feat: migrate to Pydantic v2 (#656)

* Upgrade to pydantic v2
* Replace deprecated dict with model_dump
* Replace update_forward_refs with model_rebuild
* Fix error message in test
* Fix Packages and ChannelSearch rest models

- platforms is nullable: it should be optional
- Channel description is optional - so should be ChannelSearch description

* Fix Job rest model

item_spec can't be set to required in JobBase and optional in Job
(mypy complains).
Create a new class JobCreate where item_spec is required.
In job, item_spec is optional.

* Add UserOptionalRole

User role is nullable and should be optional in get (but not in set)

* Remove nullable=True in pydantic Field

This isn't used.
To mark a field as nullable, it should be set as Optional or "| None".

Fix deprecation warning: Extra keyword arguments on `Field` is deprecated and will be removed.

* Fix Channel model

keyword should be examples (not example)

* Replace deprecated from_orm with model_validate

* Replace deprecated parse_obj with model_validate

* Fix UserWarning

UserWarning: `pydantic.error_wrappers:ValidationError` has been moved to `pydantic:ValidationError`.

* Fix test_post_new_job_invalid_items_spec

* Fix starlette Deprecation Warning

DeprecationWarning: The `allow_redirects` argument is deprecated. Use `follow_redirects` instead.

* Increase wait time for running task tests

Test failing with postgres. Task still pending after 2.5 seconds.

environment.yml

@@ -50,6 +50,6 @@ dependencies:
   - conda-content-trust
   - pyinstrument
   - pytest-asyncio
-  - pydantic <2
+  - pydantic >=2
   - pip:
       - git+https://github.com/jupyter-server/jupyter_releaser.git@v2

quetz/db_models.py

@@ -55,7 +55,7 @@ class User(Base):
         'Profile', uselist=False, back_populates='user', cascade="all,delete-orphan"
     )
 
-    role = Column(String)
+    role = Column(String, nullable=True)
 
     @classmethod
     def find(cls, db, name):

quetz/jobs/api.py

@@ -17,7 +17,7 @@
 from quetz.rest_models import PaginatedResponse
 
 from .models import JobStatus, TaskStatus
-from .rest_models import Job, JobBase, JobUpdateModel, Task
+from .rest_models import Job, JobCreate, JobUpdateModel, Task
 
 api_router = APIRouter()
 
@@ -44,7 +44,7 @@ def get_jobs(
 
 @api_router.post("/api/jobs", tags=["Jobs"], status_code=201, response_model=Job)
 def create_job(
-    job: JobBase,
+    job: JobCreate,
     dao: Dao = Depends(get_dao),
     auth: authorization.Rules = Depends(get_rules),
 ):

quetz/jobs/rest_models.py

@@ -5,7 +5,7 @@
 from typing import Optional
 
 from importlib_metadata import entry_points as get_entry_points
-from pydantic import BaseModel, Field, validator
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
 from . import handlers
 from .models import JobStatus, TaskStatus
@@ -83,7 +83,6 @@ def parse_job_name(v):
 class JobBase(BaseModel):
     """New job spec"""
 
-    items_spec: str = Field(..., title='Item selector spec')
     manifest: str = Field(None, title='Name of the function')
 
     start_at: Optional[datetime] = Field(
@@ -97,7 +96,8 @@ class JobBase(BaseModel):
         ),
     )
 
-    @validator("manifest", pre=True)
+    @field_validator("manifest", mode="before")
+    @classmethod
     def validate_job_name(cls, function_name):
         if isinstance(function_name, bytes):
             return parse_job_name(function_name)
@@ -107,6 +107,12 @@ def validate_job_name(cls, function_name):
         return function_name.encode('ascii')
 
 
+class JobCreate(JobBase):
+    """Create job spec"""
+
+    items_spec: str = Field(..., title='Item selector spec')
+
+
 class JobUpdateModel(BaseModel):
     """Modify job spec items (status and items_spec)"""
 
@@ -123,10 +129,8 @@ class Job(JobBase):
 
     status: JobStatus = Field(None, title='Status of the job (running, paused, ...)')
 
-    items_spec: str = Field(None, title='Item selector spec')
-
-    class Config:
-        orm_mode = True
+    items_spec: Optional[str] = Field(None, title='Item selector spec')
+    model_config = ConfigDict(from_attributes=True)
 
 
 class Task(BaseModel):
@@ -136,12 +140,12 @@ class Task(BaseModel):
     created: datetime = Field(None, title='Created at')
     status: TaskStatus = Field(None, title='Status of the task (running, paused, ...)')
 
-    @validator("package_version", pre=True)
+    @field_validator("package_version", mode="before")
+    @classmethod
     def convert_package_version(cls, v):
         if v:
             return {'filename': v.filename, 'id': uuid.UUID(bytes=v.id).hex}
         else:
             return {}
 
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)

quetz/main.py

@@ -17,7 +17,6 @@
 from typing import Awaitable, Callable, List, Optional, Tuple, Type
 
 import pydantic
-import pydantic.error_wrappers
 import requests
 from fastapi import (
     APIRouter,
@@ -477,7 +476,7 @@ def delete_user(
 
 @api_router.get(
     "/users/{username}/role",
-    response_model=rest_models.UserRole,
+    response_model=rest_models.UserOptionalRole,
     tags=["users"],
 )
 def get_user_role(
@@ -732,7 +731,7 @@ def post_channel(
             detail="Cannot use both `includelist` and `excludelist` together.",
         )
 
-    user_attrs = new_channel.dict(exclude_unset=True)
+    user_attrs = new_channel.model_dump(exclude_unset=True)
 
     if "size_limit" in user_attrs:
         auth.assert_set_channel_size_limit()
@@ -789,7 +788,7 @@ def patch_channel(
 ):
     auth.assert_update_channel_info(channel.name)
 
-    user_attrs = channel_data.dict(exclude_unset=True)
+    user_attrs = channel_data.model_dump(exclude_unset=True)
 
     if "size_limit" in user_attrs:
         auth.assert_set_channel_size_limit()
@@ -1064,7 +1063,7 @@ def get_package_versions(
     version_list = []
 
     for version, profile, api_key_profile in version_profile_list:
-        version_data = rest_models.PackageVersion.from_orm(version)
+        version_data = rest_models.PackageVersion.model_validate(version)
         version_list.append(version_data)
 
     return version_list
@@ -1089,7 +1088,7 @@ def get_paginated_package_versions(
     version_list = []
 
     for version, profile, api_key_profile in version_profile_list['result']:
-        version_data = rest_models.PackageVersion.from_orm(version)
+        version_data = rest_models.PackageVersion.model_validate(version)
         version_list.append(version_data)
 
     return {
@@ -1650,7 +1649,7 @@ def _delete_file(condainfo, filename):
                     summary=str(condainfo.about.get("summary", "n/a")),
                     description=str(condainfo.about.get("description", "n/a")),
                 )
-            except pydantic.error_wrappers.ValidationError as err:
+            except pydantic.ValidationError as err:
                 _delete_file(condainfo, file.filename)
                 raise errors.ValidationError(
                     "Validation Error for package: "

quetz/metrics/rest_models.py

@@ -1,17 +1,15 @@
 from datetime import datetime
 from typing import Dict, List
 
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field
 
 from quetz.metrics.db_models import IntervalType
 
 
 class PackageVersionMetricItem(BaseModel):
     timestamp: datetime
     count: int
-
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 class PackageVersionMetricSeries(BaseModel):