Merge pull request #119 from SciCatProject/pydantic-v2

Support Pydantic v2

.github/workflows/ci.yml

@@ -26,12 +26,13 @@ jobs:
           commit_message: Apply automatic formatting
 
   tests:
-    name: Tests py${{ matrix.python }} ${{ matrix.os }}
+    name: Tests ${{ matrix.os }} ${{ matrix.tox }}
     needs: formatting
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         include:
+          - {python: '3.11', os: ubuntu-22.04, tox: pydantic2-full}
           - {python: '3.11', os: ubuntu-22.04, tox: py311-full}
           - {python: '3.10', os: ubuntu-22.04, tox: py310-full}
           - {python: '3.9', os: ubuntu-22.04, tox: py39-full}

requirements-pydantic2/base.in

@@ -0,0 +1,5 @@
+email-validator
+fabric
+pydantic == 2
+python-dateutil
+requests

requirements-pydantic2/test.in

@@ -0,0 +1,8 @@
+-r base.in
+filelock
+hypothesis
+pyfakefs
+pytest
+pytest-randomly
+pytest-xdist
+pyyaml

requirements/base.in

@@ -1,5 +1,5 @@
 email-validator
 fabric
-pydantic
+pydantic < 2  # autodoc_pydantic is not compatible with pydantic 2
 python-dateutil
 requests

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:7d04d6082ad9fa4c20034b17bf0e831ba768596f
+# SHA1:a579aa51495a128838b22e1692012f3918753a8c
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -35,7 +35,7 @@ paramiko==3.2.0
     # via fabric
 pycparser==2.21
     # via cffi
-pydantic==1.10.9
+pydantic==1.10.11
     # via -r requirements/base.in
 pynacl==1.5.0
     # via paramiko
@@ -45,7 +45,7 @@ requests==2.31.0
     # via -r requirements/base.in
 six==1.16.0
     # via python-dateutil
-typing-extensions==4.6.3
+typing-extensions==4.7.1
     # via pydantic
 urllib3==2.0.3
     # via requests

requirements/ci.txt

@@ -21,11 +21,11 @@ packaging==23.1
     # via
     #   pyproject-api
     #   tox
-platformdirs==3.6.0
+platformdirs==3.8.0
     # via
     #   tox
     #   virtualenv
-pluggy==1.0.0
+pluggy==1.2.0
     # via tox
 pyproject-api==1.5.2
     # via tox

requirements/dev.txt

@@ -11,7 +11,7 @@
 -r static.txt
 -r test.txt
 -r wheels.txt
-anyio==3.7.0
+anyio==3.7.1
     # via jupyter-server
 argon2-cffi==21.3.0
     # via
@@ -41,14 +41,14 @@ json5==0.9.14
     # via jupyterlab-server
 jsonpointer==2.4
     # via jsonschema
-jsonschema[format-nongpl]==4.17.3
+jsonschema[format-nongpl]==4.18.0
     # via
     #   jupyter-events
     #   jupyterlab-server
     #   nbformat
 jupyter-events==0.6.3
     # via jupyter-server
-jupyter-server==2.6.0
+jupyter-server==2.7.0
     # via
     #   jupyterlab
     #   jupyterlab-server
@@ -76,7 +76,7 @@ pathspec==0.11.1
     # via black
 pip-compile-multi==2.6.3
     # via -r requirements/dev.in
-pip-tools==6.13.0
+pip-tools==6.14.0
     # via pip-compile-multi
 prometheus-client==0.17.0
     # via
@@ -122,11 +122,11 @@ types-requests==2.31.0.1
     # via -r requirements/dev.in
 types-urllib3==1.26.25.13
     # via types-requests
-uri-template==1.2.0
+uri-template==1.3.0
     # via jsonschema
 webcolors==1.13
     # via jsonschema
-websocket-client==1.6.0
+websocket-client==1.6.1
     # via jupyter-server
 wheel==0.40.0
     # via

requirements/docs.txt

@@ -13,8 +13,10 @@ alabaster==0.7.13
 asttokens==2.2.1
     # via stack-data
 attrs==23.1.0
-    # via jsonschema
-autodoc-pydantic==1.8.0
+    # via
+    #   jsonschema
+    #   referencing
+autodoc-pydantic==1.9.0
     # via -r requirements/docs.in
 babel==2.12.1
     # via
@@ -46,7 +48,7 @@ fastjsonschema==2.17.1
     # via nbformat
 imagesize==1.4.1
     # via sphinx
-ipykernel==6.23.2
+ipykernel==6.24.0
     # via -r requirements/docs.in
 ipython==8.14.0
     # via
@@ -60,9 +62,11 @@ jinja2==3.1.2
     #   nbconvert
     #   nbsphinx
     #   sphinx
-jsonschema==4.17.3
+jsonschema==4.18.0
     # via nbformat
-jupyter-client==8.2.0
+jsonschema-specifications==2023.6.1
+    # via jsonschema
+jupyter-client==8.3.0
     # via
     #   ipykernel
     #   nbclient
@@ -122,9 +126,9 @@ pexpect==4.8.0
     # via ipython
 pickleshare==0.7.5
     # via ipython
-platformdirs==3.6.0
+platformdirs==3.8.0
     # via jupyter-core
-prompt-toolkit==3.0.38
+prompt-toolkit==3.0.39
     # via ipython
 psutil==5.9.5
     # via ipykernel
@@ -141,14 +145,20 @@ pygments==2.15.1
     #   nbconvert
     #   pydata-sphinx-theme
     #   sphinx
-pyrsistent==0.19.3
-    # via jsonschema
 pyyaml==6.0
     # via myst-parser
 pyzmq==25.1.0
     # via
     #   ipykernel
     #   jupyter-client
+referencing==0.29.1
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+rpds-py==0.8.7
+    # via
+    #   jsonschema
+    #   referencing
 snowballstemmer==2.2.0
     # via sphinx
 soupsieve==2.4.1

requirements/static.txt

@@ -15,7 +15,7 @@ identify==2.5.24
     # via pre-commit
 nodeenv==1.8.0
     # via pre-commit
-platformdirs==3.6.0
+platformdirs==3.8.0
     # via virtualenv
 pre-commit==3.3.3
     # via -r requirements/static.in

requirements/test.txt

@@ -12,17 +12,17 @@ execnet==1.9.0
     # via pytest-xdist
 filelock==3.12.2
     # via -r requirements/test.in
-hypothesis==6.79.1
+hypothesis==6.80.0
     # via -r requirements/test.in
 iniconfig==2.0.0
     # via pytest
 packaging==23.1
     # via pytest
-pluggy==1.0.0
+pluggy==1.2.0
     # via pytest
 pyfakefs==5.2.2
     # via -r requirements/test.in
-pytest==7.3.2
+pytest==7.4.0
     # via
     #   -r requirements/test.in
     #   pytest-randomly

src/scitacean/_base_model.py

@@ -17,11 +17,14 @@
     )
 
 import dataclasses
-from typing import Any, Dict, Iterable, Optional, Type, TypeVar
+from datetime import datetime
+from typing import Any, Dict, Iterable, Optional, Type, TypeVar, Union
 
 import pydantic
+from dateutil.parser import parse as parse_datetime
 
 from ._internal.orcid import is_valid_orcid
+from ._internal.pydantic_compat import is_pydantic_v1
 from .filesystem import RemotePath
 from .logging import get_logger
 from .pid import PID
@@ -39,12 +42,19 @@ class DatasetType(*_DatasetTypeBases):
 class BaseModel(pydantic.BaseModel):
     """Base class for Pydantic models for communication with SciCat."""
 
-    class Config:
-        extra = pydantic.Extra.forbid
-        json_encoders = {
-            PID: lambda v: str(v),
-            RemotePath: lambda v: v.posix,
-        }
+    if is_pydantic_v1():
+
+        class Config:
+            extra = pydantic.Extra.forbid
+            json_encoders = {
+                PID: lambda v: str(v),
+                RemotePath: lambda v: v.posix,
+            }
+
+    else:
+        model_config = pydantic.ConfigDict(
+            extra="forbid",
+        )
 
     # Some schemas contain fields that we don't want to use in Scitacean.
     # Normally, omitting them from the model would result in an error when
@@ -58,7 +68,7 @@ def __init_subclass__(
         super().__init_subclass__(**kwargs)
 
         masked = list(masked) if masked is not None else []
-        field_names = {field.alias for field in cls.__fields__.values()}
+        field_names = {field.alias for field in cls.get_model_fields().values()}
         masked.extend(key for key in _IGNORED_KWARGS if key not in field_names)
         cls._masked_fields = tuple(masked)
 
@@ -70,6 +80,32 @@ def _delete_ignored_args(self, args: Dict[str, Any]) -> None:
         for key in self._masked_fields:
             args.pop(key, None)
 
+    if is_pydantic_v1():
+
+        @classmethod
+        def get_model_fields(cls) -> Dict[str, pydantic.fields.ModelField]:
+            return cls.__fields__
+
+        def model_dump(self, *args, **kwargs) -> Dict[str, Any]:
+            return self.dict(*args, **kwargs)
+
+        def model_dump_json(self, *args, **kwargs) -> str:
+            return self.json(*args, **kwargs)
+
+        @classmethod
+        def model_construct(cls: Type[ModelType], *args, **kwargs) -> ModelType:
+            return cls.construct(*args, **kwargs)
+
+        @classmethod
+        def model_rebuild(cls, *args, **kwargs) -> Optional[bool]:
+            return cls.update_forward_refs(*args, **kwargs)
+
+    else:
+
+        @classmethod
+        def get_model_fields(cls) -> Dict[str, pydantic.fields.FieldInfo]:
+            return cls.model_fields
+
 
 class BaseUserModel:
     """Base class for user models.
@@ -142,13 +178,31 @@ def construct(
                 "In particular, some fields may not have the correct type",
                 str(e),
             )
-        return model.construct(**fields)
+        return model.model_construct(**fields)
+
+
+def validate_datetime(value: Optional[Union[str, datetime]]) -> Optional[datetime]:
+    """Convert strings to datetimes.
+
+    This uses dateutil.parser.parse instead of Pydantic's builtin parser in order to
+    produce results that are consistent with user inputs.
+    Pydantic uses a custom type for timezones which is not fully compatible with
+    dateutil's.
+    """
+    if not isinstance(value, str):
+        return value
+    return parse_datetime(value)
+
+
+def validate_drop(_: Any) -> None:
+    """Return ``None``."""
+    return None
 
 
 def validate_emails(value: Optional[str]) -> Optional[str]:
     if value is None:
         return value
-    return ";".join(pydantic.EmailStr.validate(item) for item in value.split(";"))
+    return ";".join(pydantic.validate_email(item)[1] for item in value.split(";"))
 
 
 def validate_orcids(value: Optional[str]) -> Optional[str]:

src/scitacean/_dataset_fields.py

@@ -216,7 +216,7 @@ def used_by(self, dataset_type: DatasetType) -> bool:
             read_only=True,
             required=False,
             scicat_name="history",
-            type=History,
+            type=None,
             used_by_derived=True,
             used_by_raw=True,
         ),
@@ -766,7 +766,7 @@ def end_time(self, end_time: Optional[datetime]) -> None:
         self._end_time = end_time
 
     @property
-    def history(self) -> Optional[History]:
+    def history(self) -> Optional[None]:
         """List of objects containing old and new values."""
         return self._history
 

src/scitacean/_internal/pydantic_compat.py

@@ -0,0 +1,19 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2023 SciCat Project (https://github.com/SciCatProject/scitacean)
+from typing import Any, Literal
+
+import pydantic
+
+
+def is_pydantic_v1() -> bool:
+    return pydantic.__version__.split(".", 1)[0] == "1"
+
+
+def field_validator(
+    *args: Any,
+    mode: Literal["before", "after", "wrap", "plain"] = "after",
+    **kwargs: Any,
+) -> Any:
+    if is_pydantic_v1():
+        return pydantic.validator(*args, pre=(mode == "before"), **kwargs)
+    return pydantic.field_validator(*args, mode=mode, **kwargs)