feat: Pydantic v2

requirements.txt

@@ -1,50 +1,26 @@
 # a2wsgi==1.6.0 # This WSIGMiddleware is not compatible with starlette_context
-alembic==1.13.2
-cachetools==5.3.3
-fastapi==0.112.2
+alembic==1.14.0
+cachetools==5.5.0
+fastapi[all]==0.115.6
 json-cfg==0.4.2
 openpyxl==3.1.5
-opentelemetry-api==1.27.0
-opentelemetry-exporter-otlp==1.27.0
-opentelemetry-exporter-prometheus==0.48b0
-opentelemetry-instrumentation-fastapi==0.48b0
-opentelemetry-instrumentation-httpx==0.48b0
-opentelemetry-instrumentation-logging==0.48b0
-opentelemetry-instrumentation-requests==0.48b0
-opentelemetry-instrumentation-sqlalchemy==0.48b0
-opentelemetry-instrumentation-system-metrics==0.48b0
-opentelemetry-sdk==1.27.0
-psycopg==3.2.1
-psycopg2==2.9.9
-pydantic==1.10.17
-pyjwt[crypto]==2.9.0
-pytest-postgresql==6.0.1
+opentelemetry-api==1.28.2
+opentelemetry-exporter-otlp==1.28.2
+opentelemetry-exporter-prometheus==0.49b2
+opentelemetry-instrumentation-fastapi==0.49b2
+opentelemetry-instrumentation-httpx==0.49b2
+opentelemetry-instrumentation-logging==0.49b2
+opentelemetry-instrumentation-requests==0.49b2
+opentelemetry-instrumentation-sqlalchemy==0.49b2
+opentelemetry-instrumentation-system-metrics==0.49b2
+opentelemetry-sdk==1.28.2
+psycopg==3.2.3
+psycopg2==2.9.10
+pydantic==2.10.3
+pyjwt[crypto]==2.10.1
+pytest-postgresql==6.1.1
 python-dateutil==2.9.0.post0
 requests==2.32.3
-sentry-sdk~=2.13.0
-SQLAlchemy>=1.4.40,<=1.4.53
+sentry-sdk~=2.19.1
+SQLAlchemy>=1.4.50,<2.0.0
 starlette-context==0.3.6
-# Extras from fastapi[all], which we can't install because it requires pydantic v2: https://github.com/tiangolo/fastapi/blob/master/pyproject.toml#L79-L103
-fastapi-cli[standard]>=0.0.5
-# For the test client
-httpx>=0.23.0
-# For templates
-jinja2>=2.11.2
-# For forms and file uploads
-python-multipart>=0.0.7
-# For Starlette's SessionMiddleware, not commonly used with FastAPI
-itsdangerous>=1.1.0
-# For Starlette's schema generation, would not be used with FastAPI
-pyyaml>=5.3.1
-# For UJSONResponse
-ujson>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0
-# For ORJSONResponse
-orjson>=3.2.1
-# To validate email fields
-email-validator>=2.0.0
-# Uvicorn with uvloop
-uvicorn[standard]>=0.30.6
-# Disabled as we are still on Pydantic 1: Settings management
-# pydantic-settings>=2.0.0
-# Disabled as we are still on Pydantic 1: Extra Pydantic data types
-# pydantic-extra-types>=2.0.0

requirements_dev.txt

@@ -1,5 +1,5 @@
-black~=24.4.2
-pyright==1.1.366
+black~=24.10.0
+pyright==1.1.390
 pytest-runner~=6.0.1
-pytest~=8.2.2
-ruff==0.4.10
+pytest~=8.3.4
+ruff==0.8.2

src/app/login/UserStoreUIMap.tsx

@@ -122,7 +122,6 @@ export function AutoLoginForm({ setError, store }: IUserStoreRenderProps) {
           e.stopPropagation();
           login();
         }}
-        size="sm"
       >
         here
       </Anchor>{' '}

visyn_core/dbview.py

@@ -118,13 +118,13 @@ def is_valid_replacement(self, key, value):
         v = self.valid_replacements[key]
         if isinstance(v, list):
             return value in v
-        if v == int:
+        if v is int:
             try:
                 int(value)  # try to cast value to int
                 return True  # successful type cast
             except ValueError:
                 return False
-        if v == float:
+        if v is float:
             try:
                 float(value)  # try to cast value to float
                 return True  # successful type cast

visyn_core/id_mapping/manager.py

@@ -203,6 +203,6 @@ def create_id_mapping_manager() -> MappingManager:
     # Load mapping providers
     providers = []
     for plugin in manager.registry.list("mapping_provider"):
-        providers = providers + list(plugin.load().factory())
+        providers = providers + list(plugin.load().factory())  # type: ignore
     _log.info(f"Initializing MappingManager with {len(providers)} provider(s)")
     return MappingManager(providers)

visyn_core/plugin/model.py

@@ -2,7 +2,7 @@
 from typing import Any
 
 from fastapi import FastAPI
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 
 class RegHelper:

visyn_core/plugin/parser.py

@@ -3,7 +3,7 @@
 from functools import cached_property, lru_cache
 from importlib.metadata import EntryPoint, entry_points
 
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 from .. import manager
 from .model import AVisynPlugin, RegHelper

visyn_core/plugin/registry.py

@@ -1,4 +1,5 @@
 import logging
+from typing import Any
 
 from fastapi import FastAPI
 
@@ -30,7 +31,7 @@ def __call__(self, *args, **kwargs):
         self._cache = v
         return v
 
-    def factory(self, *args, **kwargs):
+    def factory(self, *args, **kwargs) -> Any:
         return self(*args, **kwargs)
 
 

visyn_core/rdkit/img_api.py

@@ -20,7 +20,7 @@
 def draw_smiles(
     structure: SmilesMolecule, substructure: SmilesMolecule | None = None, align: SmilesMolecule | None = None, size: int = 300
 ):
-    return draw(structure.mol, size=size, substructure=aligned(structure.mol, align and align.mol) or substructure and substructure.mol)
+    return draw(structure.mol, size=size, substructure=aligned(structure.mol, align and align.mol) or (substructure and substructure.mol))
 
 
 @app.post("/")

visyn_core/rdkit/models.py

@@ -1,35 +1,48 @@
-from typing import ClassVar
+from typing import Any, ClassVar
 
-from pydantic import BaseModel
+from pydantic import BaseModel, GetCoreSchemaHandler
+from pydantic.annotated_handlers import GetJsonSchemaHandler
+from pydantic.json_schema import JsonSchemaValue
+from pydantic_core import core_schema
 from rdkit.Chem import Mol, MolFromSmarts, MolFromSmiles  # type: ignore
 from starlette.responses import Response
 
 
 class SmilesMolecule(str):
     """We can't directly extend mol, as this would break swagger"""
 
-    parsers: ClassVar = [MolFromSmiles]
-    _mol: Mol
-
-    @property
-    def mol(self):
-        return self._mol
+    @classmethod
+    def __get_pydantic_core_schema__(
+        cls,
+        _source: type[Any],
+        _handler: GetCoreSchemaHandler,
+    ) -> core_schema.CoreSchema:
+        return core_schema.no_info_after_validator_function(cls._validate, core_schema.str_schema())
 
     @classmethod
-    def __get_validators__(cls):
-        yield cls.validate
+    def __get_pydantic_json_schema__(cls, core_schema: core_schema.CoreSchema, handler: GetJsonSchemaHandler) -> JsonSchemaValue:
+        field_schema = handler(core_schema)
+        field_schema.update(type="string", format="email")
+        return field_schema
 
     @classmethod
-    def validate(cls, value: str | None) -> "SmilesMolecule":
+    def _validate(cls, input_value: str, /) -> "SmilesMolecule":
         for parser in cls.parsers:
-            mol = parser(value)
+            mol = parser(input_value)
             if mol:
-                sm = SmilesMolecule(value)
+                sm = SmilesMolecule(input_value)
                 sm._mol = mol
                 return sm
         else:
             raise ValueError("Unparsable smiles")
 
+    parsers: ClassVar = [MolFromSmiles]
+    _mol: Mol
+
+    @property
+    def mol(self):
+        return self._mol
+
 
 class SmilesSmartsMolecule(SmilesMolecule):
     """Try parings smiles first, then smarts"""

visyn_core/security/manager.py

@@ -111,7 +111,7 @@ def _delegate_stores_until_not_none(self, store_method_name: str, *args):
             method = getattr(store, store_method_name, None)
             if callable(method):
                 try:
-                    value = method(*args)
+                    value: User | None = method(*args)  # type: ignore
                 except Exception:
                     _log.exception(f"Error executing {store_method_name} in {store}")
                 else:

visyn_core/server/utils.py

@@ -39,7 +39,7 @@ def _init_legacy_app(app: Flask):
         if manager.settings.visyn_core:
             app.config["SECRET_KEY"] = manager.settings.secret_key
 
-        @app.errorhandler(FlaskHTTPException)
+        @app.errorhandler(FlaskHTTPException)  # type: ignore
         @app.errorhandler(Exception)  # type: ignore
         async def handle_exception(e):
             """Handles Flask exceptions by returning the same JSON response as FastAPI#HTTPException would."""

visyn_core/server/visyn_server.py

@@ -6,8 +6,8 @@
 
 from fastapi import FastAPI
 from fastapi.middleware.wsgi import WSGIMiddleware
-from pydantic import create_model
-from pydantic.utils import deep_update
+from pydantic.v1 import create_model
+from pydantic.v1.utils import deep_update
 from starlette_context.middleware import RawContextMiddleware
 
 from ..settings.constants import default_logging_dict

visyn_core/settings/model.py

@@ -1,8 +1,8 @@
 import contextlib
 from typing import Any, Literal
 
-from pydantic import AnyHttpUrl, BaseConfig, BaseModel, BaseSettings, Extra, Field
-from pydantic.env_settings import EnvSettingsSource, SettingsSourceCallable
+from pydantic.v1 import AnyHttpUrl, BaseConfig, BaseModel, BaseSettings, Extra, Field
+from pydantic.v1.env_settings import EnvSettingsSource, SettingsSourceCallable
 
 from .constants import default_logging_dict
 
@@ -12,13 +12,13 @@ class DBMigrationSettings(BaseModel):
 
 
 class DisableSettings(BaseModel):
-    plugins: list[str] = []
-    extensions: list[str] = []
+    plugins: list[str] = []  # NOQA RUF012
+    extensions: list[str] = []  # NOQA RUF012
 
 
 class DummyStoreSettings(BaseModel):
     enable: bool = False
-    users: list[dict[str, Any]] = [
+    users: list[dict[str, Any]] = [  # NOQA RUF012
         {
             "name": "admin",
             "salt": "dcf46ce914154a44b1557eba91c1f50d",
@@ -44,7 +44,7 @@ class AlbSecurityStoreSettings(BaseModel):
     enable: bool = False
     cookie_name: str | None = None
     signout_url: str | None = None
-    email_token_field: str | list[str] = ["email"]
+    email_token_field: str | list[str] = ["email"]  # NOQA RUF012
     """
     Field in the JWT token that contains the email address of the user.
     """
@@ -65,7 +65,7 @@ class AlbSecurityStoreSettings(BaseModel):
     """
     The region of the ALB to fetch the public key from.
     """
-    decode_algorithms: list[str] = ["ES256"]
+    decode_algorithms: list[str] = ["ES256"]  # NOQA RUF012
     """
     The algorithm used to sign the JWT token. See https://pyjwt.readthedocs.io/en/stable/algorithms.html for details.
     """
@@ -76,13 +76,13 @@ class OAuth2SecurityStoreSettings(BaseModel):
     cookie_name: str | None = None
     signout_url: str | None = None
     access_token_header_name: str = "X-Forwarded-Access-Token"
-    email_token_field: str | list[str] = ["email"]
+    email_token_field: str | list[str] = ["email"]  # NOQA RUF012
 
 
 class NoSecurityStoreSettings(BaseModel):
     enable: bool = False
     user: str = "admin"
-    roles: list[str] = []
+    roles: list[str] = []  # NOQA RUF012
 
 
 class SecurityStoreSettings(BaseModel):
@@ -108,7 +108,7 @@ class BaseExporterTelemetrySettings(BaseModel):
     endpoint: AnyHttpUrl  # could be "http://localhost:4318"
     headers: dict[str, str] | None = None
     timeout: int | None = None
-    kwargs: dict[str, Any] = {}
+    kwargs: dict[str, Any] = {}  # NOQA RUF012
 
 
 class MetricsExporterTelemetrySettings(BaseExporterTelemetrySettings):
@@ -163,7 +163,7 @@ class SentrySettings(BaseModel):
     """
     Proxy Sentry envelopes to this URL. Used if an internal Sentry server is used, otherwise the original DSN is used.
     """
-    server_init_options: dict[str, Any] = {}
+    server_init_options: dict[str, Any] = {}  # NOQA RUF012
     """
     Options to be passed to the Sentry SDK during initialization.
     """
@@ -198,7 +198,7 @@ class VisynCoreSettings(BaseModel):
     """
 
     disable: DisableSettings = DisableSettings()
-    enabled_plugins: list[str] = []
+    enabled_plugins: list[str] = []  # NOQA RUF012
 
     # TODO: Proper typing. This is 1:1 passed to the logging.config.dictConfig(...).
     logging: dict = Field(default_logging_dict)
@@ -231,7 +231,7 @@ class GlobalSettings(BaseSettings):
     secret_key: str = "VERY_SECRET_STUFF_T0IB84wlQrdMH8RVT28w"
 
     # JWT options mostly inspired by flask-jwt-extended: https://flask-jwt-extended.readthedocs.io/en/stable/options/#general-options
-    jwt_token_location: list[str] = ["headers", "cookies"]
+    jwt_token_location: list[str] = ["headers", "cookies"]  # NOQA RUF012
     jwt_expire_in_seconds: int = 24 * 60 * 60
     jwt_refresh_if_expiring_in_seconds: int = 30 * 60
     jwt_algorithm: str = "HS256"

visyn_core/telemetry/__init__.py

@@ -57,9 +57,9 @@ def filter(self, record: logging.LogRecord) -> bool:
                     exporter=OTLPMetricExporter(
                         # If we are using the global exporter settings, append the metrics path
                         endpoint=(
-                            _append_metrics_path(exporter_settings.endpoint)
+                            _append_metrics_path(str(exporter_settings.endpoint))
                             if exporter_settings == global_exporter_settings
-                            else exporter_settings.endpoint
+                            else str(exporter_settings.endpoint)
                         ),
                         headers=exporter_settings.headers,
                         timeout=exporter_settings.timeout,
@@ -123,9 +123,9 @@ def deprecated_prometheus_metrics():
                     OTLPSpanExporter(
                         # If we are using the global exporter settings, append the traces path
                         endpoint=(
-                            _append_trace_path(exporter_settings.endpoint)
+                            _append_trace_path(str(exporter_settings.endpoint))
                             if exporter_settings == global_exporter_settings
-                            else exporter_settings.endpoint
+                            else str(exporter_settings.endpoint)
                         ),
                         headers=exporter_settings.headers,
                         timeout=exporter_settings.timeout,
@@ -168,9 +168,9 @@ def shutdown_tracer_event():
                     OTLPLogExporter(
                         # If we are using the global exporter settings, append the logs path
                         endpoint=(
-                            _append_logs_path(exporter_settings.endpoint)
+                            _append_logs_path(str(exporter_settings.endpoint))
                             if exporter_settings == global_exporter_settings
-                            else exporter_settings.endpoint
+                            else str(exporter_settings.endpoint)
                         ),
                         headers=exporter_settings.headers,
                         timeout=exporter_settings.timeout,