Add code to handle calculation options (#14)

* Adds new model "AbsorptionLayer" and model validator "set_absorption" to use the correct layer.

* Changes "AbsorptionLayer" model to use same default counter as "Layer" model

* Ensures models cannot have zero-character length names.

* Refines "update_renamed_models" in "project.py" to enable focus on specific fields

* Add "domain_contrasts", "domain_ratios" to "project.py and "ContrastWithRatio" to "models.py" for domains calculations

* Adds tests for domain calculation models

* Adds model validators to handle the "model" field of "contrasts" to "project.py"

* Tidies up code

* Addresses review comments

Author: DrPaulSharp

RAT/models.py

@@ -1,7 +1,7 @@
 """The models module. Contains the pydantic models used by RAT to store project parameters."""
 
 import numpy as np
-from pydantic import BaseModel, Field, FieldValidationInfo, field_validator, model_validator
+from pydantic import BaseModel, Field, ValidationInfo, field_validator, model_validator
 
 try:
     from enum import StrEnum
@@ -54,7 +54,7 @@ class Types(StrEnum):
 
 class Background(BaseModel, validate_assignment=True, extra='forbid'):
     """Defines the Backgrounds in RAT."""
-    name: str = Field(default_factory=lambda: 'New Background ' + next(background_number))
+    name: str = Field(default_factory=lambda: 'New Background ' + next(background_number), min_length=1)
     type: Types = Types.Constant
     value_1: str = ''
     value_2: str = ''
@@ -65,28 +65,42 @@ class Background(BaseModel, validate_assignment=True, extra='forbid'):
 
 class Contrast(BaseModel, validate_assignment=True, extra='forbid'):
     """Groups together all of the components of the model."""
-    name: str = Field(default_factory=lambda: 'New Contrast ' + next(contrast_number))
+    name: str = Field(default_factory=lambda: 'New Contrast ' + next(contrast_number), min_length=1)
     data: str = ''
     background: str = ''
     nba: str = ''
     nbs: str = ''
     scalefactor: str = ''
     resolution: str = ''
     resample: bool = False
-    model: list[str] = []  # But how many strings? How to deal with this?
+    model: list[str] = []
+
+
+class ContrastWithRatio(BaseModel, validate_assignment=True, extra='forbid'):
+    """Groups together all of the components of the model including domain terms."""
+    name: str = Field(default_factory=lambda: 'New Contrast ' + next(contrast_number), min_length=1)
+    data: str = ''
+    background: str = ''
+    nba: str = ''
+    nbs: str = ''
+    scalefactor: str = ''
+    resolution: str = ''
+    resample: bool = False
+    domain_ratio: str = ''
+    model: list[str] = []
 
 
 class CustomFile(BaseModel, validate_assignment=True, extra='forbid'):
     """Defines the files containing functions to run when using custom models."""
-    name: str = Field(default_factory=lambda: 'New Custom File ' + next(custom_file_number))
+    name: str = Field(default_factory=lambda: 'New Custom File ' + next(custom_file_number), min_length=1)
     filename: str = ''
     language: Languages = Languages.Python
     path: str = 'pwd'  # Should later expand to find current file path
 
 
 class Data(BaseModel, validate_assignment=True, extra='forbid', arbitrary_types_allowed=True):
     """Defines the dataset required for each contrast."""
-    name: str = Field(default_factory=lambda: 'New Data ' + next(data_number))
+    name: str = Field(default_factory=lambda: 'New Data ' + next(data_number), min_length=1)
     data: np.ndarray[float] = np.empty([0, 3])
     data_range: list[float] = []
     simulation_range: list[float] = [0.005, 0.7]
@@ -106,7 +120,7 @@ def check_data_dimension(cls, data: np.ndarray[float]) -> np.ndarray[float]:
 
     @field_validator('data_range', 'simulation_range')
     @classmethod
-    def check_list_elements(cls, limits: list[float], info: FieldValidationInfo) -> list[float]:
+    def check_list_elements(cls, limits: list[float], info: ValidationInfo) -> list[float]:
         """The data range and simulation range must contain exactly two parameters."""
         if len(limits) != 2:
             raise ValueError(f'{info.field_name} must contain exactly two values')
@@ -117,23 +131,34 @@ def check_list_elements(cls, limits: list[float], info: FieldValidationInfo) ->
 
 class DomainContrast(BaseModel, validate_assignment=True, extra='forbid'):
     """Groups together the layers required for each domain."""
-    name: str = Field(default_factory=lambda: 'New Domain Contrast ' + next(domain_contrast_number))
+    name: str = Field(default_factory=lambda: 'New Domain Contrast ' + next(domain_contrast_number), min_length=1)
     model: list[str] = []
 
 
-class Layer(BaseModel, validate_assignment=True, extra='forbid'):
+class Layer(BaseModel, validate_assignment=True, extra='forbid', populate_by_name=True):
     """Combines parameters into defined layers."""
-    name: str = Field(default_factory=lambda: 'New Layer ' + next(layer_number))
+    name: str = Field(default_factory=lambda: 'New Layer ' + next(layer_number), min_length=1)
+    thickness: str = ''
+    SLD: str = Field('', validation_alias='SLD_real')
+    roughness: str = ''
+    hydration: str = ''
+    hydrate_with: Hydration = Hydration.BulkOut
+
+
+class AbsorptionLayer(BaseModel, validate_assignment=True, extra='forbid', populate_by_name=True):
+    """Combines parameters into defined layers including absorption terms."""
+    name: str = Field(default_factory=lambda: 'New Layer ' + next(layer_number), min_length=1)
     thickness: str = ''
-    SLD: str = ''
+    SLD_real: str = Field('', validation_alias='SLD')
+    SLD_imaginary: str = ''
     roughness: str = ''
     hydration: str = ''
     hydrate_with: Hydration = Hydration.BulkOut
 
 
 class Parameter(BaseModel, validate_assignment=True, extra='forbid'):
-    """Defines parameters needed to specify the model"""
-    name: str = Field(default_factory=lambda: 'New Parameter ' + next(parameter_number))
+    """Defines parameters needed to specify the model."""
+    name: str = Field(default_factory=lambda: 'New Parameter ' + next(parameter_number), min_length=1)
     min: float = 0.0
     value: float = 0.0
     max: float = 0.0
@@ -152,12 +177,12 @@ def check_value_in_range(self) -> 'Parameter':
 
 class ProtectedParameter(Parameter, validate_assignment=True, extra='forbid'):
     """A Parameter with a fixed name."""
-    name: str = Field(frozen=True)
+    name: str = Field(frozen=True, min_length=1)
 
 
 class Resolution(BaseModel, validate_assignment=True, extra='forbid'):
     """Defines Resolutions in RAT."""
-    name: str = Field(default_factory=lambda: 'New Resolution ' + next(resolution_number))
+    name: str = Field(default_factory=lambda: 'New Resolution ' + next(resolution_number), min_length=1)
     type: Types = Types.Constant
     value_1: str = ''
     value_2: str = ''