chore: update pydantic dependency

deepsearch/chemistry/queries/molecules.py

@@ -1,7 +1,7 @@
 from enum import Enum
 from typing import List, Union
 
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 from deepsearch.cps.client.queries import Query
 

deepsearch/core/cli/profile.py

@@ -43,7 +43,7 @@ def add_profile(
     profile_settings = ProfileSettings(
         host=host,
         username=username,
-        api_key=api_key,
+        api_key=api_key,  # type: ignore[arg-type]
         verify_ssl=verify_ssl,
     )
 

deepsearch/core/client/config.py

@@ -1,6 +1,6 @@
 from typing import Union
 
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 
 class DeepSearchBearerTokenAuth(BaseModel):

deepsearch/core/client/settings.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Dict, Optional, Union
 
-from pydantic import BaseSettings, SecretStr
+from pydantic.v1 import BaseSettings, SecretStr
 
 
 class DumpableSettings(BaseSettings):
@@ -47,8 +47,8 @@ def from_cli_prompt(cls) -> ProfileSettings:
         return cls(
             host=input("Host: "),
             username=input("Username: "),
-            api_key=getpass("API key: "),
-            verify_ssl=input("SSL verification [y/n]: "),
+            api_key=getpass("API key: "),  # type: ignore[arg-type]
+            verify_ssl=input("SSL verification [y/n]: "),  # type: ignore[arg-type]
         )
 
 

deepsearch/core/client/settings_manager.py

@@ -5,7 +5,7 @@
 from typing import Dict, List, Optional
 
 import platformdirs
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from deepsearch.core.cli.profile_utils import (
     MSG_AMBIGUOUS_SUCCESSOR,
@@ -116,7 +116,7 @@ def _migrate_legacy_config(self) -> None:
                     new_cfg = ProfileSettings(
                         host=legacy_cfg.host,
                         username=legacy_cfg.auth.username,
-                        api_key=legacy_cfg.auth.api_key,
+                        api_key=legacy_cfg.auth.api_key,  # type: ignore[arg-type]
                         verify_ssl=legacy_cfg.verify_ssl,
                     )
                     self.save_settings(
@@ -144,7 +144,7 @@ def get_profile_settings(
         prfl_name = profile_name or self.get_active_profile()
         if prfl_name is None:
             try:  # try to instantiate from environment alone
-                return ProfileSettings()
+                return ProfileSettings()  # type: ignore[call-arg]
             except ValidationError:
                 if len(self._profile_cache) == 0:
                     raise RuntimeError(MSG_NO_PROFILES_DEFINED)

deepsearch/cps/client/api.py

@@ -3,7 +3,7 @@
 from typing import Optional
 
 import requests
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 import deepsearch.cps.apis.user
 from deepsearch.core.client import (
@@ -165,7 +165,7 @@ def from_env(cls, profile_name: Optional[str] = None) -> CpsApi:
             CpsApi: the created API object
         """
         try:
-            settings = ProfileSettings()
+            settings = ProfileSettings()  # type: ignore[call-arg]
         except ValidationError:
             settings_mgr = SettingsManager()
             settings = settings_mgr.get_profile_settings(profile_name=profile_name)

deepsearch/cps/client/components/data_indices.py

@@ -8,7 +8,7 @@
 from urllib.parse import urlparse
 
 import requests
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 from deepsearch.cps.apis import public as sw_client
 from deepsearch.cps.apis.public.models.attachment_upload_data import (

deepsearch/cps/client/components/elastic.py

@@ -3,7 +3,7 @@
 import datetime
 from typing import TYPE_CHECKING, Any, Dict, List, Union
 
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 from deepsearch.cps.apis import public as sw_client
 from deepsearch.cps.client.components.data_indices import (

deepsearch/cps/client/components/projects.py

@@ -4,7 +4,7 @@
 from enum import Enum
 from typing import TYPE_CHECKING, List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 import deepsearch.cps.apis.user
 from deepsearch.cps.apis.user.models.token_response import TokenResponse

deepsearch/cps/client/components/uploader.py

@@ -4,7 +4,7 @@
 from typing import TYPE_CHECKING, Union
 
 import requests
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 from deepsearch.cps.apis import public as sw_client
 from deepsearch.cps.apis.public.models.temporary_upload_file_result import (

deepsearch/documents/core/lookup.py

@@ -1,6 +1,6 @@
 from typing import Any, Dict, List
 
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 
 def _resolve_item(item, doc):

deepsearch/documents/core/models.py

@@ -3,7 +3,7 @@
 from textwrap import dedent
 from typing import ClassVar, Dict, List, Literal, Optional, Set, Union, get_args
 
-from pydantic import BaseModel, Field, ValidationError, conlist, parse_obj_as
+from pydantic.v1 import BaseModel, Field, ValidationError, conlist, parse_obj_as
 
 from deepsearch import CpsApi
 from deepsearch.core.util.ccs_utils import get_ccs_project_key
@@ -31,13 +31,13 @@ class S3Coordinates(BaseModel):
         "",
         description=dedent(
             """
-            Control the infix of the object keys that are saved on the document's `_s3_data`, after `key_prefix`, 
+            Control the infix of the object keys that are saved on the document's `_s3_data`, after `key_prefix`,
             and before `PDFDocuments/{document_hash}.pdf` or `PDFPages/{page_hash}.pdf`.
 
             By default, the infix is empty.
             For using the name of the index in the coordinates, you can use `key_infix_format = "{index_name}"`.
 
-            For example, if: 
+            For example, if:
 
             ```
             key_prefix = "my_prefix/"
@@ -577,8 +577,6 @@ class ConversionSettings(BaseModel):
 
     @classmethod
     def from_project(cls, api: CpsApi, proj_key: str) -> "ConversionSettings":
-        conv_settings = cls()
-
         proj_key, _ = get_ccs_project_key(api, proj_key)
 
         request_conv_settings = api.client.session.get(
@@ -587,34 +585,36 @@ def from_project(cls, api: CpsApi, proj_key: str) -> "ConversionSettings":
         request_conv_settings.raise_for_status()
         settings_dict = request_conv_settings.json()
 
-        conv_settings.pipeline = ConversionPipelineSettings.from_ccs_spec(
+        pipeline = ConversionPipelineSettings.from_ccs_spec(
             settings_dict.get("model_pipeline")
         )
-        conv_settings.ocr = OCRSettings.from_ccs_spec(settings_dict.get("ocr"))
-        conv_settings.metadata = ConversionMetadata.from_ccs_spec(
-            settings_dict.get("metadata")
+        ocr = OCRSettings.from_ccs_spec(settings_dict.get("ocr"))
+        metadata = ConversionMetadata.from_ccs_spec(settings_dict.get("metadata"))
+        return cls(
+            pipeline=pipeline,
+            ocr=ocr,
+            metadata=metadata,
         )
-        return conv_settings
 
     @classmethod
     def from_defaults(cls, api: CpsApi) -> "ConversionSettings":
-        conv_settings = cls()
-
         request_conv_settings = api.client.session.get(
             url=URLNavigator(api).url_conversion_defaults()
         )
         request_conv_settings.raise_for_status()
         settings_dict = request_conv_settings.json()
 
-        conv_settings.pipeline = ConversionPipelineSettings.from_ccs_spec(
+        pipeline = ConversionPipelineSettings.from_ccs_spec(
             settings_dict.get("model_pipeline")
         )
-        conv_settings.ocr = OCRSettings.from_ccs_spec(settings_dict.get("ocr"))
-        conv_settings.metadata = ConversionMetadata.from_ccs_spec(
-            settings_dict.get("metadata")
-        )
+        ocr = OCRSettings.from_ccs_spec(settings_dict.get("ocr"))
+        metadata = ConversionMetadata.from_ccs_spec(settings_dict.get("metadata"))
 
-        return conv_settings
+        return cls(
+            pipeline=pipeline,
+            ocr=ocr,
+            metadata=metadata,
+        )
 
     def to_ccs_spec(self):
         obj = {}

deepsearch/documents/core/utils.py

@@ -9,7 +9,7 @@
 from typing import Any, Dict, Iterator, List
 
 import requests
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 from tqdm import tqdm
 
 from deepsearch.cps.client.api import CpsApi

deepsearch/model/base/types.py

@@ -2,7 +2,7 @@
 from enum import Enum
 from typing import Any, Dict, Optional
 
-from pydantic import BaseModel, Extra, Field, PositiveFloat
+from pydantic.v1 import BaseModel, Extra, Field, PositiveFloat
 
 
 class StrictModel(BaseModel, extra=Extra.forbid):

deepsearch/model/examples/dummy_nlp_annotator/model.py

@@ -23,7 +23,7 @@ def __init__(self) -> None:
             kind=Kind.NLPModel,
             name="DummyNLPAnnotator",
             version="0.1.0",
-            supported_types=["text"],
+            supported_types=["text"],  # type: ignore[list-item]
             labels=self._generate_labels(),
         )
 

deepsearch/model/kinds/nlp/controller.py

@@ -29,16 +29,16 @@ def __init__(self, model: BaseNLPModel):
     def get_info(self) -> NLPInfoOutput:
         cfg = self._model.get_nlp_config()
         metadata = NLPModelMetadata(
-            supported_object_types=cfg.supported_types,
+            supported_object_types=cfg.supported_types,  # type: ignore[arg-type]
             **self._get_metadata().dict(),  # passing parent metadata dict as kwargs
         )
         spec = NLPInfoOutputDefinitionsSpec(
-            definition=cfg.labels,
+            definition=cfg.labels.dict(),
             metadata=metadata,
         )
         definitions = NLPInfoOutputDefinitions(
             apiVersion=self._get_api_version(),
-            kind=self.get_kind(),
+            kind=self.get_kind(),  # type: ignore[arg-type]
             spec=spec,
         )
         return NLPInfoOutput(definitions=definitions)

deepsearch/model/kinds/qagen/controller.py

@@ -24,7 +24,7 @@ def get_info(self) -> QAGenInfoOutput:
         )
         definitions = QAGenInfoOutputDefinitions(
             apiVersion=super()._get_api_version(),
-            kind=self.get_kind(),
+            kind=self.get_kind(),  # type: ignore[arg-type]
             spec=spec,
         )
         return QAGenInfoOutput(definitions=definitions)

deepsearch/model/kinds/qagen/types.py

@@ -1,6 +1,6 @@
 from typing import Any, Dict, List, Literal, Optional
 
-from pydantic import root_validator
+from pydantic.v1 import root_validator
 
 from deepsearch.model.base.types import (
     BaseAppPredInput,

deepsearch/model/server/config.py

@@ -1,4 +1,4 @@
-from pydantic import BaseSettings, SecretStr
+from pydantic.v1 import BaseSettings, SecretStr
 
 
 class Settings(BaseSettings):