ENH Bring rest of models into pydantic v2 mypy conformance. Just miss…

…ing validators.py

lute/io/models/base.py

@@ -35,9 +35,7 @@
     Optional,
     ClassVar,
     no_type_check,
-    Callable,
     cast,
-    Literal,
 )
 
 import pydantic
@@ -51,8 +49,7 @@
     # Ignore mypy and ruff for now since type checking against pydantic 1.10
     from pydantic import model_validator, field_validator  # type: ignore
     from pydantic_core import PydanticUndefined  # type: ignore
-    from pydantic_settings import SettingsConfigDict  # type: ignore
-    from pydantic_settings import BaseSettings
+    from pydantic_settings import SettingsConfigDict, BaseSettings  # type: ignore
 
     @no_type_check  # This function causes many headaches with mypy... Ignore
     def Field(

lute/io/models/sfx_find_peaks.py

@@ -48,7 +48,7 @@ class FindPeaksPyAlgosParameters(TaskParameters):
         Config = FindPeaksPyAlgosParametersConfig
 
     if PYDANTIC_V2:
-        out_file_validator = field_validator("out_file")
+        out_file_validator: ClassVar = field_validator("out_file")
     else:
         out_file_validator = validator("out_file", always=True)
 
@@ -209,17 +209,22 @@ class FindPeaksPsocakeParameters(ThirdPartyParameters):
         Config = FindPeaksPsocakeParametersConfig
 
     if PYDANTIC_V2:
-        e_validator = field_validator("e")
-        r_validator = field_validator("r")
-        set_output_path_validator = field_validator("lute_template_cfg")
-        sz_parameters_validator = field_validator("sz_parameters")
-        result_validator = model_validator(mode="after")
+        e_validator: ClassVar = field_validator("e")
+        r_validator: ClassVar = field_validator("r")
+        set_output_path_validator: ClassVar = field_validator("lute_template_cfg")
+        sz_parameters_validator: ClassVar = field_validator("sz_parameters")
+        result_validator: ClassVar = model_validator(mode="after")
     else:
         e_validator = validator("e", always=True)
         r_validator = validator("r", always=True)
         set_output_path_validator = validator("lute_template_cfg", always=True)
         sz_parameters_validator = validator("sz_parameters", always=True)
-        result_validator = root_validator(pre=False)
+        # Strictly only need pre=False for running, but it doesn't match overload
+        # variants so mypy complains when using pydantic v2. This is functionally
+        # the same for our purposes
+        result_validator = root_validator(
+            pre=False, skip_on_failure=True, allow_reuse=True
+        )
 
     class SZParameters(BaseModel):
         compressor: Literal["qoz", "sz3"] = Field(

lute/io/models/sfx_index.py

@@ -75,8 +75,8 @@ class IndexCrystFELParameters(ThirdPartyParameters):
         Config = IndexCrystFELParametersConfig
 
     if PYDANTIC_V2:
-        in_file_validator = field_validator("in_file")
-        out_file_validator = field_validator("out_file")
+        in_file_validator: ClassVar = field_validator("in_file")
+        out_file_validator: ClassVar = field_validator("out_file")
     else:
         in_file_validator = validator("in_file", always=True)
         out_file_validator = validator("out_file", always=True)
@@ -531,6 +531,15 @@ class ConcatenateStreamFilesParameters(TaskParameters):
     else:
         Config = ConcatenateStreamFilesParametersConfig
 
+    if PYDANTIC_V2:
+        in_file_validator: ClassVar = field_validator("in_file")
+        tag_validator: ClassVar = field_validator("tag")
+        out_file_validator: ClassVar = field_validator("out_file")
+    else:
+        in_file_validator = validator("in_file", always=True)
+        tag_validator = validator("tag", always=True)
+        out_file_validator = validator("out_file", always=True)
+
     in_file: str = (
         Field(
             "",
@@ -568,15 +577,6 @@ class ConcatenateStreamFilesParameters(TaskParameters):
         else Field("", description="Path to merged output stream file.", is_result=True)
     )
 
-    if PYDANTIC_V2:
-        in_file_validator = field_validator("in_file")
-        tag_validator = field_validator("tag")
-        out_file_validator = field_validator("out_file")
-    else:
-        in_file_validator = validator("in_file", always=True)
-        tag_validator = validator("tag", always=True)
-        out_file_validator = validator("out_file", always=True)
-
     @in_file_validator
     @classmethod
     def validate_in_file(cls, in_file: str, values: Dict[str, Any]) -> str:
@@ -636,6 +636,17 @@ class IndexCCTBXXFELParameters(ThirdPartyParameters):
     else:
         Config = IndexCCTBXXFELParametersConfig
 
+    if PYDANTIC_V2:
+        phil_path_validator: ClassVar = field_validator("phil_file")
+        phil_template_validator: ClassVar = field_validator("lute_template_cfg")
+        in_file_validator: ClassVar = field_validator("in_file")
+        data_spec_validator: ClassVar = field_validator("data_spec")
+    else:
+        phil_path_validator = validator("phil_file", always=True)
+        phil_template_validator = validator("lute_template_cfg", always=True)
+        in_file_validator = validator("in_file", always=True)
+        data_spec_validator = validator("data_spec", always=True)
+
     class PhilParameters(BaseModel):
         """Template parameters for CCTBX phil file."""
 
@@ -646,8 +657,10 @@ class PhilParameters(BaseModel):
             Config = PhilParametersConfig
 
         if PYDANTIC_V2:
-            output_output_dir_validator = field_validator("output_output_dir")
-            output_logging_dir_validator = field_validator("output_logging_dir")
+            output_output_dir_validator: ClassVar = field_validator("output_output_dir")
+            output_logging_dir_validator: ClassVar = field_validator(
+                "output_logging_dir"
+            )
         else:
             output_output_dir_validator = validator("output_output_dir", always=True)
             output_logging_dir_validator = validator("output_logging_dir", always=True)
@@ -947,17 +960,6 @@ def set_output_log_dir(cls, output: str, values: Dict[str, Any]) -> str:
         )
     )
 
-    if PYDANTIC_V2:
-        phil_path_validator = field_validator("phil_file")
-        phil_template_validator = field_validator("lute_template_cfg")
-        in_file_validator = field_validator("in_file")
-        data_spec_validator = field_validator("data_spec")
-    else:
-        phil_path_validator = validator("phil_file", always=True)
-        phil_template_validator = validator("lute_template_cfg", always=True)
-        in_file_validator = validator("in_file", always=True)
-        data_spec_validator = validator("data_spec", always=True)
-
     @phil_path_validator
     @classmethod
     def set_default_phil_path(cls, phil_file: str, values: Dict[str, Any]) -> str:

lute/io/models/sfx_merge.py

@@ -72,8 +72,8 @@ class MergePartialatorParameters(ThirdPartyParameters):
         Config = MergePartialatorParametersConfig
 
     if PYDANTIC_V2:
-        in_file_validator = field_validator("in_file")
-        out_file_validator = field_validator("out_file")
+        in_file_validator: ClassVar = field_validator("in_file")
+        out_file_validator: ClassVar = field_validator("out_file")
     else:
         in_file_validator = validator("in_file", always=True)
         out_file_validator = validator("out_file", always=True)
@@ -289,6 +289,13 @@ class MergeCCTBXXFELParameters(ThirdPartyParameters):
     else:
         Config = MergeCCTBXXFELParametersConfig
 
+    if PYDANTIC_V2:
+        phil_file_validator: ClassVar = field_validator("phil_file")
+        phil_template_validator: ClassVar = field_validator("lute_template_cfg")
+    else:
+        phil_file_validator = validator("phil_file", always=True)
+        phil_template_validator = validator("lute_template_cfg", always=True)
+
     class PhilParameters(BaseModel):
         """Template parameters for CCTBX phil file."""
 
@@ -461,13 +468,6 @@ class PhilParameters(BaseModel):
         )
     )
 
-    if PYDANTIC_V2:
-        phil_file_validator = field_validator("phil_file")
-        phil_template_validator = field_validator("lute_template_cfg")
-    else:
-        phil_file_validator = validator("phil_file", always=True)
-        phil_template_validator = validator("lute_template_cfg", always=True)
-
     @phil_file_validator
     @classmethod
     def set_default_phil_path(cls, phil_file: str, values: Dict[str, Any]) -> str:
@@ -514,10 +514,10 @@ class CompareHKLParameters(ThirdPartyParameters):
         Config = CompareHKLParametersConfig
 
     if PYDANTIC_V2:
-        in_files_validator = field_validator("in_files")
-        cell_file_validator = field_validator("cell_file")
-        symmetry_validator = field_validator("symmetry")
-        shell_file_validator = field_validator("shell_file")
+        in_files_validator: ClassVar = field_validator("in_files")
+        cell_file_validator: ClassVar = field_validator("cell_file")
+        symmetry_validator: ClassVar = field_validator("symmetry")
+        shell_file_validator: ClassVar = field_validator("shell_file")
     else:
         in_files_validator = validator("in_files", always=True)
         cell_file_validator = validator("cell_file", always=True)
@@ -716,9 +716,9 @@ class ManipulateHKLParameters(ThirdPartyParameters):
         Config = ManipulateHKLParametersConfig
 
     if PYDANTIC_V2:
-        in_file_validator = field_validator("in_file")
-        out_file_validator = field_validator("out_file")
-        cell_file_validator = field_validator("cell_file")
+        in_file_validator: ClassVar = field_validator("in_file")
+        out_file_validator: ClassVar = field_validator("out_file")
+        cell_file_validator: ClassVar = field_validator("cell_file")
     else:
         in_file_validator = validator("in_file", always=True)
         out_file_validator = validator("out_file", always=True)

lute/io/models/sfx_solve.py

@@ -59,13 +59,18 @@ class DimpleSolveParameters(ThirdPartyParameters):
         Config = DimpleSolveParametersConfig
 
     if PYDANTIC_V2:
-        in_file_validator = field_validator("in_file")
-        out_dir_validator = field_validator("out_dir")
-        result_validator = model_validator(mode="after")
+        in_file_validator: ClassVar = field_validator("in_file")
+        out_dir_validator: ClassVar = field_validator("out_dir")
+        result_validator: ClassVar = model_validator(mode="after")
     else:
         in_file_validator = validator("in_file", always=True)
         out_dir_validator = validator("out_dir", always=True)
-        result_validator = root_validator(pre=False)
+        # Strictly only need pre=False for running, but it doesn't match overload
+        # variants so mypy complains when using pydantic v2. This is functionally
+        # the same for our purposes
+        result_validator = root_validator(
+            pre=False, skip_on_failure=True, allow_reuse=True
+        )
 
     executable: str = Field(
         "/sdf/group/lcls/ds/tools/ccp4-8.0/bin/dimple",
@@ -277,7 +282,7 @@ class RunSHELXCParameters(ThirdPartyParameters):
     """
 
     if PYDANTIC_V2:
-        in_file_validator = field_validator("in_file")
+        in_file_validator: ClassVar = field_validator("in_file")
     else:
         in_file_validator = validator("in_file", always=True)
 

lute/io/models/smd.py

@@ -73,13 +73,18 @@ class SubmitSMDParameters(ThirdPartyParameters):
         Config = SubmitSMDParametersConfig
 
     if PYDANTIC_V2:
-        producer_validator = field_validator("producer")
-        producer_template_validator = field_validator("lute_template_cfg")
-        result_validator = model_validator(mode="after")
+        producer_validator: ClassVar = field_validator("producer")
+        producer_template_validator: ClassVar = field_validator("lute_template_cfg")
+        result_validator: ClassVar = model_validator(mode="after")
     else:
         producer_validator = validator("producer", always=True)
         producer_template_validator = validator("lute_template_cfg", always=True)
-        result_validator = root_validator(pre=False)
+        # Strictly only need pre=False for running, but it doesn't match overload
+        # variants so mypy complains when using pydantic v2. This is functionally
+        # the same for our purposes
+        result_validator = root_validator(
+            pre=False, skip_on_failure=True, allow_reuse=True
+        )
 
     class ProducerParameters(BaseModel):
         class ROIParams(BaseModel):

lute/io/models/tests.py

@@ -126,7 +126,7 @@ class TestReadOutputParameters(TaskParameters):
     in_file: str = Field("", description="File to read in. (Full path)")
 
     if PYDANTIC_V2:
-        in_file_validator = field_validator("in_file")
+        in_file_validator: ClassVar = field_validator("in_file")
     else:
         in_file_validator = validator("in_file", always=True)