Migrate to pydantic v2 API (#13)

* make tests compatible with pytest >= 8.0.0

* migrate to pydantic v2

* remove redundant import

pyproject.toml

@@ -27,7 +27,7 @@ dynamic = ["version"]
 dependencies = [
     "numpy",
     "pandas",
-    "pydantic",
+    "pydantic>=2",
 ]
 
 # extras
@@ -112,11 +112,10 @@ test = "pytest {args:tests}"
 matrix-name-format = "{variable}_{value}"
 
 [[tool.hatch.envs.all.matrix]]
-pydantic_version = ["1","2"]
+pydantic_version = ["2"]
 
 [tool.hatch.envs.all.overrides]
 matrix.pydantic_version.dependencies = [
-    { value="pydantic<2", if = ["1"] },
     { value="pydantic>=2", if = ["2"] }
 ]
 

src/imodmodel/models.py

@@ -1,10 +1,9 @@
 import os
 import warnings
-from typing import Tuple, List, Optional, Union
+from typing import List, Optional, Tuple, Union
 
 import numpy as np
-from pydantic import BaseModel, validator
-from pydantic.version import VERSION as PYDANTIC_VERSION
+from pydantic import BaseModel, ConfigDict, field_validator
 
 
 class ID(BaseModel):
@@ -20,10 +19,6 @@ class GeneralStorage(BaseModel):
     index: Union[float, int, Tuple[int, int], Tuple[int, int, int, int]]
     value: Union[float, int, Tuple[int, int], Tuple[int, int, int, int]]
 
-    if PYDANTIC_VERSION < '2.0':
-        class Config:
-            smart_union = True
-
 
 class ModelHeader(BaseModel):
     """https://bio3d.colorado.edu/imod/doc/binspec.html"""
@@ -55,7 +50,8 @@ class ModelHeader(BaseModel):
     beta: float
     gamma: float
 
-    @validator('name', pre=True)
+    @field_validator('name', mode="before")
+    @classmethod
     def decode_null_terminated_byte_string(cls, value: bytes):
         end = value.find(b'\x00')
         return value[:end].decode('utf-8')
@@ -84,7 +80,8 @@ class ObjectHeader(BaseModel):
     meshsize: int
     surfsize: int
 
-    @validator('name', pre=True)
+    @field_validator('name', mode="before")
+    @classmethod
     def decode_null_terminated_byte_string(cls, value: bytes):
         end = value.find(b'\x00')
         return value[:end].decode('utf-8')
@@ -104,8 +101,7 @@ class Contour(BaseModel):
     points: np.ndarray  # pt
     extra: List[GeneralStorage] = []
 
-    class Config:
-        arbitrary_types_allowed = True
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
 
 class MeshHeader(BaseModel):
@@ -123,10 +119,9 @@ class Mesh(BaseModel):
     raw_indices: np.ndarray
     extra: List[GeneralStorage] = []
 
-    class Config:
-        arbitrary_types_allowed = True
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    @validator('raw_indices')
+    @field_validator('raw_indices')
     @classmethod
     def validate_indices(cls, indices: np.ndarray):
         if indices.ndim > 1:
@@ -140,7 +135,7 @@ def validate_indices(cls, indices: np.ndarray):
                 warnings.warn(f'Unsupported mesh type: {i}')
         return indices
 
-    @validator('raw_vertices')
+    @field_validator('raw_vertices')
     @classmethod
     def validate_vertices(cls, vertices: np.ndarray):
         if vertices.ndim > 1:
@@ -242,7 +237,7 @@ class ImodModel(BaseModel):
     id: ID
     header: ModelHeader
     objects: List[Object]
-    imat: Optional[IMAT]
+    imat: Optional[IMAT] = None
     extra: List[GeneralStorage] = []
 
     @classmethod