update to pydantic 2

This commit is contained in:
sneakers-the-rat 2023-08-31 15:36:58 -07:00
parent 3568037a1e
commit 4ee77dbb2e
11 changed files with 303 additions and 114 deletions

View file

@ -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'
)

View file

@ -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

View file

@ -1,5 +1,16 @@
# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
[[package]]
name = "annotated-types"
version = "0.5.0"
description = "Reusable constraint types to use with typing.Annotated"
optional = false
python-versions = ">=3.7"
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[[package]]
name = "antlr4-python3-runtime"
version = "4.9.3"
@ -1351,55 +1362,140 @@ pyasn1 = ">=0.4.6,<0.6.0"
[[package]]
name = "pydantic"
version = "1.10.12"
description = "Data validation and settings management using python type hints"
version = "2.3.0"
description = "Data validation using Python type hints"
optional = false
python-versions = ">=3.7"
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{file = "pydantic_core-2.6.3.tar.gz", hash = "sha256:1508f37ba9e3ddc0189e6ff4e2228bd2d3c3a4641cbe8c07177162f76ed696c7"},
]
[package.dependencies]
typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
[[package]]
name = "pygments"
@ -2427,4 +2523,4 @@ docs = []
[metadata]
lock-version = "2.0"
python-versions = "^3.9"
content-hash = "7f1c4bbcfac50aaa741976f74d8ceac46ba630ea5ed649b90184f9698c05d536"
content-hash = "64b3d27885bd38afe892c662d06a69f48e980d5464922329aad071e2893f40d9"

View file

@ -13,7 +13,7 @@ include = ["README.md", "src/nwb_schema_language/schema", "project"]
[tool.poetry.dependencies]
python = "^3.9"
linkml-runtime = "^1.1.24"
pydantic = "<2"
pydantic = "^2.3.0"
[tool.poetry-dynamic-versioning]
enable = true

View file

@ -1,6 +1,7 @@
import warnings
from typing import List, Union
try:
pass
from .datamodel.nwb_schema_pydantic import Namespace, \
Namespaces, \
Schema, \
@ -13,5 +14,5 @@ try:
FlatDtype
DTypeType = 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!')

View file

@ -1,3 +1,3 @@
from .nwb_schema_language import *
# from .nwb_schema_language import *
# create additional derived

View file

@ -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()

View file

@ -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:

180
poetry.lock generated
View file

@ -1,5 +1,16 @@
# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
[[package]]
name = "annotated-types"
version = "0.5.0"
description = "Reusable constraint types to use with typing.Annotated"
optional = false
python-versions = ">=3.7"
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"},
]
[[package]]
name = "ansi2html"
version = "1.8.0"
@ -1089,55 +1100,140 @@ refresh = ["bioregistry[refresh] (>=0.8.0,<0.9.0)", "rdflib[refresh] (>=6.2.0,<7
[[package]]
name = "pydantic"
version = "1.10.12"
description = "Data validation and settings management using python type hints"
version = "2.3.0"
description = "Data validation using Python type hints"
optional = false
python-versions = ">=3.7"
files = [
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]
[package.dependencies]
typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
[[package]]
name = "pygments"
@ -2062,4 +2158,4 @@ tests = ["pytest", "pytest-depends"]
[metadata]
lock-version = "2.0"
python-versions = "^3.11"
content-hash = "d76271be11498c9055d0692800a4e1ddcb81d9807e6ff993472ea2ab7eb076b0"
content-hash = "b552d70308f5b757a624b3d0046e54af4297bfba994a8019f4b366cce2fbe06f"

View file

@ -15,7 +15,6 @@ python = "^3.11"
pyyaml = "^6.0"
linkml-runtime = "^1.5.6"
#nwb_schema_language = { path = './nwb_schema_language', develop = true, optional = true }
pydantic = "<2"
rich = "^13.5.2"
linkml = "^1.5.7"
pytest = { version="^7.4.0", optional=true}
@ -23,6 +22,7 @@ pytest-depends = {version="^1.0.1", optional=true}
dash = {version="^2.12.1", optional=true}
dash-cytoscape = {version="^0.3.0", optional=true}
nptyping = "^2.5.0"
pydantic = "^2.3.0"
[tool.poetry.extras]
dev = ["nwb_schema_language"]

View file

@ -40,7 +40,7 @@ def test_generate_pydantic(tmp_output_dir):
generator = NWBPydanticGenerator(
str(schema),
pydantic_version='1',
pydantic_version='2',
emit_metadata=True,
gen_classvars=True,
gen_slots=True