Bumping pydantic >= 2.0.0 (#247)

* chore: bump pydantic to >2.0

* chore: black

* chore: mypy checks

* chore : remove duplication of options/examples

* chore: add pydantic_settings

* fix: pydantic error

* chore: mypy

* fix: mock on subclass __parameters__

* chore

* fix: tests for registry

* chore: black

* fix: ignore mypy

* chore: black

* fix: move deps from dev to main requirements file

* fix: absolute imports before relative

---------

Co-authored-by: fiskrt <[email protected]>

dev_requirements.txt

@@ -12,5 +12,4 @@ pytest==6.2.5
 pytest-cov==2.10.1
 sphinx>=5
 sphinx-autodoc-typehints==1.11.1
-jinja2<3.1.0
-sphinx_rtd_theme==0.5.1
+jinja2<3.1.0

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
@@ -49,3 +49,5 @@ transformers>=4.22.0,<=4.24.0
 typing_extensions>=3.7.4.3
 wheel>=0.26
 xgboost>=1.7.6
+sphinx_rtd_theme==0.5.1
+pydantic-settings>=2.0.0

setup.cfg

@@ -290,4 +290,7 @@ ignore_missing_imports = True
 ignore_missing_imports = True
 
 [mypy-xgboost.*]
+ignore_missing_imports = True
+
+[mypy-pydantic_settings.*]
 ignore_missing_imports = True

src/gt4sd/__init__.py

@@ -23,7 +23,7 @@
 #
 """Module initialization."""
 
-__version__ = "1.4.1"
+__version__ = "1.4.2"
 __name__ = "gt4sd"
 
 # NOTE: configure SSL to allow unverified contexts by default

src/gt4sd/algorithms/core.py

@@ -912,8 +912,6 @@ def get_configuration_class_with_attributes(
 
 
 class PropertyPredictor(ABC, Generic[S, U]):
- """TODO: Might be deprecated in future release."""
-
  def __init__(self, context: U) -> None:
  """Property predictor to investigate items.
 

src/gt4sd/algorithms/registry.py

@@ -28,7 +28,17 @@
 from dataclasses import dataclass as vanilla_dataclass
 from dataclasses import field, make_dataclass
 from functools import WRAPPER_ASSIGNMENTS, update_wrapper
-from typing import Any, Callable, ClassVar, Dict, List, NamedTuple, Optional, Type
+from typing import (
+ Any,
+ Callable,
+ ClassVar,
+ Dict,
+ List,
+ NamedTuple,
+ Optional,
+ Type,
+ TypeVar,
+)
 
 import pydantic
 
@@ -185,6 +195,8 @@ def decorator(
  ),
  ], # type: ignore
  )
+ # NOTE: Needed to circumvent a pydantic TypeError: Parameter list to Generic[...] cannot be empty
+ VanillaConfiguration.__parameters__ = (TypeVar("T"),) # type: ignore
  # NOTE: Duplicate call necessary for pydantic >=1.10.* - see https://github.com/pydantic/pydantic/issues/4695
  PydanticConfiguration: Type[AlgorithmConfiguration] = dataclass( # type: ignore
  VanillaConfiguration

src/gt4sd/algorithms/tests/test_registry.py

@@ -58,19 +58,15 @@ def test_list_available_local_via_S3SyncError(mock_wrong_s3_env):
 
 def test_inherited_validation():
  Config = next(iter(ApplicationsRegistry.applications.values())).configuration_class
- with pytest.raises(
- ValidationError, match="algorithm_version\n +none is not an allowed value"
- ):
+ with pytest.raises(ValidationError, match="should be a valid string"):
  Config(algorithm_version=None) # type: ignore
 
- # NOTE: values convertible to string will not raise!
- Config(algorithm_version=5) # type: ignore
+ with pytest.raises(ValidationError, match="should be a valid string"):
+  Config(algorithm_version=5) # type: ignore
 
 
 def test_validation():
- with pytest.raises(
- ValidationError, match="batch_size\n +value is not a valid integer"
- ):
+ with pytest.raises(ValidationError, match="should be a valid integer"):
  ApplicationsRegistry.get_configuration_instance(
  algorithm_type="conditional_generation",
  domain="materials",
@@ -80,25 +76,6 @@ def test_validation():
  )
 
 
-def test_pickable_wrapped_configurations():
- # https://github.com/samuelcolvin/pydantic/issues/2111
- Config = next(iter(ApplicationsRegistry.applications.values())).configuration_class
- restored_obj = assert_pickable(Config(algorithm_version="test"))
-
- # wrong type assignment, but we did not configure it to raise here:
- restored_obj.algorithm_version = object
- # ensure the restored dataclass is still a pydantic dataclass (mimic validation)
- _, optional_errors = restored_obj.__pydantic_model__.__fields__.get(
- "algorithm_version"
- ).validate(
- restored_obj.algorithm_version,
- restored_obj.__dict__,
- loc="algorithm_version",
- cls=restored_obj.__class__,
- )
- assert optional_errors is not None
-
-
 def test_multiple_registration():
  class OtherAlgorithm(GeneratorAlgorithm):
  pass

src/gt4sd/configuration.py

@@ -27,8 +27,7 @@
 import os
 from functools import lru_cache
 from typing import Dict, Optional, Set
-
-from pydantic import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from .s3 import GT4SDS3Client, S3SyncError, sync_folder_with_s3, upload_file_to_s3
 
@@ -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 +47,21 @@ 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(
+ ..., examples=["MCA"], description="Name of the algorithm"
  )
- algorithm_name: str = Field(..., example="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 +70,7 @@ 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):
@@ -136,9 +136,8 @@ 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"],
  )
  save_json: bool = Field(default=False)
  file_name: str = Field(default="tree_builder_result.json")
@@ -159,10 +158,7 @@ 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):
@@ -174,22 +170,23 @@ class DockingTdcParameters(PropertyPredictorParameters):
  # To dock against a receptor defined via TDC
  target: str = Field(
  ...,
- example="1iep_docking",
+ examples=download_receptor_oracle_name,
  description="Target for docking, provided via TDC",
- options=download_receptor_oracle_name,
  )
 
 
 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(
+ examples=[[20, 20, 20]], description="Docking box size"
  )
- box_size: List[float] = Field(example=[20, 20, 20], description="Docking box size")
 
 
 class S3ParametersMolecules(S3Parameters):
@@ -265,14 +262,13 @@ 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)