From 4ee77dbb2e728eebc72c5be1ba1cf34d08d215de Mon Sep 17 00:00:00 2001 From: sneakers-the-rat Date: Thu, 31 Aug 2023 15:36:58 -0700 Subject: [PATCH] update to pydantic 2 --- nwb_linkml/adapters/classes.py | 2 +- nwb_schema_language/Makefile | 2 +- nwb_schema_language/poetry.lock | 180 ++++++++++++++---- nwb_schema_language/pyproject.toml | 2 +- .../src/nwb_schema_language/__init__.py | 3 +- .../nwb_schema_language/datamodel/__init__.py | 2 +- .../datamodel/nwb_schema_pydantic.py | 40 ++-- .../schema/nwb_schema_language.yaml | 2 +- poetry.lock | 180 ++++++++++++++---- pyproject.toml | 2 +- tests/test_generate.py | 2 +- 11 files changed, 303 insertions(+), 114 deletions(-) diff --git a/nwb_linkml/adapters/classes.py b/nwb_linkml/adapters/classes.py index 1dd0f8a..f145a55 100644 --- a/nwb_linkml/adapters/classes.py +++ b/nwb_linkml/adapters/classes.py @@ -178,7 +178,7 @@ class ClassAdapter(Adapter): name_slot = SlotDefinition( name='name', required=True, - ifabsent=self.cls.name, + ifabsent=f'string({self.cls.name})', equals_string=self.cls.name, range='string' ) diff --git a/nwb_schema_language/Makefile b/nwb_schema_language/Makefile index 0692fd9..9d6f45f 100644 --- a/nwb_schema_language/Makefile +++ b/nwb_schema_language/Makefile @@ -107,7 +107,7 @@ gen-project: $(PYMODEL) $(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL) gen-pydantic: $(PYMODEL) - $(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) --pydantic_version 1 > $(PYMODEL)/nwb_schema_pydantic.py + $(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) --pydantic_version 2 > $(PYMODEL)/nwb_schema_pydantic.py $(RUN) run_patches --phase post_generation_pydantic test: test-schema test-python test-examples diff --git a/nwb_schema_language/poetry.lock b/nwb_schema_language/poetry.lock index 31113a2..2a1efac 100644 --- a/nwb_schema_language/poetry.lock +++ b/nwb_schema_language/poetry.lock @@ -1,5 +1,16 @@ # This file is automatically @generated by Poetry 1.5.1 and should not be 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Union[List[CompoundDtype], FlatDtype, ReferenceDtype] -except NameError: +except (NameError, RecursionError): warnings.warn('Error importing pydantic classes, passing because we might be in the process of patching them, but it is likely they are broken and you will be unable to use them!') \ No newline at end of file diff --git a/nwb_schema_language/src/nwb_schema_language/datamodel/__init__.py b/nwb_schema_language/src/nwb_schema_language/datamodel/__init__.py index 2536e1a..309e640 100644 --- a/nwb_schema_language/src/nwb_schema_language/datamodel/__init__.py +++ b/nwb_schema_language/src/nwb_schema_language/datamodel/__init__.py @@ -1,3 +1,3 @@ -from .nwb_schema_language import * +# from .nwb_schema_language import * # create additional derived \ No newline at end of file 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 59e2ad4..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 @@ -13,13 +13,9 @@ else: metamodel_version = "None" version = "None" -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, +class ConfiguredBaseModel(BaseModel, validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, + validate_default = True, extra = 'forbid', arbitrary_types_allowed = True, use_enum_values = True): @@ -115,7 +111,7 @@ class Namespace(ConfiguredBaseModel): name: str = Field(...) full_name: Optional[str] = Field(None, description="""Optional string with extended full name for the namespace.""") version: str = Field(...) - date: Optional[date] = Field(None, description="""Date that a namespace was last modified or released""") + date: Optional[datetime ] = Field(None, description="""Date that a namespace was last modified or released""") 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.""") @@ -216,18 +212,18 @@ class Dataset(DtypeMixin): -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Namespace.update_forward_refs() -Namespaces.update_forward_refs() -Schema.update_forward_refs() -Group.update_forward_refs() -Groups.update_forward_refs() -Link.update_forward_refs() -Datasets.update_forward_refs() -ReferenceDtype.update_forward_refs() -CompoundDtype.update_forward_refs() -DtypeMixin.update_forward_refs() -Attribute.update_forward_refs() -Dataset.update_forward_refs() - +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +Namespace.model_rebuild() +Namespaces.model_rebuild() +Schema.model_rebuild() +Group.model_rebuild() +Groups.model_rebuild() +Link.model_rebuild() +Datasets.model_rebuild() +ReferenceDtype.model_rebuild() +CompoundDtype.model_rebuild() +DtypeMixin.model_rebuild() +Attribute.model_rebuild() +Dataset.model_rebuild() + diff --git a/nwb_schema_language/src/nwb_schema_language/schema/nwb_schema_language.yaml b/nwb_schema_language/src/nwb_schema_language/schema/nwb_schema_language.yaml index 923f433..ff06a56 100644 --- a/nwb_schema_language/src/nwb_schema_language/schema/nwb_schema_language.yaml +++ b/nwb_schema_language/src/nwb_schema_language/schema/nwb_schema_language.yaml @@ -179,7 +179,7 @@ slots: required: true pattern: "^(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-]+)*))?$" date: - range: date + range: datetime slot_uri: schema:dateModified description: Date that a namespace was last modified or released examples: diff --git a/poetry.lock b/poetry.lock index 5682954..cf3250e 100644 --- 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