Updates indices (#71)

* Applies use of strings for Classlist __getitem__

* Bug fix for qzshift index in inputs.py

* Bug fix

Author: DrPaulSharp

RATapi/inputs.py

@@ -128,7 +128,7 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
     contrast_background_params = []
 
     for contrast in project.contrasts:
-        background = project.backgrounds[project.backgrounds.index(contrast.background)]
+        background = project.backgrounds[contrast.background]
         if background.type == TypeOptions.Data:
             contrast_background_params.append(-1)
         else:
@@ -138,7 +138,7 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
     contrast_resolution_params = []
 
     for contrast in project.contrasts:
-        resolution = project.resolutions[project.resolutions.index(contrast.resolution)]
+        resolution = project.resolutions[contrast.resolution]
         if resolution.type == TypeOptions.Data:
             contrast_resolution_params.append(-1)
         else:
@@ -160,7 +160,7 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
     problem.resolutionParams = [param.value for param in project.resolution_parameters]
     problem.contrastBulkIns = [project.bulk_in.index(contrast.bulk_in, True) for contrast in project.contrasts]
     problem.contrastBulkOuts = [project.bulk_out.index(contrast.bulk_out, True) for contrast in project.contrasts]
-    problem.contrastQzshifts = [0] * len(project.contrasts)  # This is marked as "to do" in RAT
+    problem.contrastQzshifts = [1] * len(project.contrasts)  # This is marked as "to do" in RAT
     problem.contrastScalefactors = [
         project.scalefactors.index(contrast.scalefactor, True) for contrast in project.contrasts
     ]
@@ -239,9 +239,7 @@ def make_data_present(project: RATapi.Project) -> list[int]:
         The "dataPresent" field of the problem input used in the compiled RAT code.
 
     """
-    return [
-        1 if project.data[project.data.index(contrast.data)].data.size != 0 else 0 for contrast in project.contrasts
-    ]
+    return [1 if project.data[contrast.data].data.size != 0 else 0 for contrast in project.contrasts]
 
 
 def check_indices(problem: ProblemDefinition) -> None:

RATapi/project.py

@@ -285,7 +285,7 @@ def model_post_init(self, __context: Any) -> None:
             )
         elif "Substrate Roughness" not in [name.title() for name in self.get_all_protected_parameters()["parameters"]]:
             # If substrate roughness is included as a standard parameter replace it with a protected parameter
-            substrate_roughness_values = self.parameters[self.parameters.index("Substrate Roughness")].model_dump()
+            substrate_roughness_values = self.parameters["Substrate Roughness"].model_dump()
             self.parameters.remove("Substrate Roughness")
             self.parameters.insert(0, RATapi.models.ProtectedParameter(**substrate_roughness_values))