adapt to current pydantic version

src/cryo_challenge/data/_validation/config_validators.py

@@ -2,7 +2,7 @@
 import numpy as np
 import pandas as pd
 import os
-from pydantic import BaseModel, validator, root_validator
+from pydantic import BaseModel, field_validator, model_validator
 from typing import Optional, List
 
 
@@ -259,21 +259,21 @@ class SVDNormalizeParams(BaseModel):
     bfactor: float = None
     box_size_ds: Optional[int] = None
 
-    @validator("mask_path")
+    @field_validator("mask_path")
     def check_mask_path_exists(cls, value):
         if value is not None:
             if not os.path.exists(value):
                 raise ValueError(f"Mask file {value} does not exist.")
         return value
 
-    @validator("bfactor")
+    @field_validator("bfactor")
     def check_bfactor(cls, value):
         if value is not None:
             if value < 0:
                 raise ValueError("B-factor must be non-negative.")
         return value
 
-    @validator("box_size_ds")
+    @field_validator("box_size_ds")
     def check_box_size_ds(cls, value):
         if value is not None:
             if value < 0:
@@ -285,7 +285,7 @@ class SVDGtParams(BaseModel):
     gt_vols_file: str
     skip_vols: int = 1
 
-    @validator("gt_vols_file")
+    @field_validator("gt_vols_file")
     def check_mask_path_exists(cls, value):
         if not os.path.exists(value):
             raise ValueError(f"Could not find file {value}.")
@@ -300,7 +300,7 @@ def check_mask_path_exists(cls, value):
             )
         return value
 
-    @validator("skip_vols")
+    @field_validator("skip_vols")
     def check_skip_vols(cls, value):
         if value is not None:
             if value < 0:
@@ -327,10 +327,10 @@ class SVDConfig(BaseModel):
     gt_params: Optional[SVDGtParams] = None
     output_params: SVDOutputParams
 
-    @root_validator
-    def check_path_to_submissions(cls, values):
-        path_to_submissions = values.get("path_to_submissions")
-        excluded_submissions = values.get("excluded_submissions")
+    @model_validator(mode="after")
+    def check_path_to_submissions(self):
+        path_to_submissions = self.path_to_submissions
+        excluded_submissions = self.excluded_submissions
 
         if not os.path.exists(path_to_submissions):
             raise ValueError(f"Could not find path {path_to_submissions}.")
@@ -354,21 +354,21 @@ def check_path_to_submissions(cls, values):
                 f"No submission files found after excluding {excluded_submissions}."
             )
 
-        return values
+        return self
 
-    @validator("dtype")
+    @field_validator("dtype")
     def check_dtype(cls, value):
         if value not in ["float32", "float64"]:
             raise ValueError(f"Invalid dtype {value}.")
         return value
 
-    @validator("svd_max_rank")
+    @field_validator("svd_max_rank")
     def check_svd_max_rank(cls, value):
         if value < 1 and value is not None:
             raise ValueError("Max rank must be at least 1.")
         return value
 
-    @validator("voxel_size")
+    @field_validator("voxel_size")
     def check_voxel_size(cls, value):
         if value <= 0:
             raise ValueError("Voxel size must be positive.")