Attempt lite migration to pydantic v2

optimade/adapters/base.py

@@ -21,7 +21,7 @@
 import re
 from typing import Any, Callable, Dict, List, Optional, Tuple, Type, Union
 
-from pydantic import BaseModel  # pylint: disable=no-name-in-module
+from pydantic.v1 import BaseModel  # pylint: disable=no-name-in-module
 
 from optimade.adapters.logger import LOGGER
 from optimade.models.entries import EntryResource

optimade/models/baseinfo.py

@@ -2,7 +2,7 @@
 import re
 from typing import Dict, List, Optional
 
-from pydantic import AnyHttpUrl, BaseModel, Field, root_validator, validator
+from pydantic.v1 import AnyHttpUrl, BaseModel, Field, root_validator, validator
 
 from optimade.models.jsonapi import Resource
 from optimade.models.utils import SemanticVersion, StrictField

optimade/models/entries.py

@@ -2,7 +2,7 @@
 from datetime import datetime
 from typing import Dict, List, Optional
 
-from pydantic import BaseModel, validator  # pylint: disable=no-name-in-module
+from pydantic.v1 import BaseModel, validator  # pylint: disable=no-name-in-module
 
 from optimade.models.jsonapi import Attributes, Relationships, Resource
 from optimade.models.optimade_json import DataType, Relationship

optimade/models/index_metadb.py

@@ -2,7 +2,7 @@
 from enum import Enum
 from typing import Dict, Union
 
-from pydantic import BaseModel, Field  # pylint: disable=no-name-in-module
+from pydantic.v1 import BaseModel, Field  # pylint: disable=no-name-in-module
 
 from optimade.models.baseinfo import BaseInfoAttributes, BaseInfoResource
 from optimade.models.jsonapi import BaseResource

optimade/models/jsonapi.py

@@ -3,7 +3,7 @@
 from datetime import datetime, timezone
 from typing import Any, Dict, List, Optional, Type, Union
 
-from pydantic import (  # pylint: disable=no-name-in-module
+from pydantic.v1 import (  # pylint: disable=no-name-in-module
     AnyUrl,
     BaseModel,
     parse_obj_as,

optimade/models/links.py

@@ -2,7 +2,7 @@
 from enum import Enum
 from typing import Optional, Union
 
-from pydantic import AnyUrl, root_validator  # pylint: disable=no-name-in-module
+from pydantic.v1 import AnyUrl, root_validator  # pylint: disable=no-name-in-module
 
 from optimade.models.entries import EntryResource
 from optimade.models.jsonapi import Attributes, Link

optimade/models/optimade_json.py

@@ -4,7 +4,7 @@
 from enum import Enum
 from typing import Any, Dict, List, Optional, Type, Union
 
-from pydantic import AnyHttpUrl, AnyUrl, BaseModel, EmailStr, root_validator
+from pydantic.v1 import AnyHttpUrl, AnyUrl, BaseModel, EmailStr, root_validator
 
 from optimade.models import jsonapi
 from optimade.models.utils import SemanticVersion, StrictField

optimade/models/references.py

@@ -1,8 +1,13 @@
 # pylint: disable=line-too-long,no-self-argument
 from typing import List, Optional
 
-from pydantic import AnyUrl, BaseModel, validator  # pylint: disable=no-name-in-module
+from pydantic.v1 import (
+    AnyUrl,
+    BaseModel,
+    validator,
+)
 
+# pylint: disable=no-name-in-module
 from optimade.models.entries import EntryResource, EntryResourceAttributes
 from optimade.models.utils import OptimadeField, SupportLevel
 

optimade/models/responses.py

@@ -1,7 +1,7 @@
 # pylint: disable=no-self-argument
 from typing import Any, Dict, List, Optional, Union
 
-from pydantic import Field, root_validator
+from pydantic.v1 import Field, root_validator
 
 from optimade.models.baseinfo import BaseInfoResource
 from optimade.models.entries import EntryInfoResource, EntryResource

optimade/models/structures.py

@@ -4,7 +4,7 @@
 from enum import Enum, IntEnum
 from typing import List, Optional, Union
 
-from pydantic import BaseModel, conlist, root_validator, validator
+from pydantic.v1 import BaseModel, conlist, root_validator, validator
 
 from optimade.models.entries import EntryResource, EntryResourceAttributes
 from optimade.models.utils import (

optimade/models/utils.py

@@ -7,8 +7,8 @@
 from functools import reduce
 from typing import TYPE_CHECKING, List, Optional, Union
 
-from pydantic import Field
-from pydantic.fields import FieldInfo
+from pydantic.v1 import Field
+from pydantic.v1.fields import FieldInfo
 
 if TYPE_CHECKING:  # pragma: no cover
     from typing import Any

optimade/server/config.py

@@ -4,14 +4,13 @@
 from pathlib import Path
 from typing import Any, Dict, List, Literal, Optional, Tuple, Union
 
-from pydantic import (  # pylint: disable=no-name-in-module
+from pydantic.v1 import (  # pylint: disable=no-name-in-module
     AnyHttpUrl,
-    BaseSettings,
     Field,
     root_validator,
     validator,
 )
-from pydantic.env_settings import SettingsSourceCallable
+from pydantic_settings import BaseSettings, PydanticBaseSettingsSource
 
 from optimade import __api_version__, __version__
 from optimade.models import Implementation, Provider
@@ -71,14 +70,14 @@ def config_file_settings(settings: BaseSettings) -> Dict[str, Any]:
     """Configuration file settings source.
 
     Based on the example in the
-    [pydantic documentation](https://pydantic-docs.helpmanual.io/usage/settings/#adding-sources),
+    [pydantic documentation](https://docs.pydantic.dev/latest/usage/pydantic_settings/#customise-settings-sources),
     this function loads ServerConfig settings from a configuration file.
 
     The file must be of either type JSON or YML/YAML.
 
     Parameters:
-        settings: The `pydantic.BaseSettings` class using this function as a
-            `pydantic.SettingsSourceCallable`.
+        settings: The `pydantic_settings.BaseSettings` class using this function as a
+            `pydantic_settings.PydanticBaseSettingsSource`.
 
     Returns:
         Dictionary of settings as read from a file.
@@ -345,10 +344,10 @@ class Config:
         @classmethod
         def customise_sources(
             cls,
-            init_settings: SettingsSourceCallable,
-            env_settings: SettingsSourceCallable,
-            file_secret_settings: SettingsSourceCallable,
-        ) -> Tuple[SettingsSourceCallable, ...]:
+            init_settings: PydanticBaseSettingsSource,
+            env_settings: PydanticBaseSettingsSource,
+            file_secret_settings: PydanticBaseSettingsSource,
+        ) -> Tuple[PydanticBaseSettingsSource, ...]:
             """
             **Priority of config settings sources**:
 

optimade/server/exception_handlers.py

@@ -5,7 +5,7 @@
 from fastapi.encoders import jsonable_encoder
 from fastapi.exceptions import RequestValidationError, StarletteHTTPException
 from lark.exceptions import VisitError
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from optimade.exceptions import BadRequest, OptimadeHTTPException
 from optimade.models import ErrorResponse, ErrorSource, OptimadeError

optimade/server/query_params.py

@@ -3,7 +3,7 @@
 from warnings import warn
 
 from fastapi import Query
-from pydantic import EmailStr  # pylint: disable=no-name-in-module
+from pydantic.v1 import EmailStr  # pylint: disable=no-name-in-module
 
 from optimade.exceptions import BadRequest
 from optimade.server.config import CONFIG

optimade/utils.py

@@ -6,7 +6,7 @@
 import json
 from typing import Container, Iterable, List, Optional
 
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from optimade.models.links import LinksResource
 

optimade/validator/config.py

@@ -9,7 +9,7 @@
 
 from typing import Any, Container, Dict, List, Set
 
-from pydantic import BaseSettings, Field
+from pydantic.v1 import BaseSettings, Field
 
 from optimade.models import (
     DataType,

optimade/validator/utils.py

@@ -21,7 +21,7 @@
 from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import requests
-from pydantic import Field, ValidationError
+from pydantic.v1 import Field, ValidationError
 
 from optimade import __version__
 from optimade.models import (
@@ -366,7 +366,7 @@ def wrapper(
             else:
                 message = msg.split("\n")
                 if validator.verbosity > 1:
-                    # ValidationErrors from pydantic already include very detailed errors
+                    # ValidationErrors from pydantic.v1 already include very detailed errors
                     # that get duplicated in the traceback
                     if not isinstance(result, ValidationError):
                         message += traceback.split("\n")

pyproject.toml

@@ -26,7 +26,8 @@ classifiers = [
 requires-python = ">=3.9"
 dependencies = [
     "lark~=1.1",
-    "pydantic~=1.10,>=1.10.2,!=1.10.7",
+    "pydantic~=2.0",
+    "pydantic-settings~=2.0",
     "email_validator>=1.2",
     "requests~=2.28",
 ]
@@ -65,7 +66,6 @@ elastic = ["elasticsearch-dsl~=7.4,<8.0", "elasticsearch~=7.17"]
 mongo = ["pymongo~=4.0", "mongomock~=4.1"]
 server = [
     "uvicorn[standard]~=0.19",
-    "fastapi>=0.103.1",
     "pyyaml~=6.0",
     "optimade[mongo]",
 ]
@@ -150,6 +150,7 @@ filterwarnings = [
     "ignore:.*has an unrecognised prefix.*:",
     "ignore:.*pkg_resources is deprecated as an API*:DeprecationWarning",
     "ignore:.*Deprecated call to `pkg_resources.declare_namespace*:DeprecationWarning",
+    "ignore:.*Support for class-based `config` is deprecated, use ConfigDict instead*:DeprecationWarning",
 ]
 testpaths = "tests"
 addopts = "-rs"

requirements.txt

@@ -1,6 +1,7 @@
 email_validator==2.0.0.post2
 lark==1.1.7
-pydantic==1.10.9
+pydantic==2.4.1
+pydantic_settings==2.0.3
 pyyaml==6.0
 requests==2.31.0
 uvicorn==0.23.2

tests/models/test_entries.py

@@ -1,5 +1,5 @@
 import pytest
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from optimade.models.entries import EntryRelationships
 

tests/models/test_jsonapi.py

@@ -1,5 +1,5 @@
 import pytest
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 
 def test_hashability():

tests/models/test_links.py

@@ -14,7 +14,7 @@ def test_good_links(starting_links, mapper):
 
 def test_bad_links(starting_links, mapper):
     """Check badly formed links"""
-    from pydantic import ValidationError
+    from pydantic.v1 import ValidationError
 
     bad_links = [
         {"aggregate": "wrong"},

tests/models/test_optimade_json.py

@@ -1,5 +1,5 @@
 import pytest
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from optimade.models import DataType, Provider
 

tests/models/test_references.py

@@ -1,6 +1,6 @@
 # pylint: disable=no-member
 import pytest
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from optimade.models.references import ReferenceResource
 
@@ -22,7 +22,7 @@ def test_more_good_references(good_references, mapper):
 
 def test_bad_references(mapper):
     """Check badly formed references"""
-    from pydantic import ValidationError
+    from pydantic.v1 import ValidationError
 
     bad_refs = [
         {"id": "AAAA", "type": "references", "doi": "10.1234/1234"},  # bad id

tests/models/test_structures.py

@@ -2,7 +2,7 @@
 import itertools
 
 import pytest
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from optimade.models.structures import CORRELATED_STRUCTURE_FIELDS, StructureResource
 from optimade.warnings import MissingExpectedField

tests/models/test_utils.py

@@ -1,7 +1,7 @@
 from typing import Callable, List
 
 import pytest
-from pydantic import BaseModel, Field, ValidationError
+from pydantic.v1 import BaseModel, Field, ValidationError
 
 from optimade.models.utils import OptimadeField, StrictField, SupportLevel