/test_dataclass_extensions_376.py
new file mode 100644
index 00000000..11010d5c
--- /dev/null
+++ b/tests/test_issues/test_dataclass_extensions_376.py
@@ -0,0 +1,46 @@
+import sys
+import unittest
+from dataclasses import dataclass
+from typing import Optional
+import pytest
+
+# Only import the LinkML patch module on supported Python versions
+# Python 3.13+ removed dataclasses._create_fn, which breaks this patch.
+# The test will be skipped on versions > 3.13.0.
+if sys.version_info < (3, 13):
+    import linkml_runtime.utils.dataclass_extensions_376 as dc_tweak
+    DC_IN = dc_tweak.DC_CREATE_FN
+else:
+    dc_tweak = None
+    DC_IN = False
+
+
+@pytest.mark.skipif(sys.version_info >= (3, 13), reason="LinkML dataclass patch no longer supported in Python 3.13+")
+class DataclassExtensionsTestCase(unittest.TestCase):
+    """Test the dataclass_extensions_376 module with Python <3.13"""
+
+    @dataclass
+    class TestClass:
+        a: Optional[int] = 0
+        b: Optional[str] = None
+
+        def __post_init__(self, **kwargs):
+            if kwargs:
+                unknown_args = sorted(kwargs.keys())
+                first_arg = unknown_args[0]
+                raise ValueError(f"Unknown argument: {first_arg} = {repr(kwargs[first_arg])}")
+
+    def test_kwargs_passed_to_post_init(self):
+        self.TestClass(a=1, b="test")
+
+        with self.assertRaises(ValueError) as e:
+            self.TestClass(a=1, b="test", c="unknown")
+        self.assertEqual("Unknown argument: c = 'unknown'", str(e.exception))
+
+        with self.assertRaises(ValueError) as e:
+            self.TestClass(a=1, b="test", c="unknown", z="also_unknown")
+        self.assertEqual("Unknown argument: c = 'unknown'", str(e.exception))
+
+
+if __name__ == '__main__':
+    unittest.main()

From aaae754ea538d4a5a92488ef668f982b08603f0c Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 31 Mar 2025 11:30:52 -0700
Subject: [PATCH 06/16] remove unused toml addition

---
 .../utils/dataclass_extensions_376.py         |  2 +-
 poetry.lock                                   | 30 +++++++++----------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
index d61dffa1..d20a68fa 100644
--- a/linkml_runtime/utils/dataclass_extensions_376.py
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -14,7 +14,7 @@
 
 # Emit deprecation warning in all other Python versions
 warnings.warn(
-    "The LinkML dataclass extension monkeypatch is deprecated and will be removed in a future release.\n"
+    "The LinkML dataclass extension is deprecated and will be removed in a future release.\n"
     "Consider upgrading to LinkML >=1.9.0 or switching to Pydantic.",
     DeprecationWarning,
     stacklevel=2
diff --git a/poetry.lock b/poetry.lock
index 3732d198..c5ecd50b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -28,12 +28,12 @@ files = [
 ]
 
 [package.extras]
-benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
+cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
+dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
 docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
-tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
+tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\""]
 
 [[package]]
 name = "cattrs"
@@ -56,8 +56,8 @@ typing-extensions = {version = ">=4.1.0,<4.6.3 || >4.6.3", markers = "python_ver
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
-msgspec = ["msgspec (>=0.18.5)"]
-orjson = ["orjson (>=3.9.2)"]
+msgspec = ["msgspec (>=0.18.5) ; implementation_name == \"cpython\""]
+orjson = ["orjson (>=3.9.2) ; implementation_name == \"cpython\""]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
 ujson = ["ujson (>=5.7.0)"]
@@ -265,7 +265,7 @@ files = [
 ]
 
 [package.extras]
-toml = ["tomli"]
+toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
 
 [[package]]
 name = "curies"
@@ -308,7 +308,7 @@ files = [
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools", "tox"]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools ; python_version >= \"3.12\"", "tox"]
 
 [[package]]
 name = "exceptiongroup"
@@ -370,7 +370,7 @@ files = [
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
@@ -583,7 +583,7 @@ typing-extensions = ">=4.12.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
-timezone = ["tzdata"]
+timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
 
 [[package]]
 name = "pydantic-core"
@@ -1141,7 +1141,7 @@ files = [
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
 h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
@@ -1249,11 +1249,11 @@ files = [
 ]
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
 type = ["pytest-mypy"]
 
 [metadata]

From 9e6ed7e77d57494e745d693d10c88b849d183802 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 31 Mar 2025 11:52:08 -0700
Subject: [PATCH 07/16] refactor to pytest instead of unittest

---
 .../utils/dataclass_extensions_376.py         | 38 +++++++++++++------
 .../test_dataclass_extensions_376.py          | 33 ++++++++--------
 2 files changed, 45 insertions(+), 26 deletions(-)

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
index d20a68fa..008cddfe 100644
--- a/linkml_runtime/utils/dataclass_extensions_376.py
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -2,25 +2,25 @@
 import dataclasses
 import warnings
 
-# Raise helpful error in unsupported Python versions
+# Block unsupported Python versions
 if sys.version_info >= (3, 13):
     raise RuntimeError(
-        "The LinkML dataclass_extensions_376 is no longer compatible with Python 3.13 or newer.\n\n"
-        "Python 3.13 removed _create_fn), which this extension relies on.\n\n"
+        "The LinkML dataclass_extensions_376 patch is no longer compatible with Python 3.13 or newer.\n\n"
+        "Python 3.13 removed internal support for `_create_fn`, which this patch depends on.\n\n"
         "To resolve this:\n"
-        "  • Upgrade your LinkML schema and code to use LinkML >= 1.9.0, which no longer requires this patch\n"
-        "  • Or migrate to Pydantic models for runtime dataclass behavior\n\n"
+        "  • Upgrade your LinkML schema and code to use LinkML >= 1.9.0, which no longer uses this patch\n"
+        "  • Or migrate to Pydantic models for dataclass behavior\n\n"
     )
 
-# Emit deprecation warning in all other Python versions
+# Warn that this extension is deprecated
 warnings.warn(
-    "The LinkML dataclass extension is deprecated and will be removed in a future release.\n"
-    "Consider upgrading to LinkML >=1.9.0 or switching to Pydantic.",
+    "The LinkML dataclass extension patch is deprecated and will be removed in a future release.\n"
+    "Consider upgrading to LinkML >= 1.9.0 or switching Python class generation to Pydantic.",
     DeprecationWarning,
-    stacklevel=2
+    stacklevel=2,
 )
 
-# Patch _create_fn if it still exists
+# Conditionally patch only if _create_fn exists
 if hasattr(dataclasses, "_create_fn"):
     loc_fn = dataclasses._create_fn
 
@@ -34,5 +34,21 @@ def dc_create_fn(name, args, body, *_posargs, **_kwargs):
 
     dataclasses._create_fn = dc_create_fn
     dataclasses_init_fn_with_kwargs = dataclasses._init_fn
-    DC_CREATE_FN = True
 
+    warnings.warn(
+        "LinkML dataclass patch successfully applied.",
+        UserWarning,
+        stacklevel=2,
+    )
+else:
+    raise RuntimeError(
+        "The LinkML dataclass_extensions_376 patch could not be applied: `dataclasses._create_fn` is missing.\n\n"
+        "This likely indicates a nonstandard or altered Python environment, or partial compatibility with this patch.\n\n"
+        "To proceed:\n"
+        "  • Use a supported Python version where `_create_fn` is present (Python < 3.13)\n"
+        "  • Or upgrade to LinkML >= 1.9.0 to remove reliance on this patch\n"
+        "  • Or migrate to Pydantic models\n\n"
+    )
+
+# Used to signal that this patch was imported/applied
+DC_CREATE_FN = True
\ No newline at end of file
diff --git a/tests/test_issues/test_dataclass_extensions_376.py b/tests/test_issues/test_dataclass_extensions_376.py
index 11010d5c..d2941b4b 100644
--- a/tests/test_issues/test_dataclass_extensions_376.py
+++ b/tests/test_issues/test_dataclass_extensions_376.py
@@ -1,14 +1,14 @@
 import sys
-import unittest
+import pytest
 from dataclasses import dataclass
 from typing import Optional
-import pytest
+import importlib
 
 # Only import the LinkML patch module on supported Python versions
 # Python 3.13+ removed dataclasses._create_fn, which breaks this patch.
-# The test will be skipped on versions > 3.13.0.
 if sys.version_info < (3, 13):
     import linkml_runtime.utils.dataclass_extensions_376 as dc_tweak
+
     DC_IN = dc_tweak.DC_CREATE_FN
 else:
     dc_tweak = None
@@ -16,8 +16,8 @@
 
 
 @pytest.mark.skipif(sys.version_info >= (3, 13), reason="LinkML dataclass patch no longer supported in Python 3.13+")
-class DataclassExtensionsTestCase(unittest.TestCase):
-    """Test the dataclass_extensions_376 module with Python <3.13"""
+def test_kwargs_passed_to_post_init():
+    """Test that kwargs are passed to __post_init__ in patched dataclass"""
 
     @dataclass
     class TestClass:
@@ -30,17 +30,20 @@ def __post_init__(self, **kwargs):
                 first_arg = unknown_args[0]
                 raise ValueError(f"Unknown argument: {first_arg} = {repr(kwargs[first_arg])}")
 
-    def test_kwargs_passed_to_post_init(self):
-        self.TestClass(a=1, b="test")
+    # No extra kwargs – should not raise
+    TestClass(a=1, b="test")
 
-        with self.assertRaises(ValueError) as e:
-            self.TestClass(a=1, b="test", c="unknown")
-        self.assertEqual("Unknown argument: c = 'unknown'", str(e.exception))
+    # One unknown kwarg – should raise
+    with pytest.raises(ValueError, match="Unknown argument: c = 'unknown'"):
+        TestClass(a=1, b="test", c="unknown")
 
-        with self.assertRaises(ValueError) as e:
-            self.TestClass(a=1, b="test", c="unknown", z="also_unknown")
-        self.assertEqual("Unknown argument: c = 'unknown'", str(e.exception))
+    # Multiple unknown kwargs – should raise, first alphabetically
+    with pytest.raises(ValueError, match="Unknown argument: c = 'unknown'"):
+        TestClass(a=1, b="test", c="unknown", z="also_unknown")
 
 
-if __name__ == '__main__':
-    unittest.main()
+@pytest.mark.skipif(sys.version_info < (3, 13), reason="This test only applies to Python 3.13+")
+def test_patch_fails_on_python_3_13_plus():
+    """Ensure the patch raises a RuntimeError on Python 3.13+"""
+    with pytest.raises(RuntimeError, match="no longer compatible with Python 3.13 or newer"):
+        importlib.import_module("linkml_runtime.utils.dataclass_extensions_376")

From 7c2164cfa6d9d4654d91171ab99e97b9622efb52 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 31 Mar 2025 12:40:39 -0700
Subject: [PATCH 08/16] fix tests to always emit warning

---
 .../utils/dataclass_extensions_376.py         | 70 ++++++++-----------
 .../test_dataclass_extensions_376.py          | 13 ++--
 2 files changed, 37 insertions(+), 46 deletions(-)

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
index 008cddfe..17cc1bd1 100644
--- a/linkml_runtime/utils/dataclass_extensions_376.py
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -1,54 +1,40 @@
 import sys
-import dataclasses
 import warnings
 
-# Block unsupported Python versions
-if sys.version_info >= (3, 13):
-    raise RuntimeError(
-        "The LinkML dataclass_extensions_376 patch is no longer compatible with Python 3.13 or newer.\n\n"
-        "Python 3.13 removed internal support for `_create_fn`, which this patch depends on.\n\n"
-        "To resolve this:\n"
-        "  • Upgrade your LinkML schema and code to use LinkML >= 1.9.0, which no longer uses this patch\n"
-        "  • Or migrate to Pydantic models for dataclass behavior\n\n"
-    )
-
-# Warn that this extension is deprecated
 warnings.warn(
     "The LinkML dataclass extension patch is deprecated and will be removed in a future release.\n"
-    "Consider upgrading to LinkML >= 1.9.0 or switching Python class generation to Pydantic.",
+    "If you're currently using Python < 3.13, where this patch still applies, you should:\n"
+    "  • Upgrade your LinkML tooling to version >= 1.9.0 (which no longer needs this patch), OR\n"
+    "  • Migrate to Pydantic models if you're using LinkML's generated classes at runtime.\n\n"
+    "If you're currently using Python >= 3.13, this patch is ignored.",
     DeprecationWarning,
-    stacklevel=2,
+    stacklevel=2
 )
 
-# Conditionally patch only if _create_fn exists
-if hasattr(dataclasses, "_create_fn"):
-    loc_fn = dataclasses._create_fn
+# In Python < 3.13, still apply the dataclass extension patch
+if sys.version_info < (3, 13):
+    import dataclasses
 
-    def dc_create_fn(name, args, body, *_posargs, **_kwargs):
-        if name == '__init__' and dataclasses._POST_INIT_NAME in body[-1]:
-            pi_parms = body[-1].rsplit(')', 1)[0]
-            body[-1] = pi_parms + ('' if pi_parms[-1] == '(' else ',') + ' **_kwargs)'
-            return loc_fn(name, list(args) + ["**_kwargs"], body, *_posargs, **_kwargs)
-        else:
-            return loc_fn(name, args, body, *_posargs, **_kwargs)
+    if hasattr(dataclasses, "_create_fn"):
+        loc_fn = dataclasses._create_fn
 
-    dataclasses._create_fn = dc_create_fn
-    dataclasses_init_fn_with_kwargs = dataclasses._init_fn
+        def dc_create_fn(name, args, body, *_posargs, **_kwargs):
+            if name == '__init__' and dataclasses._POST_INIT_NAME in body[-1]:
+                pi_parms = body[-1].rsplit(')', 1)[0]
+                body[-1] = pi_parms + ('' if pi_parms[-1] == '(' else ',') + ' **_kwargs)'
+                return loc_fn(name, list(args) + ["**_kwargs"], body, *_posargs, **_kwargs)
+            else:
+                return loc_fn(name, args, body, *_posargs, **_kwargs)
 
-    warnings.warn(
-        "LinkML dataclass patch successfully applied.",
-        UserWarning,
-        stacklevel=2,
-    )
-else:
-    raise RuntimeError(
-        "The LinkML dataclass_extensions_376 patch could not be applied: `dataclasses._create_fn` is missing.\n\n"
-        "This likely indicates a nonstandard or altered Python environment, or partial compatibility with this patch.\n\n"
-        "To proceed:\n"
-        "  • Use a supported Python version where `_create_fn` is present (Python < 3.13)\n"
-        "  • Or upgrade to LinkML >= 1.9.0 to remove reliance on this patch\n"
-        "  • Or migrate to Pydantic models\n\n"
-    )
+        dataclasses._create_fn = dc_create_fn
+        dataclasses_init_fn_with_kwargs = dataclasses._init_fn
 
-# Used to signal that this patch was imported/applied
-DC_CREATE_FN = True
\ No newline at end of file
+        DC_CREATE_FN = True
+    else:
+        warnings.warn(
+            "The LinkML dataclass patch could not be applied because `dataclasses._create_fn` is missing.\n"
+            "This may indicate a nonstandard Python environment. "
+            "Please upgrade to LinkML >= 1.9.0 or migrate to Pydantic.",
+            RuntimeWarning,
+            stacklevel=2,
+        )
diff --git a/tests/test_issues/test_dataclass_extensions_376.py b/tests/test_issues/test_dataclass_extensions_376.py
index d2941b4b..ae4aa4af 100644
--- a/tests/test_issues/test_dataclass_extensions_376.py
+++ b/tests/test_issues/test_dataclass_extensions_376.py
@@ -43,7 +43,12 @@ def __post_init__(self, **kwargs):
 
 
 @pytest.mark.skipif(sys.version_info < (3, 13), reason="This test only applies to Python 3.13+")
-def test_patch_fails_on_python_3_13_plus():
-    """Ensure the patch raises a RuntimeError on Python 3.13+"""
-    with pytest.raises(RuntimeError, match="no longer compatible with Python 3.13 or newer"):
-        importlib.import_module("linkml_runtime.utils.dataclass_extensions_376")
+def test_patch_module_is_ignored_on_python_3_13_plus():
+    """Ensure the patch module is importable and emits a DeprecationWarning on Python 3.13+"""
+    with pytest.warns(DeprecationWarning, match="deprecated and will be removed in a future release"):
+        import importlib.util
+
+        spec = importlib.util.find_spec("linkml_runtime.utils.dataclass_extensions_376")
+        mod = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(mod)
+

From 968e3ef9f605d908f01254f2d7725e7e9cfebb1c Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 31 Mar 2025 15:28:27 -0700
Subject: [PATCH 09/16] alternative approach, just gut the module.

---
 .../utils/dataclass_extensions_376.py         | 32 +--------
 .../test_dataclass_extensions_376.py          | 69 +++++++------------
 2 files changed, 29 insertions(+), 72 deletions(-)

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
index 17cc1bd1..0a0e0475 100644
--- a/linkml_runtime/utils/dataclass_extensions_376.py
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -5,36 +5,10 @@
     "The LinkML dataclass extension patch is deprecated and will be removed in a future release.\n"
     "If you're currently using Python < 3.13, where this patch still applies, you should:\n"
     "  • Upgrade your LinkML tooling to version >= 1.9.0 (which no longer needs this patch), OR\n"
-    "  • Migrate to Pydantic models if you're using LinkML's generated classes at runtime.\n\n"
-    "If you're currently using Python >= 3.13, this patch is ignored.",
+    "  • Migrate to Pydantic models if you're using LinkML's generated classes at runtime.\n",
     DeprecationWarning,
     stacklevel=2
 )
 
-# In Python < 3.13, still apply the dataclass extension patch
-if sys.version_info < (3, 13):
-    import dataclasses
-
-    if hasattr(dataclasses, "_create_fn"):
-        loc_fn = dataclasses._create_fn
-
-        def dc_create_fn(name, args, body, *_posargs, **_kwargs):
-            if name == '__init__' and dataclasses._POST_INIT_NAME in body[-1]:
-                pi_parms = body[-1].rsplit(')', 1)[0]
-                body[-1] = pi_parms + ('' if pi_parms[-1] == '(' else ',') + ' **_kwargs)'
-                return loc_fn(name, list(args) + ["**_kwargs"], body, *_posargs, **_kwargs)
-            else:
-                return loc_fn(name, args, body, *_posargs, **_kwargs)
-
-        dataclasses._create_fn = dc_create_fn
-        dataclasses_init_fn_with_kwargs = dataclasses._init_fn
-
-        DC_CREATE_FN = True
-    else:
-        warnings.warn(
-            "The LinkML dataclass patch could not be applied because `dataclasses._create_fn` is missing.\n"
-            "This may indicate a nonstandard Python environment. "
-            "Please upgrade to LinkML >= 1.9.0 or migrate to Pydantic.",
-            RuntimeWarning,
-            stacklevel=2,
-        )
+dataclasses_init_fn_with_kwargs = None
+DC_CREATE_FN = False
\ No newline at end of file
diff --git a/tests/test_issues/test_dataclass_extensions_376.py b/tests/test_issues/test_dataclass_extensions_376.py
index ae4aa4af..c6f46442 100644
--- a/tests/test_issues/test_dataclass_extensions_376.py
+++ b/tests/test_issues/test_dataclass_extensions_376.py
@@ -1,54 +1,37 @@
 import sys
 import pytest
-from dataclasses import dataclass
-from typing import Optional
-import importlib
+import importlib.util
 
-# Only import the LinkML patch module on supported Python versions
-# Python 3.13+ removed dataclasses._create_fn, which breaks this patch.
-if sys.version_info < (3, 13):
-    import linkml_runtime.utils.dataclass_extensions_376 as dc_tweak
 
-    DC_IN = dc_tweak.DC_CREATE_FN
-else:
-    dc_tweak = None
-    DC_IN = False
+def import_patch_module():
+    """Fresh import to ensure warning is triggered"""
+    spec = importlib.util.find_spec("linkml_runtime.utils.dataclass_extensions_376")
+    mod = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(mod)
+    return mod
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 13), reason="LinkML dataclass patch no longer supported in Python 3.13+")
-def test_kwargs_passed_to_post_init():
-    """Test that kwargs are passed to __post_init__ in patched dataclass"""
+def test_patch_module_emits_deprecation_warning():
+    """All Python versions: emits DeprecationWarning and defines compatibility symbols"""
+    with pytest.warns(DeprecationWarning):
+        mod = import_patch_module()
 
-    @dataclass
-    class TestClass:
-        a: Optional[int] = 0
-        b: Optional[str] = None
+    assert hasattr(mod, "DC_CREATE_FN")
+    assert hasattr(mod, "dataclasses_init_fn_with_kwargs")
+    assert mod.DC_CREATE_FN is False
+    assert mod.dataclasses_init_fn_with_kwargs is None
 
-        def __post_init__(self, **kwargs):
-            if kwargs:
-                unknown_args = sorted(kwargs.keys())
-                first_arg = unknown_args[0]
-                raise ValueError(f"Unknown argument: {first_arg} = {repr(kwargs[first_arg])}")
 
-    # No extra kwargs – should not raise
-    TestClass(a=1, b="test")
+@pytest.mark.skipif(sys.version_info >= (3, 13), reason="dataclass patch behavior was only relevant pre-3.13")
+def test_behavior_without_patch_pre_3_13():
+    """Ensure standard dataclass behavior (no patch) in <3.13"""
+    import dataclasses
 
-    # One unknown kwarg – should raise
-    with pytest.raises(ValueError, match="Unknown argument: c = 'unknown'"):
-        TestClass(a=1, b="test", c="unknown")
-
-    # Multiple unknown kwargs – should raise, first alphabetically
-    with pytest.raises(ValueError, match="Unknown argument: c = 'unknown'"):
-        TestClass(a=1, b="test", c="unknown", z="also_unknown")
-
-
-@pytest.mark.skipif(sys.version_info < (3, 13), reason="This test only applies to Python 3.13+")
-def test_patch_module_is_ignored_on_python_3_13_plus():
-    """Ensure the patch module is importable and emits a DeprecationWarning on Python 3.13+"""
-    with pytest.warns(DeprecationWarning, match="deprecated and will be removed in a future release"):
-        import importlib.util
-
-        spec = importlib.util.find_spec("linkml_runtime.utils.dataclass_extensions_376")
-        mod = importlib.util.module_from_spec(spec)
-        spec.loader.exec_module(mod)
+    with pytest.raises(TypeError):
+        @dataclasses.dataclass
+        class Example:
+            a: int
+            def __post_init__(self, **kwargs): pass
 
+        # This will fail because unknown kwarg 'extra' is not accepted
+        Example(a=1, extra="not allowed")

From 8fcfb009a6f4cddee86ade03c097ca041298e81e Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Tue, 1 Apr 2025 15:42:24 -0700
Subject: [PATCH 10/16] test out change to dataclasses_init_fn_with_kwargs =
 dataclasses._init_fn

---
 linkml_runtime/utils/dataclass_extensions_376.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/linkml_runtime/utils/dataclass_extensions_376.py b/linkml_runtime/utils/dataclass_extensions_376.py
index 0a0e0475..4321855d 100644
--- a/linkml_runtime/utils/dataclass_extensions_376.py
+++ b/linkml_runtime/utils/dataclass_extensions_376.py
@@ -1,5 +1,6 @@
 import sys
 import warnings
+import dataclasses
 
 warnings.warn(
     "The LinkML dataclass extension patch is deprecated and will be removed in a future release.\n"
@@ -10,5 +11,5 @@
     stacklevel=2
 )
 
-dataclasses_init_fn_with_kwargs = None
+dataclasses_init_fn_with_kwargs = dataclasses._init_fn
 DC_CREATE_FN = False
\ No newline at end of file

From 193cdb5b677561d40de9218d91c07d477b945d28 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Tue, 1 Apr 2025 16:12:40 -0700
Subject: [PATCH 11/16] fix tests

---
 .../test_dataclass_extensions_376.py           | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/tests/test_issues/test_dataclass_extensions_376.py b/tests/test_issues/test_dataclass_extensions_376.py
index c6f46442..093a233e 100644
--- a/tests/test_issues/test_dataclass_extensions_376.py
+++ b/tests/test_issues/test_dataclass_extensions_376.py
@@ -1,6 +1,7 @@
 import sys
 import pytest
 import importlib.util
+import dataclasses
 
 
 def import_patch_module():
@@ -10,7 +11,6 @@ def import_patch_module():
     spec.loader.exec_module(mod)
     return mod
 
-
 def test_patch_module_emits_deprecation_warning():
     """All Python versions: emits DeprecationWarning and defines compatibility symbols"""
     with pytest.warns(DeprecationWarning):
@@ -19,19 +19,9 @@ def test_patch_module_emits_deprecation_warning():
     assert hasattr(mod, "DC_CREATE_FN")
     assert hasattr(mod, "dataclasses_init_fn_with_kwargs")
     assert mod.DC_CREATE_FN is False
-    assert mod.dataclasses_init_fn_with_kwargs is None
-
 
-@pytest.mark.skipif(sys.version_info >= (3, 13), reason="dataclass patch behavior was only relevant pre-3.13")
-def test_behavior_without_patch_pre_3_13():
-    """Ensure standard dataclass behavior (no patch) in <3.13"""
-    import dataclasses
+    # Check consistency with actual dataclasses module
+    init_fn = getattr(dataclasses, "_init_fn", None)
+    assert mod.dataclasses_init_fn_with_kwargs == init_fn
 
-    with pytest.raises(TypeError):
-        @dataclasses.dataclass
-        class Example:
-            a: int
-            def __post_init__(self, **kwargs): pass
 
-        # This will fail because unknown kwarg 'extra' is not accepted
-        Example(a=1, extra="not allowed")

From 13dccbef2ccd3e6d8165af3956e6eca909540756 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 2 Apr 2025 11:49:34 -0700
Subject: [PATCH 12/16] relock with poetry 2.0

---
 poetry.lock | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index c5ecd50b..9cb73736 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -28,12 +28,12 @@ files = [
 ]
 
 [package.extras]
-benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
-tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\""]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "cattrs"
@@ -56,8 +56,8 @@ typing-extensions = {version = ">=4.1.0,<4.6.3 || >4.6.3", markers = "python_ver
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
-msgspec = ["msgspec (>=0.18.5) ; implementation_name == \"cpython\""]
-orjson = ["orjson (>=3.9.2) ; implementation_name == \"cpython\""]
+msgspec = ["msgspec (>=0.18.5)"]
+orjson = ["orjson (>=3.9.2)"]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
 ujson = ["ujson (>=5.7.0)"]
@@ -265,7 +265,7 @@ files = [
 ]
 
 [package.extras]
-toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
+toml = ["tomli"]
 
 [[package]]
 name = "curies"
@@ -308,7 +308,7 @@ files = [
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools ; python_version >= \"3.12\"", "tox"]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools", "tox"]
 
 [[package]]
 name = "exceptiongroup"
@@ -370,7 +370,7 @@ files = [
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
@@ -583,7 +583,7 @@ typing-extensions = ">=4.12.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
-timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
+timezone = ["tzdata"]
 
 [[package]]
 name = "pydantic-core"
@@ -1141,7 +1141,7 @@ files = [
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
 h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
@@ -1249,11 +1249,11 @@ files = [
 ]
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
-test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
 type = ["pytest-mypy"]
 
 [metadata]

From 632f6fbde26315225fe071362a627270e35a28be Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 2 Apr 2025 11:54:59 -0700
Subject: [PATCH 13/16] use same poetry version

---
 poetry.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 9cb73736..3732d198 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"

From dc19eded398c6fdf694fb1c3d9cc0dfed8af024a Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 2 Apr 2025 12:05:16 -0700
Subject: [PATCH 14/16] test previous version of poetry

---
 .github/workflows/test-upstream.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-upstream.yaml b/.github/workflows/test-upstream.yaml
index 1aab649c..a841cc31 100644
--- a/.github/workflows/test-upstream.yaml
+++ b/.github/workflows/test-upstream.yaml
@@ -118,7 +118,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install poetry
-        run: pipx install poetry
+        run: pipx install poetry==2.0.0
+
+      - name: Check Poetry version
+        run: poetry --version
 
       - name: Install dynamic versioning plugin
         run: poetry self add "poetry-dynamic-versioning[plugin]"

From ea110a06a57902fe3f5a287affacbfc8be02385c Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 2 Apr 2025 12:10:21 -0700
Subject: [PATCH 15/16] poetry 1.x

---
 .github/workflows/test-upstream.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-upstream.yaml b/.github/workflows/test-upstream.yaml
index a841cc31..c767647a 100644
--- a/.github/workflows/test-upstream.yaml
+++ b/.github/workflows/test-upstream.yaml
@@ -118,7 +118,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install poetry
-        run: pipx install poetry==2.0.0
+        run: pipx install poetry==1.*
 
       - name: Check Poetry version
         run: poetry --version

From 8f4ede4258d76c988263f31cbf73d58127a39044 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Fri, 4 Apr 2025 14:53:28 -0700
Subject: [PATCH 16/16] null change to retrigger actions using upstream -
 hopefully - branch

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 4020b7c9..d48c3cc2 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
 [![PyPIDownloadsMonth](https://img.shields.io/pypi/dm/linkml-runtime?logo=PyPI&color=blue)](https://pypi.org/project/linkml-runtime)
 [![codecov](https://codecov.io/gh/linkml/linkml-runtime/branch/main/graph/badge.svg?token=FOBHNSK5WG)](https://codecov.io/gh/linkml/linkml-runtime)
 
-Runtime support for linkml generated data classes
+Runtime support for linkml generated data classes.
 
 ## About