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Fix deprecated class Config in pydantic models #359

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Merged
dweindl merged 1 commit into from
Mar 17, 2025
Merged

Fix deprecated class Config in pydantic models #359

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46 changes: 23 additions & 23 deletions petab/v2/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import sympy as sp
from pydantic import (
BaseModel,
ConfigDict,
Field,
ValidationInfo,
field_validator,
Expand Down Expand Up @@ -149,9 +150,9 @@ def sympify(cls, v):

return sympify_petab(v)

class Config:
populate_by_name = True
arbitrary_types_allowed = True
model_config = ConfigDict(
arbitrary_types_allowed=True, populate_by_name=True
)


class ObservablesTable(BaseModel):
Expand Down Expand Up @@ -224,10 +225,11 @@ class Change(BaseModel):
operation_type: OperationType = Field(alias=C.OPERATION_TYPE)
target_value: sp.Basic | None = Field(alias=C.TARGET_VALUE, default=None)

class Config:
populate_by_name = True
arbitrary_types_allowed = True
use_enum_values = True
model_config = ConfigDict(
arbitrary_types_allowed=True,
populate_by_name=True,
use_enum_values=True,
)

@model_validator(mode="before")
@classmethod
Expand Down Expand Up @@ -264,8 +266,7 @@ class ChangeSet(BaseModel):
id: str = Field(alias=C.CONDITION_ID)
changes: list[Change]

class Config:
populate_by_name = True
model_config = ConfigDict(populate_by_name=True)

@field_validator("id")
@classmethod
Expand Down Expand Up @@ -354,8 +355,7 @@ class ExperimentPeriod(BaseModel):
start: float = Field(alias=C.TIME)
condition_id: str = Field(alias=C.CONDITION_ID)

class Config:
populate_by_name = True
model_config = ConfigDict(populate_by_name=True)

@field_validator("condition_id")
@classmethod
Expand All @@ -378,9 +378,9 @@ class Experiment(BaseModel):
id: str = Field(alias=C.EXPERIMENT_ID)
periods: list[ExperimentPeriod] = []

class Config:
populate_by_name = True
arbitrary_types_allowed = True
model_config = ConfigDict(
arbitrary_types_allowed=True, populate_by_name=True
)

@field_validator("id")
@classmethod
Expand Down Expand Up @@ -471,9 +471,9 @@ class Measurement(BaseModel):
alias=C.NOISE_PARAMETERS, default_factory=list
)

class Config:
populate_by_name = True
arbitrary_types_allowed = True
model_config = ConfigDict(
arbitrary_types_allowed=True, populate_by_name=True
)

@field_validator(
"experiment_id",
Expand Down Expand Up @@ -566,8 +566,7 @@ class Mapping(BaseModel):
petab_id: str = Field(alias=C.PETAB_ENTITY_ID)
model_id: str = Field(alias=C.MODEL_ENTITY_ID)

class Config:
populate_by_name = True
model_config = ConfigDict(populate_by_name=True)

@field_validator(
"petab_id",
Expand Down Expand Up @@ -636,10 +635,11 @@ class Parameter(BaseModel):
estimate: bool = Field(alias=C.ESTIMATE, default=True)
# TODO priors

class Config:
populate_by_name = True
arbitrary_types_allowed = True
use_enum_values = True
model_config = ConfigDict(
arbitrary_types_allowed=True,
populate_by_name=True,
use_enum_values=True,
)

@field_validator("id")
@classmethod
Expand Down