From 39c600fda1f3f4ea2fe625066300415e5093aac7 Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <JLSaunders987@gmail.com>
Date: Mon, 9 Oct 2023 15:06:53 -0700
Subject: [PATCH] Regenerate nwb_schema_language models

---
 docs/conf.py                                  |   10 +-
 nwb_linkml/pyproject.toml                     |    3 +-
 .../src/nwb_linkml/adapters/__init__.py       |    2 +
 nwb_linkml/src/nwb_linkml/adapters/adapter.py |   57 +-
 nwb_linkml/src/nwb_linkml/io/schema.py        |   35 +-
 nwb_linkml/src/nwb_linkml/maps/hdf5.py        |   27 -
 nwb_linkml/tests/fixtures.py                  |   64 +-
 .../tests/test_adapters/test_adapter.py       |   91 +-
 nwb_schema_language/poetry.lock               | 1063 +++++++++--------
 .../project/excel/nwb_schema_language.xlsx    |  Bin 10405 -> 10407 bytes
 .../graphql/nwb_schema_language.graphql       |    2 +-
 .../jsonld/nwb_schema_language.context.jsonld |    4 +-
 .../project/jsonld/nwb_schema_language.jsonld |    8 +-
 .../nwb_schema_language.schema.json           |    2 +-
 .../protobuf/nwb_schema_language.proto        |    2 +-
 .../project/shex/nwb_schema_language.shex     |    2 +-
 .../project/sqlschema/nwb_schema_language.sql |    2 +-
 .../src/nwb_schema_language/__init__.py       |    1 -
 .../datamodel/nwb_schema_language.py          |   14 +-
 .../datamodel/nwb_schema_pydantic.py          |    4 +-
 20 files changed, 771 insertions(+), 622 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 3028388..ede0055 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -20,7 +20,8 @@ extensions = [
     'sphinx.ext.napoleon',
     'sphinx.ext.autodoc',
     'sphinxcontrib.autodoc_pydantic',
-    'sphinx.ext.intersphinx'
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.doctest'
 ]
 
 templates_path = ['_templates']
@@ -68,3 +69,10 @@ graphviz_output_format = "svg"
 autodoc_pydantic_model_show_json_error_strategy = 'coerce'
 autodoc_pydantic_model_show_json = False
 autodoc_mock_imports = ['nptyping']
+
+# doctest
+doctest_global_setup = """
+from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition, SchemaDefinition
+from pydantic import BaseModel, Field
+import numpy as np
+"""
\ No newline at end of file
diff --git a/nwb_linkml/pyproject.toml b/nwb_linkml/pyproject.toml
index de909f3..8453772 100644
--- a/nwb_linkml/pyproject.toml
+++ b/nwb_linkml/pyproject.toml
@@ -72,7 +72,8 @@ build-backend = "poetry.core.masonry.api"
 addopts = [
     "--cov=nwb_linkml",
     "--cov-append",
-    "--cov-config=.coveragerc"
+    "--cov-config=.coveragerc",
+    "--doctest-modules"
 ]
 testpaths = [
     "tests",
diff --git a/nwb_linkml/src/nwb_linkml/adapters/__init__.py b/nwb_linkml/src/nwb_linkml/adapters/__init__.py
index 784ff3f..9ce6c4b 100644
--- a/nwb_linkml/src/nwb_linkml/adapters/__init__.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/__init__.py
@@ -1,4 +1,6 @@
+from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.classes import ClassAdapter
 from nwb_linkml.adapters.group import GroupAdapter
 from nwb_linkml.adapters.schema import SchemaAdapter
+
diff --git a/nwb_linkml/src/nwb_linkml/adapters/adapter.py b/nwb_linkml/src/nwb_linkml/adapters/adapter.py
index 0b5161e..6d94937 100644
--- a/nwb_linkml/src/nwb_linkml/adapters/adapter.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/adapter.py
@@ -1,10 +1,11 @@
 """
 Base class for adapters
 """
+import pdb
 from abc import abstractmethod
 import warnings
 from dataclasses import dataclass, field
-from typing import List, Dict, Type, Generator, Any, Tuple, Optional, TypeVar, TypeVarTuple, Unpack
+from typing import List, Dict, Type, Generator, Any, Tuple, Optional, TypeVar, TypeVarTuple, Unpack, Literal
 from pydantic import BaseModel, Field, validator
 from linkml_runtime.linkml_model import Element, SchemaDefinition, ClassDefinition, SlotDefinition, TypeDefinition
 
@@ -35,15 +36,8 @@ class BuildResult:
 
         self.schemas.extend(self._dedupe(self.schemas, other.schemas))
         self.classes.extend(self._dedupe(self.classes, other.classes))
-        # existing_names = [c.name for c in self.classes]
-        # for newc in other.classes:
-        #     if newc.name in existing_names:
-        #         warnings.warn(f'Not creating duplicate class for {newc.name}')
-        #         continue
-        #     self.classes.append(newc)
-        # self.classes.extend(other.classes)
-        self.slots.extend(other.slots)
-        self.types.extend(other.types)
+        self.slots.extend(self._dedupe(self.slots, other.slots))
+        self.types.extend(self._dedupe(self.types, other.types))
         return self
 
     def __repr__(self):  # pragma: no cover
@@ -76,7 +70,13 @@ class Adapter(BaseModel):
         Generate the corresponding linkML element for this adapter
         """
 
-    def walk(self, input: BaseModel | list | dict):
+    def walk(self, input: BaseModel | list | dict) -> Generator[BaseModel | Any | None, None, None]:
+        """
+        Iterate through all items in the given model.
+
+        Could be a staticmethod or a function, but bound to adapters to make it available to them :)
+        """
+
         yield input
         if isinstance(input, BaseModel):
 
@@ -92,7 +92,7 @@ class Adapter(BaseModel):
                 if isinstance(val, (BaseModel, dict, list)):
                     yield from self.walk(val)
 
-        elif isinstance(input, dict):
+        elif isinstance(input, dict): # pragma: no cover - not used in our adapters, but necessary for logical completeness
             for key, val in input.items():
                 yield (key, val)
                 if isinstance(val, (BaseModel, dict, list)):
@@ -108,12 +108,45 @@ class Adapter(BaseModel):
             pass
 
     def walk_fields(self, input: BaseModel | list | dict, field: str | Tuple[str, ...]):
+        """
+        Recursively walk input for fields that match ``field``
+
+        Args:
+            input (:class:`pydantic.BaseModel`) : Model to walk (or a list or dictionary to walk too)
+            field (str, Tuple[str, ...]):
+
+        Returns:
+
+        """
         if isinstance(field, str):
             field = (field,)
         for item in self.walk(input):
             if isinstance(item, tuple) and item[0] in field and item[1] is not None:
                 yield item[1]
 
+    def walk_field_values(self, input: BaseModel | list | dict, field: str, value: Optional[Any] = None ) -> Generator[BaseModel, None, None]:
+        """
+        Recursively walk input for **models** that contain a ``field`` as a direct child with a value matching ``value``
+
+        Args:
+            input (:class:`pydantic.BaseModel`): Model to walk
+            field (str): Name of field - unlike :meth:`.walk_fields`, only one field can be given
+            value (Any): Value to match for given field. If ``None`` , return models that have the field
+
+        Returns:
+            :class:`pydantic.BaseModel` the matching model
+        """
+        for item in self.walk(input):
+            if isinstance(item, BaseModel):
+                if field in item.model_fields:
+                    if value is None:
+                        yield item
+                    field_value = item.model_dump().get(field, None)
+                    if value == field_value:
+                        yield item
+
+
+
 
     def walk_types(self, input: BaseModel | list | dict, get_type: T | List[Unpack[Ts]] | Tuple[Unpack[T]]) -> Generator[T, None, None]:
         if not isinstance(get_type, (list, tuple)):
diff --git a/nwb_linkml/src/nwb_linkml/io/schema.py b/nwb_linkml/src/nwb_linkml/io/schema.py
index 18e990e..819e8a8 100644
--- a/nwb_linkml/src/nwb_linkml/io/schema.py
+++ b/nwb_linkml/src/nwb_linkml/io/schema.py
@@ -69,13 +69,19 @@ def load_schema_file(path:Path, yaml:Optional[dict] = None) -> SchemaAdapter:
     )
     return schema
 
-def load_namespace_adapter(namespace: Path | NamespaceRepo | Namespaces, path:Optional[Path]=None) -> NamespacesAdapter:
+def load_namespace_adapter(
+        namespace: Path | NamespaceRepo | Namespaces,
+        path:Optional[Path]=None,
+        version: Optional[str]=None
+) -> NamespacesAdapter:
     """
     Load all schema referenced by a namespace file
 
     Args:
         namespace (:class:`:class:`.Namespace`):
-        path (:class:`pathlib.Path`): Location of the namespace file - all relative paths are interpreted relative to this
+        path (:class:`pathlib.Path`): Optional: Location of the namespace file - all relative paths are interpreted relative to this
+        version (str): Optional: tag or commit to check out namespace is a :class:`.NamespaceRepo`. If ``None``, use ``HEAD`` if not already checked out,
+            or otherwise use whatever version is already checked out.
 
     Returns:
         :class:`.NamespacesAdapter`
@@ -87,7 +93,7 @@ def load_namespace_adapter(namespace: Path | NamespaceRepo | Namespaces, path:Op
         path = namespace
         namespaces = _load_namespaces(path)
     elif isinstance(namespace, NamespaceRepo):
-        path = namespace.provide_from_git()
+        path = namespace.provide_from_git(commit=version)
         namespaces = _load_namespaces(namespace)
 
     elif isinstance(namespace, Namespaces):
@@ -116,10 +122,27 @@ def load_namespace_adapter(namespace: Path | NamespaceRepo | Namespaces, path:Op
 
     return adapter
 
-def load_nwb_core() -> NamespacesAdapter:
+def load_nwb_core(core_version="2.6.0", hdmf_version="1.5.0") -> NamespacesAdapter:
+    """
+    Convenience function for loading the NWB core schema + hdmf-common as a namespace adapter.
+
+    .. note::
+
+        NWB Core schema are implicitly linked to a specific version of HDMF common by virtue of which version
+        of `hdmf-common-schema` is checked out as a submodule in the repository. We don't
+        attempt to resolve that linkage here because it's not in the schema, but the defaults
+        are for the latest nwb core ( ``'2.6.0'`` ) and its linked hdmf-common version ( ``'1.5.0'`` )
+
+    Args:
+        core_version (str): an entry in :attr:`.NWB_CORE_REPO.versions`
+        hdmf_version (str): an entry in :attr:`.NWB_CORE_REPO.versions`
+
+    Returns:
+
+    """
     # First get hdmf-common:
-    hdmf_schema = load_namespace_adapter(HDMF_COMMON_REPO)
-    schema = load_namespace_adapter(NWB_CORE_REPO)
+    hdmf_schema = load_namespace_adapter(HDMF_COMMON_REPO, version=hdmf_version)
+    schema = load_namespace_adapter(NWB_CORE_REPO, version=core_version)
 
     schema.imported.append(hdmf_schema)
 
diff --git a/nwb_linkml/src/nwb_linkml/maps/hdf5.py b/nwb_linkml/src/nwb_linkml/maps/hdf5.py
index edd9727..542d49e 100644
--- a/nwb_linkml/src/nwb_linkml/maps/hdf5.py
+++ b/nwb_linkml/src/nwb_linkml/maps/hdf5.py
@@ -529,12 +529,6 @@ class CompleteModelGroups(HDF5Map):
         unpacked_results, errors, completes = resolve_references(src.result, completed)
         res.update(unpacked_results)
 
-        # # final cleanups
-        # for key, val in res.items():
-        #     # if we're supposed to be a list, but instead we're an array, fix that!
-        #
-
-        #try:
         instance = src.model(**res)
         return H5ReadResult(
             path=src.path,
@@ -548,19 +542,6 @@ class CompleteModelGroups(HDF5Map):
             applied=src.applied + ['CompleteModelGroups'],
             errors=errors
         )
-        # except ValidationError:
-        #     # didn't get it! try again next time
-        #     return H5ReadResult(
-        #         path=src.path,
-        #         source=src,
-        #         result=src,
-        #         model=src.model,
-        #         completed=True,
-        #         completes=completes,
-        #         neurodata_type=src.neurodata_type,
-        #         namespace=src.namespace,
-        #         applied=src.applied + ['CompleteModelGroups']
-        #     )
 
 class CompleteNWBFile(HDF5Map):
     """
@@ -721,14 +702,6 @@ class ReadQueue(BaseModel):
             self.apply_phase(phase, max_passes=max_passes-1)
 
 
-
-
-
-
-
-
-
-
 def flatten_hdf(h5f:h5py.File | h5py.Group, skip='specifications') -> Dict[str, H5SourceItem]:
     """
     Flatten all child elements of hdf element into a dict of :class:`.H5SourceItem` s keyed by their path
diff --git a/nwb_linkml/tests/fixtures.py b/nwb_linkml/tests/fixtures.py
index bc1c81c..162257e 100644
--- a/nwb_linkml/tests/fixtures.py
+++ b/nwb_linkml/tests/fixtures.py
@@ -1,6 +1,6 @@
 import pytest
 import os
-from typing import NamedTuple
+from typing import NamedTuple, Optional
 
 from linkml_runtime.dumpers import yaml_dumper
 
@@ -49,9 +49,13 @@ def set_config_vars(tmp_output_dir):
 
 
 
-@pytest.fixture(scope="session")
-def nwb_core_fixture() -> NamespacesAdapter:
-    nwb_core = io.load_nwb_core()
+@pytest.fixture(
+    scope="session",
+    params=[
+    {'core_version': "2.6.0", 'hdmf_version': '1.5.0'}
+])
+def nwb_core_fixture(request) -> NamespacesAdapter:
+    nwb_core = io.load_nwb_core(**request.param)
     nwb_core.populate_imports()
     return nwb_core
 
@@ -63,34 +67,16 @@ def data_dir() -> Path:
 
 class TestSchemas(NamedTuple):
     core: SchemaDefinition
-    core_path: Path
     imported: SchemaDefinition
-    imported_path: Path
     namespace: SchemaDefinition
-    namespace_path: Path
+    core_path: Optional[Path] = None
+    imported_path: Optional[Path] = None
+    namespace_path: Optional[Path] = None
 
 @pytest.fixture(scope="module")
-def linkml_schema(tmp_output_dir_mod) -> TestSchemas:
-    """
-    A test schema that includes
-
-    - Two schemas, one importing from the other
-    - Arraylike
-    - Required/static "name" field
-    - linkml metadata like tree_root
-    - skipping classes
-    """
-    test_schema_path = tmp_output_dir_mod / 'test_schema'
-    test_schema_path.mkdir()
-
-    core_path = test_schema_path / 'core.yaml'
-    imported_path = test_schema_path / 'imported.yaml'
-    namespace_path = test_schema_path / 'namespace.yaml'
+def linkml_schema_bare() -> TestSchemas:
 
     schema = TestSchemas(
-        core_path=core_path,
-        imported_path=imported_path,
-        namespace_path=namespace_path,
         core=SchemaDefinition(
             name="core",
             id="core",
@@ -235,6 +221,32 @@ def linkml_schema(tmp_output_dir_mod) -> TestSchemas:
             imports=['core', 'imported']
         )
     )
+    return schema
+
+@pytest.fixture(scope="module")
+def linkml_schema(tmp_output_dir_mod, linkml_schema_bare) -> TestSchemas:
+    """
+    A test schema that includes
+
+    - Two schemas, one importing from the other
+    - Arraylike
+    - Required/static "name" field
+    - linkml metadata like tree_root
+    - skipping classes
+    """
+    schema = linkml_schema_bare
+
+    test_schema_path = tmp_output_dir_mod / 'test_schema'
+    test_schema_path.mkdir()
+
+    core_path = test_schema_path / 'core.yaml'
+    imported_path = test_schema_path / 'imported.yaml'
+    namespace_path = test_schema_path / 'namespace.yaml'
+
+    schema.core_path = core_path,
+    schema.imported_path = imported_path,
+    schema.namespace_path = namespace_path,
+
     yaml_dumper.dump(schema.core, schema.core_path)
     yaml_dumper.dump(schema.imported, schema.imported_path)
     yaml_dumper.dump(schema.namespace, schema.namespace_path)
diff --git a/nwb_linkml/tests/test_adapters/test_adapter.py b/nwb_linkml/tests/test_adapters/test_adapter.py
index 60f43c1..d13c7c6 100644
--- a/nwb_linkml/tests/test_adapters/test_adapter.py
+++ b/nwb_linkml/tests/test_adapters/test_adapter.py
@@ -1,7 +1,21 @@
+import pdb
+
 import pytest
 from ..fixtures import nwb_core_fixture
 
-from nwb_schema_language import Dataset, Group, Schema
+from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, SlotDefinition, TypeDefinition
+from nwb_schema_language import Dataset, Group, Schema, CompoundDtype
+
+from nwb_linkml.adapters import BuildResult
+
+from ..fixtures import linkml_schema_bare
+
+def test_walk(nwb_core_fixture):
+    """
+    Not sure exactly what should be tested here, for now just testing that we get an expected value
+    """
+    everything = nwb_core_fixture.walk(nwb_core_fixture)
+    assert len(list(everything)) == 9959
 
 @pytest.mark.parametrize(
     ['walk_class', 'known_number'],
@@ -17,12 +31,77 @@ def test_walk_types(nwb_core_fixture, walk_class, known_number):
     class_list = list(classes)
     assert len(class_list) == known_number
 
-    # pdb.set_trace()
+def test_walk_fields(nwb_core_fixture):
+    dtype = nwb_core_fixture.walk_fields(nwb_core_fixture, 'dtype')
 
 
-def test_build_result_add():
+def test_walk_field_values(nwb_core_fixture):
+    dtype_models = list(nwb_core_fixture.walk_field_values(nwb_core_fixture, 'dtype', value=None))
+
+    compounds = [d for d in dtype_models if isinstance(d.dtype, list) and len(d.dtype) > 0 and isinstance(d.dtype[0], CompoundDtype)]
+
+
+def test_build_result(linkml_schema_bare):
     """
-    Build results can
-    Returns:
+    build results can hold lists of class, slot, and type definitions
+    """
+    schema = linkml_schema_bare
+    sch = schema.core
+    cls = sch.classes['MainTopLevel']
+    slot1 = cls.attributes['name']
+    typ = sch.types['numeric']
+
+    # Build result should hold the results and coerce to list type
+    res = BuildResult(
+        schemas=sch,
+        classes=cls,
+        slots=slot1,
+        types=typ
+    )
+    for field in ('schemas', 'classes', 'slots', 'types'):
+        assert isinstance(getattr(res, field), list)
+        assert len(getattr(res, field)) == 1
+
+@pytest.mark.parametrize(
+    'sch_type',
+    ('schemas', 'classes', 'slots', 'types')
+)
+def test_build_result_add(linkml_schema_bare, sch_type):
+    """
+    Build results can be added together without duplicating
+    """
+    schema = linkml_schema_bare
+    if sch_type == 'schemas':
+        obj = schema.core
+        other_obj = SchemaDefinition(name="othername", id="othername", version="1.0.1")
+    elif sch_type == 'classes':
+        obj = schema.core.classes['MainTopLevel']
+        other_obj = ClassDefinition(name="othername")
+    elif sch_type == 'slots':
+        obj = schema.core.classes['MainTopLevel'].attributes['name']
+        other_obj = SlotDefinition(name="othername", range="string")
+    elif sch_type == 'types':
+        obj = schema.core.types['numeric']
+        other_obj = TypeDefinition(name="othername", typeof="float")
+    else:
+        raise ValueError(f"Dont know how to test type {sch_type}")
+
+    res1 = BuildResult(**{sch_type: [obj]})
+    res2 = BuildResult(**{sch_type: [obj]})
+    assert len(getattr(res1, sch_type)) == 1
+    assert len(getattr(res2, sch_type)) == 1
+
+    assert len(getattr(res1 + res2, sch_type)) == 1
+    assert len(getattr(res2 + res1, sch_type)) == 1
+
+    # and then addition works as normal for not same named items
+    res3 = BuildResult(**{sch_type: [other_obj]})
+    assert len(getattr(res1 + res3, sch_type)) == 2
+    assert len(getattr(res2 + res3, sch_type)) == 2
+
+    res_combined_2 = res1 + res3
+    assert getattr(res_combined_2, sch_type)[-1] is other_obj
+
+
+
 
-    """
\ No newline at end of file
diff --git a/nwb_schema_language/poetry.lock b/nwb_schema_language/poetry.lock
index 2a1efac..1859ded 100644
--- a/nwb_schema_language/poetry.lock
+++ b/nwb_schema_language/poetry.lock
@@ -1,14 +1,14 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
-version = "0.5.0"
+version = "0.6.0"
 description = "Reusable constraint types to use with typing.Annotated"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
-    {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
+    {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
+    {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
 ]
 
 [[package]]
@@ -23,17 +23,22 @@ files = [
 
 [[package]]
 name = "arrow"
-version = "1.2.3"
+version = "1.3.0"
 description = "Better dates & times for Python"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
-    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+    {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
+    {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
 ]
 
 [package.dependencies]
 python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
 
 [[package]]
 name = "attrs"
@@ -73,18 +78,18 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bioregistry"
-version = "0.6.108"
+version = "0.10.55"
 description = "Integrated registry of biological databases and nomenclatures"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 click = "*"
-curies = ">=0.5.1"
+curies = ">=0.6.0"
 more-click = ">=0.1.2"
 pydantic = "*"
 pystow = ">=0.1.13"
@@ -93,13 +98,13 @@ tqdm = "*"
 
 [package.extras]
 align = ["beautifulsoup4", "class-resolver", "defusedxml", "fairsharing-client (>=0.1.0)", "pyyaml", "tabulate"]
-charts = ["matplotlib", "matplotlib-venn", "pandas", "seaborn"]
-docs = ["autodoc-pydantic", "sphinx", "sphinx-autodoc-typehints (==1.21.1)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+charts = ["jinja2", "matplotlib", "matplotlib-venn", "pandas", "seaborn"]
+docs = ["autodoc-pydantic", "sphinx", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
 export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
 gha = ["more-itertools"]
-health = ["click-default-group", "pandas", "pyyaml", "tabulate"]
-tests = ["coverage", "more-itertools", "pytest"]
-web = ["bootstrap-flask (<=2.0.0)", "flasgger", "flask", "markdown", "pyyaml", "rdflib", "rdflib-jsonld"]
+health = ["click-default-group", "jinja2", "pandas", "pyyaml", "tabulate"]
+tests = ["coverage", "httpx", "more-itertools", "pytest"]
+web = ["bootstrap-flask (<=2.0.0)", "curies[fastapi]", "fastapi", "flask (<2.2.4)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint", "rdflib-jsonld", "uvicorn", "werkzeug (<2.3.0)"]
 
 [[package]]
 name = "cachetools"
@@ -149,97 +154,112 @@ files = [
 
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 name = "charset-normalizer"
-version = "3.2.0"
+version = "3.3.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
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 python-versions = ">=3.7.0"
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 ]
 
 [[package]]
 name = "click"
-version = "8.1.6"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
 ]
 
 [package.dependencies]
@@ -258,13 +278,13 @@ files = [
 
 [[package]]
 name = "curies"
-version = "0.6.0"
+version = "0.6.4"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "curies-0.6.0-py3-none-any.whl", hash = "sha256:0bf79e2176b2e44dee7fefadcd1f2d69e643fea124dc4a8d0dbf47ca5e1589f2"},
-    {file = "curies-0.6.0.tar.gz", hash = "sha256:a31533ae9caeec332f9bb33e21366ab7ec32437c5f347fc9d85aa77cc48093cc"},
+    {file = "curies-0.6.4-py3-none-any.whl", hash = "sha256:d19e2f61d8a37560e96a5676a5f98cf056f4e2206e281bdcca74934e7623b9d8"},
+    {file = "curies-0.6.4.tar.gz", hash = "sha256:c896e6d8d7f469c9ce52f781c8c35d25c46619e977cc6c932f34d98bf33e3749"},
 ]
 
 [package.dependencies]
@@ -290,17 +310,6 @@ files = [
     {file = "daff-1.3.46.tar.gz", hash = "sha256:22d0da9fd6a3275b54c926a9c97b180f9258aad65113ea18f3fec52cbadcd818"},
 ]
 
-[[package]]
-name = "decorator"
-version = "5.1.1"
-description = "Decorators for Humans"
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
-    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
-]
-
 [[package]]
 name = "deprecated"
 version = "1.2.14"
@@ -398,13 +407,13 @@ beautifulsoup4 = "*"
 
 [[package]]
 name = "google-api-core"
-version = "2.11.1"
+version = "2.12.0"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-core-2.11.1.tar.gz", hash = "sha256:25d29e05a0058ed5f19c61c0a78b1b53adea4d9364b464d014fbda941f6d1c9a"},
-    {file = "google_api_core-2.11.1-py3-none-any.whl", hash = "sha256:d92a5a92dc36dd4f4b9ee4e55528a90e432b059f93aee6ad857f9de8cc7ae94a"},
+    {file = "google-api-core-2.12.0.tar.gz", hash = "sha256:c22e01b1e3c4dcd90998494879612c38d0a3411d1f7b679eb89e2abe3ce1f553"},
+    {file = "google_api_core-2.12.0-py3-none-any.whl", hash = "sha256:ec6054f7d64ad13b41e43d96f735acbd763b0f3b695dabaa2d579673f6a6e160"},
 ]
 
 [package.dependencies]
@@ -420,13 +429,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 
 [[package]]
 name = "google-api-python-client"
-version = "2.97.0"
+version = "2.102.0"
 description = "Google API Client Library for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-python-client-2.97.0.tar.gz", hash = "sha256:48277291894876a1ca7ed4127e055e81f81e6343ced1b544a7200ae2c119dcd7"},
-    {file = "google_api_python_client-2.97.0-py2.py3-none-any.whl", hash = "sha256:5215f4cd577753fc4192ccfbe0bb8b55d4bb5fd68fa6268ac5cf271b6305de31"},
+    {file = "google-api-python-client-2.102.0.tar.gz", hash = "sha256:906ff9b672a4d5ddad8f4073a040e59f1fba6734909c14cd49938e37be53691d"},
+    {file = "google_api_python_client-2.102.0-py2.py3-none-any.whl", hash = "sha256:ce2fb4d80eb24519ced44a1e79030866cc8a6379ed5ba6c76ba46e772cc68137"},
 ]
 
 [package.dependencies]
@@ -438,21 +447,19 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.22.0"
+version = "2.23.3"
 description = "Google Authentication Library"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "google-auth-2.22.0.tar.gz", hash = "sha256:164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce"},
-    {file = "google_auth-2.22.0-py2.py3-none-any.whl", hash = "sha256:d61d1b40897407b574da67da1a833bdc10d5a11642566e506565d1b1a46ba873"},
+    {file = "google-auth-2.23.3.tar.gz", hash = "sha256:6864247895eea5d13b9c57c9e03abb49cb94ce2dc7c58e91cba3248c7477c9e3"},
+    {file = "google_auth-2.23.3-py2.py3-none-any.whl", hash = "sha256:a8f4608e65c244ead9e0538f181a96c6e11199ec114d41f1d7b1bffa96937bda"},
 ]
 
 [package.dependencies]
 cachetools = ">=2.0.0,<6.0"
 pyasn1-modules = ">=0.2.1"
 rsa = ">=3.1.4,<5"
-six = ">=1.9.0"
-urllib3 = "<2.0"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0.dev0)", "requests (>=2.20.0,<3.0.0.dev0)"]
@@ -463,29 +470,28 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
 
 [[package]]
 name = "google-auth-httplib2"
-version = "0.1.0"
+version = "0.1.1"
 description = "Google Authentication Library: httplib2 transport"
 optional = false
 python-versions = "*"
 files = [
-    {file = "google-auth-httplib2-0.1.0.tar.gz", hash = "sha256:a07c39fd632becacd3f07718dfd6021bf396978f03ad3ce4321d060015cc30ac"},
-    {file = "google_auth_httplib2-0.1.0-py2.py3-none-any.whl", hash = "sha256:31e49c36c6b5643b57e82617cb3e021e3e1d2df9da63af67252c02fa9c1f4a10"},
+    {file = "google-auth-httplib2-0.1.1.tar.gz", hash = "sha256:c64bc555fdc6dd788ea62ecf7bccffcf497bf77244887a3f3d7a5a02f8e3fc29"},
+    {file = "google_auth_httplib2-0.1.1-py2.py3-none-any.whl", hash = "sha256:42c50900b8e4dcdf8222364d1f0efe32b8421fb6ed72f2613f12f75cc933478c"},
 ]
 
 [package.dependencies]
 google-auth = "*"
-httplib2 = ">=0.15.0"
-six = "*"
+httplib2 = ">=0.19.0"
 
 [[package]]
 name = "google-auth-oauthlib"
-version = "1.0.0"
+version = "1.1.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "google-auth-oauthlib-1.0.0.tar.gz", hash = "sha256:e375064964820b47221a7e1b7ee1fd77051b6323c3f9e3e19785f78ab67ecfc5"},
-    {file = "google_auth_oauthlib-1.0.0-py2.py3-none-any.whl", hash = "sha256:95880ca704928c300f48194d1770cf5b1462835b6e49db61445a520f793fd5fb"},
+    {file = "google-auth-oauthlib-1.1.0.tar.gz", hash = "sha256:83ea8c3b0881e453790baff4448e8a6112ac8778d1de9da0b68010b843937afb"},
+    {file = "google_auth_oauthlib-1.1.0-py2.py3-none-any.whl", hash = "sha256:089c6e587d36f4803ac7e0720c045c6a8b1fd1790088b8424975b90d0ee61c12"},
 ]
 
 [package.dependencies]
@@ -603,13 +609,13 @@ test = ["faulthandler", "objgraph", "psutil"]
 
 [[package]]
 name = "gspread"
-version = "5.10.0"
+version = "5.11.3"
 description = "Google Spreadsheets Python API"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "gspread-5.10.0-py3-none-any.whl", hash = "sha256:f58b15d950ef5c45c8607edb3687188d5a543f2b66242f9c26fbb0d2cf36169d"},
-    {file = "gspread-5.10.0.tar.gz", hash = "sha256:2b6bba6dc111580170346a9bcd1893e0e8c52f67a9e537caec7b7a1e27c14435"},
+    {file = "gspread-5.11.3-py3-none-any.whl", hash = "sha256:665a77fe9be4a79b606e6beb9baf8855d63dce211055cb1df1de9c2c70deb882"},
+    {file = "gspread-5.11.3.tar.gz", hash = "sha256:7512ade467590d5ee8d49e8981c7f1ba5813fd56e78cb4dcd7a77e0cb4ce2b86"},
 ]
 
 [package.dependencies]
@@ -811,20 +817,17 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpath-ng"
-version = "1.5.3"
+version = "1.6.0"
 description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
 optional = false
 python-versions = "*"
 files = [
-    {file = "jsonpath-ng-1.5.3.tar.gz", hash = "sha256:a273b182a82c1256daab86a313b937059261b5c5f8c4fa3fc38b882b344dd567"},
-    {file = "jsonpath_ng-1.5.3-py2-none-any.whl", hash = "sha256:f75b95dbecb8a0f3b86fd2ead21c2b022c3f5770957492b9b6196ecccfeb10aa"},
-    {file = "jsonpath_ng-1.5.3-py3-none-any.whl", hash = "sha256:292a93569d74029ba75ac2dc3d3630fc0e17b2df26119a165fa1d498ca47bf65"},
+    {file = "jsonpath-ng-1.6.0.tar.gz", hash = "sha256:5483f8e9d74c39c9abfab554c070ae783c1c8cbadf5df60d561bc705ac68a07e"},
+    {file = "jsonpath_ng-1.6.0-py3-none-any.whl", hash = "sha256:6fd04833412c4b3d9299edf369542f5e67095ca84efa17cbb7f06a34958adc9f"},
 ]
 
 [package.dependencies]
-decorator = "*"
 ply = "*"
-six = "*"
 
 [[package]]
 name = "jsonpointer"
@@ -839,13 +842,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.0"
+version = "4.19.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
-    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
+    {file = "jsonschema-4.19.1-py3-none-any.whl", hash = "sha256:cd5f1f9ed9444e554b38ba003af06c0a8c2868131e56bfbef0550fb450c0330e"},
+    {file = "jsonschema-4.19.1.tar.gz", hash = "sha256:ec84cc37cfa703ef7cd4928db24f9cb31428a5d0fa77747b8b51a847458e0bbf"},
 ]
 
 [package.dependencies]
@@ -882,13 +885,13 @@ referencing = ">=0.28.0"
 
 [[package]]
 name = "linkml"
-version = "1.5.7"
+version = "1.6.1"
 description = "Linked Open Data Modeling Language"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8,<4.0"
 files = [
-    {file = "linkml-1.5.7-py3-none-any.whl", hash = "sha256:677f4c5809dc51b151b86accc69e77482ad86b9c1326a212cef9b4a2a9a96c10"},
-    {file = "linkml-1.5.7.tar.gz", hash = "sha256:bca3dd56837ced79749656843e1e20b8d1db1a89287e7b29d1ee145e4a75ad4d"},
+    {file = "linkml-1.6.1-py3-none-any.whl", hash = "sha256:7501cb9c7b2c13ca78fc7121ae8b5457fb5771138714da31cc11f971062070ee"},
+    {file = "linkml-1.6.1.tar.gz", hash = "sha256:65f73cf29a77518972238e71e91e012c081cf2e43d71d8965ca414c78c11e08e"},
 ]
 
 [package.dependencies]
@@ -901,7 +904,7 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1.5.4"
+linkml-runtime = ">=1.6.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
@@ -937,13 +940,13 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.5.6"
+version = "1.6.0"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml_runtime-1.5.6-py3-none-any.whl", hash = "sha256:b869f7adf340b7df73f4fefa28a402de5719bbd7d172590e8a7ae9c25e179d77"},
-    {file = "linkml_runtime-1.5.6.tar.gz", hash = "sha256:eb5f506f7ec08c44e49578d0ecc80e2d3d922756c2430e06906ee9502cca1b4c"},
+    {file = "linkml_runtime-1.6.0-py3-none-any.whl", hash = "sha256:1b6b698f8cf23d63ff833ae0be8055b2e945e1c0ef06a1ed6db359247194a2eb"},
+    {file = "linkml_runtime-1.6.0.tar.gz", hash = "sha256:a06df7431a9b929afe242598800d99cec83bb31cbdc1f5d2d70e6b26c67dc337"},
 ]
 
 [package.dependencies]
@@ -963,20 +966,20 @@ requests = "*"
 
 [[package]]
 name = "markdown"
-version = "3.4.4"
+version = "3.5"
 description = "Python implementation of John Gruber's Markdown."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Markdown-3.4.4-py3-none-any.whl", hash = "sha256:a4c1b65c0957b4bd9e7d86ddc7b3c9868fb9670660f6f99f6d1bca8954d5a941"},
-    {file = "Markdown-3.4.4.tar.gz", hash = "sha256:225c6123522495d4119a90b3a3ba31a1e87a70369e03f14799ea9c0d7183a3d6"},
+    {file = "Markdown-3.5-py3-none-any.whl", hash = "sha256:4afb124395ce5fc34e6d9886dab977fd9ae987fc6e85689f08278cf0c69d4bf3"},
+    {file = "Markdown-3.5.tar.gz", hash = "sha256:a807eb2e4778d9156c8f07876c6e4d50b5494c5665c4834f67b06459dfd877b3"},
 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.0)", "mkdocs-nature (>=0.4)"]
+docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.5)", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-nature (>=0.6)", "mkdocs-section-index", "mkdocstrings[python]"]
 testing = ["coverage", "pyyaml"]
 
 [[package]]
@@ -1051,13 +1054,13 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.5.2"
+version = "1.5.3"
 description = "Project documentation with Markdown."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "mkdocs-1.5.2-py3-none-any.whl", hash = "sha256:60a62538519c2e96fe8426654a67ee177350451616118a41596ae7c876bb7eac"},
-    {file = "mkdocs-1.5.2.tar.gz", hash = "sha256:70d0da09c26cff288852471be03c23f0f521fc15cf16ac89c7a3bfb9ae8d24f9"},
+    {file = "mkdocs-1.5.3-py3-none-any.whl", hash = "sha256:3b3a78e736b31158d64dbb2f8ba29bd46a379d0c6e324c2246c3bc3d2189cfc1"},
+    {file = "mkdocs-1.5.3.tar.gz", hash = "sha256:eb7c99214dcb945313ba30426c2451b735992c73c2e10838f76d09e39ff4d0e2"},
 ]
 
 [package.dependencies]
@@ -1102,13 +1105,13 @@ requests = ">=2.26"
 
 [[package]]
 name = "mkdocs-material-extensions"
-version = "1.1.1"
+version = "1.2"
 description = "Extension pack for Python Markdown and MkDocs Material."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "mkdocs_material_extensions-1.1.1-py3-none-any.whl", hash = "sha256:e41d9f38e4798b6617ad98ca8f7f1157b1e4385ac1459ca1e4ea219b556df945"},
-    {file = "mkdocs_material_extensions-1.1.1.tar.gz", hash = "sha256:9c003da71e2cc2493d910237448c672e00cefc800d3d6ae93d2fc69979e3bd93"},
+    {file = "mkdocs_material_extensions-1.2-py3-none-any.whl", hash = "sha256:c767bd6d6305f6420a50f0b541b0c9966d52068839af97029be14443849fb8a1"},
+    {file = "mkdocs_material_extensions-1.2.tar.gz", hash = "sha256:27e2d1ed2d031426a6e10d5ea06989d67e90bb02acd588bc5673106b5ee5eedf"},
 ]
 
 [[package]]
@@ -1202,13 +1205,13 @@ et-xmlfile = "*"
 
 [[package]]
 name = "packaging"
-version = "23.1"
+version = "23.2"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"},
-    {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
+    {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
+    {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
 ]
 
 [[package]]
@@ -1235,13 +1238,13 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "3.10.0"
+version = "3.11.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "platformdirs-3.10.0-py3-none-any.whl", hash = "sha256:d7c24979f292f916dc9cbf8648319032f551ea8c49a4c9bf2fb556a02070ec1d"},
-    {file = "platformdirs-3.10.0.tar.gz", hash = "sha256:b45696dab2d7cc691a3226759c0d3b00c47c8b6e293d96f6436f733303f77f6d"},
+    {file = "platformdirs-3.11.0-py3-none-any.whl", hash = "sha256:e9d171d00af68be50e9202731309c4e658fd8bc76f55c11c7dd760d023bda68e"},
+    {file = "platformdirs-3.11.0.tar.gz", hash = "sha256:cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3"},
 ]
 
 [package.extras]
@@ -1250,13 +1253,13 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
-    {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
 [package.extras]
@@ -1315,24 +1318,24 @@ refresh = ["bioregistry[refresh] (>=0.8.0,<0.9.0)", "rdflib[refresh] (>=6.2.0,<7
 
 [[package]]
 name = "protobuf"
-version = "4.24.0"
+version = "4.24.4"
 description = ""
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "protobuf-4.24.0-cp310-abi3-win32.whl", hash = "sha256:81cb9c4621d2abfe181154354f63af1c41b00a4882fb230b4425cbaed65e8f52"},
-    {file = "protobuf-4.24.0-cp310-abi3-win_amd64.whl", hash = "sha256:6c817cf4a26334625a1904b38523d1b343ff8b637d75d2c8790189a4064e51c3"},
-    {file = "protobuf-4.24.0-cp37-abi3-macosx_10_9_universal2.whl", hash = "sha256:ae97b5de10f25b7a443b40427033e545a32b0e9dda17bcd8330d70033379b3e5"},
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 ]
 
 [[package]]
@@ -1996,17 +2004,17 @@ pyasn1 = ">=0.1.3"
 
 [[package]]
 name = "ruamel-yaml"
-version = "0.17.32"
+version = "0.17.35"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
 optional = false
 python-versions = ">=3"
 files = [
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 ]
 
 [package.dependencies]
-"ruamel.yaml.clib" = {version = ">=0.2.7", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.12\""}
+"ruamel.yaml.clib" = {version = ">=0.2.7", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.13\""}
 
 [package.extras]
 docs = ["ryd"]
@@ -2014,83 +2022,82 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
 
 [[package]]
 name = "ruamel-yaml-clib"
-version = "0.2.7"
+version = "0.2.8"
 description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
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 ]
 
 [[package]]
 name = "schemasheets"
-version = "0.1.23"
+version = "0.1.24"
 description = "Package to author schemas using spreadsheets"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
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 ]
 
 [package.dependencies]
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-Jinja2 = ">=3.0.3,<4.0.0"
-linkml = ">=1.4,<2.0"
-linkml-runtime = ">=1.4,<2.0"
+bioregistry = ">0.5.0"
+Jinja2 = ">=3.0.3"
+linkml = ">=1.5.0"
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 ontodev-cogs = ">=0.3.3,<0.4.0"
 
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+    {file = "SQLAlchemy-2.0.21-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:513fd5b6513d37e985eb5b7ed89da5fd9e72354e3523980ef00d439bc549c9e9"},
+    {file = "SQLAlchemy-2.0.21-cp39-cp39-win32.whl", hash = "sha256:f9fefd6298433b6e9188252f3bff53b9ff0443c8fde27298b8a2b19f6617eeb9"},
+    {file = "SQLAlchemy-2.0.21-cp39-cp39-win_amd64.whl", hash = "sha256:2e617727fe4091cedb3e4409b39368f424934c7faa78171749f704b49b4bb4ce"},
+    {file = "SQLAlchemy-2.0.21-py3-none-any.whl", hash = "sha256:ea7da25ee458d8f404b93eb073116156fd7d8c2a776d8311534851f28277b4ce"},
+    {file = "SQLAlchemy-2.0.21.tar.gz", hash = "sha256:05b971ab1ac2994a14c56b35eaaa91f86ba080e9ad481b20d99d77f381bb6258"},
 ]
 
 [package.dependencies]
-greenlet = {version = "!=0.4.17", markers = "platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\""}
+greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
 typing-extensions = ">=4.2.0"
 
 [package.extras]
@@ -2313,14 +2320,25 @@ slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
-name = "typing-extensions"
-version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+name = "types-python-dateutil"
+version = "2.8.19.14"
+description = "Typing stubs for python-dateutil"
 optional = false
-python-versions = ">=3.7"
+python-versions = "*"
 files = [
-    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
-    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
+    {file = "types-python-dateutil-2.8.19.14.tar.gz", hash = "sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b"},
+    {file = "types_python_dateutil-2.8.19.14-py3-none-any.whl", hash = "sha256:f977b8de27787639986b4e28963263fd0e5158942b3ecef91b9335c130cb1ce9"},
+]
+
+[[package]]
+name = "typing-extensions"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
 ]
 
 [[package]]
@@ -2350,19 +2368,20 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.16"
+version = "2.0.6"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7"
 files = [
-    {file = "urllib3-1.26.16-py2.py3-none-any.whl", hash = "sha256:8d36afa7616d8ab714608411b4a3b13e58f463aee519024578e062e141dce20f"},
-    {file = "urllib3-1.26.16.tar.gz", hash = "sha256:8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14"},
+    {file = "urllib3-2.0.6-py3-none-any.whl", hash = "sha256:7a7c7003b000adf9e7ca2a377c9688bbc54ed41b985789ed576570342a375cd2"},
+    {file = "urllib3-2.0.6.tar.gz", hash = "sha256:b19e1a85d206b56d7df1d5e683df4a7725252a964e3993648dd0fb5a1c157564"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "watchdog"
@@ -2504,17 +2523,17 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.16.2"
+version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
-    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
 testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [extras]
diff --git a/nwb_schema_language/project/excel/nwb_schema_language.xlsx b/nwb_schema_language/project/excel/nwb_schema_language.xlsx
index 13103d694f6b2a6e34e0de059c6e27cbefae3c74..5fb4563269cd7cc070679180e1a57897525c3b0d 100644
GIT binary patch
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diff --git a/nwb_schema_language/project/graphql/nwb_schema_language.graphql b/nwb_schema_language/project/graphql/nwb_schema_language.graphql
index ebbaa47..0d05849 100644
--- a/nwb_schema_language/project/graphql/nwb_schema_language.graphql
+++ b/nwb_schema_language/project/graphql/nwb_schema_language.graphql
@@ -82,7 +82,7 @@ type Namespace
     name: String!
     fullName: String
     version: String!
-    date: Date
+    date: Datetime
     author: [String]!
     contact: [String]!
     schema: [Schema]
diff --git a/nwb_schema_language/project/jsonld/nwb_schema_language.context.jsonld b/nwb_schema_language/project/jsonld/nwb_schema_language.context.jsonld
index fe62a5f..e412375 100644
--- a/nwb_schema_language/project/jsonld/nwb_schema_language.context.jsonld
+++ b/nwb_schema_language/project/jsonld/nwb_schema_language.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-08-30T20:53:58",
+      "generation_date": "2023-10-09T15:03:06",
       "source": "nwb_schema_language.yaml"
    },
    "@context": {
@@ -23,7 +23,7 @@
          "@type": "@id"
       },
       "date": {
-         "@type": "xsd:date",
+         "@type": "xsd:dateTime",
          "@id": "schema:dateModified"
       },
       "default_value": {
diff --git a/nwb_schema_language/project/jsonld/nwb_schema_language.jsonld b/nwb_schema_language/project/jsonld/nwb_schema_language.jsonld
index 3ecfbe3..9bfbd78 100644
--- a/nwb_schema_language/project/jsonld/nwb_schema_language.jsonld
+++ b/nwb_schema_language/project/jsonld/nwb_schema_language.jsonld
@@ -588,7 +588,7 @@
       "domain_of": [
         "Namespace"
       ],
-      "range": "date",
+      "range": "datetime",
       "@type": "SlotDefinition"
     },
     {
@@ -1504,9 +1504,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "nwb_schema_language.yaml",
-  "source_file_date": "2023-08-30T20:53:55",
-  "source_file_size": 10793,
-  "generation_date": "2023-08-30T20:53:59",
+  "source_file_date": "2023-08-31T15:31:11",
+  "source_file_size": 10797,
+  "generation_date": "2023-10-09T15:03:07",
   "settings": [
     {
       "setting_key": "email",
diff --git a/nwb_schema_language/project/jsonschema/nwb_schema_language.schema.json b/nwb_schema_language/project/jsonschema/nwb_schema_language.schema.json
index 969bd36..ec86735 100644
--- a/nwb_schema_language/project/jsonschema/nwb_schema_language.schema.json
+++ b/nwb_schema_language/project/jsonschema/nwb_schema_language.schema.json
@@ -408,7 +408,7 @@
                 },
                 "date": {
                     "description": "Date that a namespace was last modified or released",
-                    "format": "date",
+                    "format": "date-time",
                     "type": "string"
                 },
                 "doc": {
diff --git a/nwb_schema_language/project/protobuf/nwb_schema_language.proto b/nwb_schema_language/project/protobuf/nwb_schema_language.proto
index 219be35..0918c65 100644
--- a/nwb_schema_language/project/protobuf/nwb_schema_language.proto
+++ b/nwb_schema_language/project/protobuf/nwb_schema_language.proto
@@ -66,7 +66,7 @@ message Namespace
   string name = 0
   string fullName = 0
   string version = 0
-  date date = 0
+  datetime date = 0
  repeated  string author = 0
  repeated  string contact = 0
  repeated  schema schema = 0
diff --git a/nwb_schema_language/project/shex/nwb_schema_language.shex b/nwb_schema_language/project/shex/nwb_schema_language.shex
index 3769b16..c4c8efa 100644
--- a/nwb_schema_language/project/shex/nwb_schema_language.shex
+++ b/nwb_schema_language/project/shex/nwb_schema_language.shex
@@ -145,7 +145,7 @@ linkml:Sparqlpath xsd:string
           <name> @linkml:String ;
           <full_name> @linkml:String ? ;
           <version> @linkml:String ;
-          schema1:dateModified @linkml:Date ? ;
+          schema1:dateModified @linkml:Datetime ? ;
           schema1:author @linkml:String + ;
           schema1:email @linkml:String + ;
           <schema_> @<Schema> *
diff --git a/nwb_schema_language/project/sqlschema/nwb_schema_language.sql b/nwb_schema_language/project/sqlschema/nwb_schema_language.sql
index bbb9284..b4c0182 100644
--- a/nwb_schema_language/project/sqlschema/nwb_schema_language.sql
+++ b/nwb_schema_language/project/sqlschema/nwb_schema_language.sql
@@ -74,7 +74,7 @@ CREATE TABLE "Namespace" (
 	name TEXT NOT NULL, 
 	full_name TEXT, 
 	version TEXT NOT NULL, 
-	date DATE, 
+	date DATETIME, 
 	author TEXT NOT NULL, 
 	contact TEXT NOT NULL, 
 	schema_ TEXT, 
diff --git a/nwb_schema_language/src/nwb_schema_language/__init__.py b/nwb_schema_language/src/nwb_schema_language/__init__.py
index 8f4c2f6..d7281ec 100644
--- a/nwb_schema_language/src/nwb_schema_language/__init__.py
+++ b/nwb_schema_language/src/nwb_schema_language/__init__.py
@@ -1,7 +1,6 @@
 import warnings
 from typing import List, Union
 try:
-    pass
     from .datamodel.nwb_schema_pydantic import Namespace, \
         Namespaces, \
         Schema, \
diff --git a/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py
index 2084de0..1aa0343 100644
--- a/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py
+++ b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py
@@ -1,5 +1,5 @@
 # Auto generated from nwb_schema_language.yaml by pythongen.py version: 0.0.1
-# Generation date: 2023-08-30T20:54:02
+# Generation date: 2023-10-09T15:03:09
 # Schema: nwb-schema-language
 #
 # id: https://w3id.org/p2p_ld/nwb-schema-language
@@ -21,8 +21,8 @@ from linkml_runtime.utils.formatutils import camelcase, underscore, sfx
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
 from rdflib import Namespace, URIRef
 from linkml_runtime.utils.curienamespace import CurieNamespace
-from linkml_runtime.linkml_model.types import Boolean, Date, String
-from linkml_runtime.utils.metamodelcore import Bool, XSDDate
+from linkml_runtime.linkml_model.types import Boolean, Datetime, String
+from linkml_runtime.utils.metamodelcore import Bool, XSDDateTime
 
 metamodel_version = "1.7.0"
 version = None
@@ -58,7 +58,7 @@ class Namespace(YAMLRoot):
     author: Union[str, List[str]] = None
     contact: Union[str, List[str]] = None
     full_name: Optional[str] = None
-    date: Optional[Union[str, XSDDate]] = None
+    date: Optional[Union[str, XSDDateTime]] = None
     schema_: Optional[Union[Union[dict, "Schema"], List[Union[dict, "Schema"]]]] = empty_list()
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
@@ -92,8 +92,8 @@ class Namespace(YAMLRoot):
         if self.full_name is not None and not isinstance(self.full_name, str):
             self.full_name = str(self.full_name)
 
-        if self.date is not None and not isinstance(self.date, XSDDate):
-            self.date = XSDDate(self.date)
+        if self.date is not None and not isinstance(self.date, XSDDateTime):
+            self.date = XSDDateTime(self.date)
 
         if not isinstance(self.schema_, list):
             self.schema_ = [self.schema_] if self.schema_ is not None else []
@@ -629,7 +629,7 @@ slots.version = Slot(uri=NWB_SCHEMA_LANGUAGE.version, name="version", curie=NWB_
                    pattern=re.compile(r'^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$'))
 
 slots.date = Slot(uri=SCHEMA.dateModified, name="date", curie=SCHEMA.curie('dateModified'),
-                   model_uri=NWB_SCHEMA_LANGUAGE.date, domain=None, range=Optional[Union[str, XSDDate]])
+                   model_uri=NWB_SCHEMA_LANGUAGE.date, domain=None, range=Optional[Union[str, XSDDateTime]])
 
 slots.author = Slot(uri=SCHEMA.author, name="author", curie=SCHEMA.curie('author'),
                    model_uri=NWB_SCHEMA_LANGUAGE.author, domain=None, range=Union[str, List[str]])
diff --git a/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py
index 9762fab..f041572 100644
--- a/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py
+++ b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py
@@ -112,8 +112,8 @@ class Namespace(ConfiguredBaseModel):
     full_name: Optional[str] = Field(None, description="""Optional string with extended full name for the namespace.""")
     version: str = Field(...)
     date: Optional[datetime ] = Field(None, description="""Date that a namespace was last modified or released""")
-    author: List[str] | str = Field(default_factory=list, description="""List of strings with the names of the authors of the namespace.""")
-    contact: List[str] | str = Field(default_factory=list, description="""List of strings with the contact information for the authors. Ordering of the contacts should match the ordering of the authors.""")
+    author: List[str] = Field(default_factory=list, description="""List of strings with the names of the authors of the namespace.""")
+    contact: List[str] = Field(default_factory=list, description="""List of strings with the contact information for the authors. Ordering of the contacts should match the ordering of the authors.""")
     schema_: Optional[List[Schema]] = Field(alias="schema", default_factory=list, description="""List of the schema to be included in this namespace.""")