chore: bump pydantic to >2.0

requirements.txt

@@ -21,7 +21,7 @@ numpy>=1.16.5,<1.24.0
 pandas<=2.0.3
 protobuf<3.20
 pyarrow>=8.0.0
-pydantic>=1.7.3,<2.0.0
+pydantic>=2.0.0
 pymatgen>=2022.11.7
 PyTDC==0.3.7
 pytorch_lightning<=1.7.7

src/gt4sd/configuration.py

@@ -28,9 +28,8 @@
 from functools import lru_cache
 from typing import Dict, Optional, Set
 
-from pydantic import BaseSettings
-
 from .s3 import GT4SDS3Client, S3SyncError, sync_folder_with_s3, upload_file_to_s3
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
@@ -65,10 +64,7 @@ class GT4SDConfiguration(BaseSettings):
  gt4sd_s3_secure_hub: bool = True
  gt4sd_s3_bucket_hub_algorithms: str = "gt4sd-cos-hub-algorithms-artifacts"
  gt4sd_s3_bucket_hub_properties: str = "gt4sd-cos-hub-properties-artifacts"
-
- class Config:
- # immutable and in turn hashable, that is required for lru_cache
- frozen = True
+ model_config = SettingsConfigDict(frozen=True)
 
  @staticmethod
  @lru_cache(maxsize=None)

src/gt4sd/properties/core.py

@@ -47,19 +47,19 @@ class S3Parameters(PropertyPredictorParameters):
  algorithm_type: str = "prediction"
 
  domain: DomainSubmodule = Field(
- ..., example="molecules", description="Submodule of gt4sd.properties"
+ ..., examples=["molecules"], description="Submodule of gt4sd.properties"
  )
- algorithm_name: str = Field(..., example="MCA", description="Name of the algorithm")
+ algorithm_name: str = Field(..., examples=["MCA"], description="Name of the algorithm")
  algorithm_version: str = Field(
- ..., example="v0", description="Version of the algorithm"
+ ..., examples=["v0"], description="Version of the algorithm"
  )
- algorithm_application: str = Field(..., example="Tox21")
+ algorithm_application: str = Field(..., examples=["Tox21"])
 
 
 class ApiTokenParameters(PropertyPredictorParameters):
  api_token: str = Field(
  ...,
- example="apk-c9db......",
+ examples=["apk-c9db......"],
  description="The API token/key to access the service",
  )
 
@@ -68,7 +68,7 @@ class IpAdressParameters(PropertyPredictorParameters):
 
  host_ip: str = Field(
  ...,
- example="xx.xx.xxx.xxx",
+ examples=["xx.xx.xxx.xxx"],
  description="The host IP address to access the service",
  )
 

src/gt4sd/properties/molecules/core.py

@@ -59,7 +59,7 @@
 from paccmann_generator.drug_evaluators import OrganDB as _OrganTox
 from paccmann_generator.drug_evaluators import SCScore
 from paccmann_generator.drug_evaluators import Tox21 as _Tox21
-from pydantic import Field
+from pydantic import ConfigDict, Field
 from tdc import Oracle
 from tdc.metadata import download_receptor_oracle_name
 
@@ -119,12 +119,12 @@ class ScscoreConfiguration(PropertyPredictorParameters):
 
 
 class SimilaritySeedParameters(PropertyPredictorParameters):
- smiles: str = Field(..., example="c1ccccc1")
+ smiles: str = Field(..., examples=["c1ccccc1"])
  fp_key: str = "ECFP4"
 
 
 class ActivityAgainstTargetParameters(PropertyPredictorParameters):
- target: str = Field(..., example="drd2", description="name of the target.")
+ target: str = Field(..., examples=["drd2"], description="name of the target.")
 
 
 class AskcosParameters(IpAdressParameters):
@@ -136,7 +136,7 @@ class Output(str, Enum):
 
  output: Output = Field(
  default=Output.plausability,
- example=Output.synthesizability,
+ examples=[Output.synthesizability],
  description="Main output return type from ASKCOS",
  options=["plausibility", "num_step", "synthesizability", "price"],
  )
@@ -159,10 +159,7 @@ class Output(str, Enum):
  min_chempop_products: int = Field(default=5)
  filter_threshold: float = Field(default=0.1)
  return_first: str = Field(default="true")
-
- # Convert enum items back to strings
- class Config:
- use_enum_values = True
+ model_config = ConfigDict(use_enum_values=True)
 
 
 class MoleculeOneParameters(ApiTokenParameters):
@@ -174,7 +171,7 @@ class DockingTdcParameters(PropertyPredictorParameters):
  # To dock against a receptor defined via TDC
  target: str = Field(
  ...,
- example="1iep_docking",
+ examples=["1iep_docking"],
  description="Target for docking, provided via TDC",
  options=download_receptor_oracle_name,
  )
@@ -184,12 +181,12 @@ class DockingParameters(PropertyPredictorParameters):
  # To dock against a user-provided receptor
  name: str = Field(default="pyscreener")
  receptor_pdb_file: str = Field(
- example="/tmp/2hbs.pdb", description="Path to receptor PDB file"
+ examples=["/tmp/2hbs.pdb"], description="Path to receptor PDB file"
  )
  box_center: List[int] = Field(
- example=[15.190, 53.903, 16.917], description="Docking box center"
+ examples=[[15.190, 53.903, 16.917]], description="Docking box center"
  )
- box_size: List[float] = Field(example=[20, 20, 20], description="Docking box size")
+ box_size: List[float] = Field(examples=[[20, 20, 20]], description="Docking box size")
 
 
 class S3ParametersMolecules(S3Parameters):
@@ -265,12 +262,12 @@ class ToxType(str, Enum):
  algorithm_application: str = "OrganTox"
  site: Organs = Field(
  ...,
- example=Organs.kidney,
+ examples=[Organs.kidney],
  description="name of the target site of interest.",
  )
  toxicity_type: ToxType = Field(
  default=ToxType.all,
- example=ToxType.chronic,
+ examples=[ToxType.chronic],
  description="type of toxicity for which predictions are made.",
  options=["chronic", "subchronic", "multigenerational", "all"],
  )

src/gt4sd/properties/proteins/core.py

@@ -46,7 +46,7 @@
 class AmideConfiguration(PropertyPredictorParameters):
  amide: bool = Field(
  False,
- example=False,
+ examples=[False],
  description="whether the sequences are C-terminally amidated.",
  )
 
@@ -58,7 +58,7 @@ class PhConfiguration(PropertyPredictorParameters):
 class AmidePhConfiguration(PropertyPredictorParameters):
  amide: bool = Field(
  False,
- example=False,
+ examples=[False],
  description="whether the sequences are C-terminally amidated.",
  )
  ph: float = 7.0

src/gt4sd/tests/utils.py

@@ -29,7 +29,7 @@
 from pathlib import PosixPath
 
 import importlib_resources
-from pydantic import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
 class GT4SDTestSettings(BaseSettings):
@@ -40,10 +40,7 @@ class GT4SDTestSettings(BaseSettings):
  gt4sd_s3_secret_key: str = "5748375c761a4f09c30a68cd15e218e3b27ca3e2aebd7726"
  gt4sd_s3_secure: bool = True
  gt4sd_ci: bool = False
-
- class Config:
- # immutable and in turn hashable, that is required for lru_cache
- frozen = True
+ model_config = SettingsConfigDict(frozen=True)
 
  @staticmethod
  @lru_cache(maxsize=None)