Updating to sqlmodel 0.0.14

[nsheff]

This morning, sqlmodel with support for pydantic v2 was released. Not sure if we need to update anything, but we should adapt the pydantic 2 models.

[khoroshevskyi]

How much effort will it take to update pipestat to support pydantic2.0? I want to create a script, that will be making zip file with all geo peps, but unfortunately pepdbagent supports pydantic>2, and pephubclient pydantic<2. I can't update pephubclient, because if I update it, looper will be broken.

How fast can update it? @donaldcampbelljr do you have any ideas about his update?

[donaldcampbelljr]

I'll begin looking at this this afternoon or tomorrow and let you know if I'm running into any issues.

[donaldcampbelljr]

Some notes: -we are technically already using sqlmodel 0.014 in pipestat (but it supports backwards compatibility with pydantic 1) -installing pydantic 2.5.3 (newest version) causes pytest errors: sqlalchemy.exc.IntegrityError: (psycopg.errors.NotNullViolation) -pydantic has a tool to do migration https://docs.pydantic.dev/latest/migration/

• To check diffs: (venv) drc@databio:~/GITHUB/pipestat/pipestat$ bump-pydantic --diff ./pipestat/

Results:

[15:26:13] Start bump-pydantic.                                                                                                                                                                                               main.py:61
           Found 21 files to process.                                                                                                                                                                                         main.py:78
--- pipestat/backends/db_backend/db_parsed_schema.py
+++ pipestat/backends/db_backend/db_parsed_schema.py
@@ -5,7 +5,7 @@
 import logging
 from pathlib import Path
 from typing import Any, Dict, List, Mapping, Optional
-from pydantic import create_model
+from pydantic import ConfigDict, create_model

 from sqlalchemy import Column, null
 from sqlalchemy.dialects.postgresql import JSONB
@@ -54,9 +54,7 @@
 def get_base_model():
     class BaseModel(SQLModel):
         __table_args__ = {"extend_existing": True}
-
-        class Config:
-            arbitrary_types_allowed = True
+        model_config = ConfigDict(arbitrary_types_allowed=True)

     # return SQLModel
     return BaseModel
[15:26:27] Found 1 errors. Please check the log.txt file.

1 Error is related to https://github.com/pydantic/bump-pydantic/issues/124 and only affects the filebackend (which does not use sqlmodel, so it can be ignored).

After conversion, only db_parsed_schema.py modified, still getting sqlalchemy.exc.IntegrityError: (psycopg.errors.NotNullViolation), but it is the only errror at the moment.