mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-12 17:54:29 +00:00
update to pydantic 2
This commit is contained in:
parent
3568037a1e
commit
4ee77dbb2e
11 changed files with 303 additions and 114 deletions
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@ -178,7 +178,7 @@ class ClassAdapter(Adapter):
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name_slot = SlotDefinition(
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name='name',
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required=True,
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ifabsent=self.cls.name,
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ifabsent=f'string({self.cls.name})',
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equals_string=self.cls.name,
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range='string'
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)
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@ -107,7 +107,7 @@ gen-project: $(PYMODEL)
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$(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
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gen-pydantic: $(PYMODEL)
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$(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) --pydantic_version 1 > $(PYMODEL)/nwb_schema_pydantic.py
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$(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) --pydantic_version 2 > $(PYMODEL)/nwb_schema_pydantic.py
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$(RUN) run_patches --phase post_generation_pydantic
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test: test-schema test-python test-examples
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180
nwb_schema_language/poetry.lock
generated
180
nwb_schema_language/poetry.lock
generated
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@ -1,5 +1,16 @@
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# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
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[[package]]
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name = "annotated-types"
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version = "0.5.0"
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description = "Reusable constraint types to use with typing.Annotated"
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optional = false
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python-versions = ">=3.7"
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files = [
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{file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
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{file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
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]
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[[package]]
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name = "antlr4-python3-runtime"
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version = "4.9.3"
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@ -1351,55 +1362,140 @@ pyasn1 = ">=0.4.6,<0.6.0"
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[[package]]
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name = "pydantic"
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version = "1.10.12"
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description = "Data validation and settings management using python type hints"
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version = "2.3.0"
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description = "Data validation using Python type hints"
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optional = false
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python-versions = ">=3.7"
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]
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[package.dependencies]
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typing-extensions = ">=4.2.0"
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annotated-types = ">=0.4.0"
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pydantic-core = "2.6.3"
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typing-extensions = ">=4.6.1"
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[package.extras]
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dotenv = ["python-dotenv (>=0.10.4)"]
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email = ["email-validator (>=1.0.3)"]
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email = ["email-validator (>=2.0.0)"]
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[[package]]
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name = "pydantic-core"
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version = "2.6.3"
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description = ""
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optional = false
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python-versions = ">=3.7"
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{file = "pydantic_core-2.6.3-pp39-pypy39_pp73-macosx_11_0_arm64.whl", hash = "sha256:48c1ed8b02ffea4d5c9c220eda27af02b8149fe58526359b3c07eb391cb353a2"},
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{file = "pydantic_core-2.6.3-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8b2b1bfed698fa410ab81982f681f5b1996d3d994ae8073286515ac4d165c2e7"},
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{file = "pydantic_core-2.6.3-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bf9d42a71a4d7a7c1f14f629e5c30eac451a6fc81827d2beefd57d014c006c4a"},
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{file = "pydantic_core-2.6.3-pp39-pypy39_pp73-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:4292ca56751aebbe63a84bbfc3b5717abb09b14d4b4442cc43fd7c49a1529efd"},
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{file = "pydantic_core-2.6.3-pp39-pypy39_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:7dc2ce039c7290b4ef64334ec7e6ca6494de6eecc81e21cb4f73b9b39991408c"},
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||||
{file = "pydantic_core-2.6.3-pp39-pypy39_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:615a31b1629e12445c0e9fc8339b41aaa6cc60bd53bf802d5fe3d2c0cda2ae8d"},
|
||||
{file = "pydantic_core-2.6.3-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:1fa1f6312fb84e8c281f32b39affe81984ccd484da6e9d65b3d18c202c666149"},
|
||||
{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"
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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!')
|
||||
|
|
@ -1,3 +1,3 @@
|
|||
from .nwb_schema_language import *
|
||||
# from .nwb_schema_language import *
|
||||
|
||||
# create additional derived
|
||||
|
|
@ -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()
|
||||
|
||||
|
|
|
|||
|
|
@ -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
180
poetry.lock
generated
|
|
@ -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 = [
|
||||
{file = "pydantic-1.10.12-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a1fcb59f2f355ec350073af41d927bf83a63b50e640f4dbaa01053a28b7a7718"},
|
||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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{file = "pydantic-1.10.12.tar.gz", hash = "sha256:0fe8a415cea8f340e7a9af9c54fc71a649b43e8ca3cc732986116b3cb135d303"},
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{file = "pydantic-2.3.0.tar.gz", hash = "sha256:1607cc106602284cd4a00882986570472f193fde9cb1259bceeaedb26aa79a6d"},
|
||||
]
|
||||
|
||||
[package.dependencies]
|
||||
typing-extensions = ">=4.2.0"
|
||||
annotated-types = ">=0.4.0"
|
||||
pydantic-core = "2.6.3"
|
||||
typing-extensions = ">=4.6.1"
|
||||
|
||||
[package.extras]
|
||||
dotenv = ["python-dotenv (>=0.10.4)"]
|
||||
email = ["email-validator (>=1.0.3)"]
|
||||
email = ["email-validator (>=2.0.0)"]
|
||||
|
||||
[[package]]
|
||||
name = "pydantic-core"
|
||||
version = "2.6.3"
|
||||
description = ""
|
||||
optional = false
|
||||
python-versions = ">=3.7"
|
||||
files = [
|
||||
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{file = "pydantic_core-2.6.3.tar.gz", hash = "sha256:1508f37ba9e3ddc0189e6ff4e2228bd2d3c3a4641cbe8c07177162f76ed696c7"},
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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"
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||||
content-hash = "b552d70308f5b757a624b3d0046e54af4297bfba994a8019f4b366cce2fbe06f"
|
||||
|
|
|
|||
|
|
@ -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}
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||||
|
|
@ -23,6 +22,7 @@ pytest-depends = {version="^1.0.1", optional=true}
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|||
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"]
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
Loading…
Reference in a new issue