Updates API and tests with recently added input and output objects (#124)

* Converts background function to python

* Adds resolutions to inputs and outputs

* Adds additional problem_definition fields to test data

* Updates submodule

* Adds names to "test_inputs.py"

* Fixes pickle bug

* Renames "non_polarised" to "normal_reflectivity"

* Adds names and checks to "test_run.py"

* Suppresses warnings in tests

* Adds backgrounds and resolutions to "check_results_equal"

* Addresses review comments

Author: DrPaulSharp

RATapi/examples/__init__.py

@@ -3,11 +3,11 @@
 from RATapi.examples.domains.domains_custom_layers import domains_custom_layers
 from RATapi.examples.domains.domains_custom_XY import domains_custom_XY
 from RATapi.examples.domains.domains_standard_layers import domains_standard_layers
-from RATapi.examples.non_polarised.DSPC_custom_layers import DSPC_custom_layers
-from RATapi.examples.non_polarised.DSPC_custom_XY import DSPC_custom_XY
-from RATapi.examples.non_polarised.DSPC_data_background import DSPC_data_background
-from RATapi.examples.non_polarised.DSPC_function_background import DSPC_function_background
-from RATapi.examples.non_polarised.DSPC_standard_layers import DSPC_standard_layers
+from RATapi.examples.normal_reflectivity.DSPC_custom_layers import DSPC_custom_layers
+from RATapi.examples.normal_reflectivity.DSPC_custom_XY import DSPC_custom_XY
+from RATapi.examples.normal_reflectivity.DSPC_data_background import DSPC_data_background
+from RATapi.examples.normal_reflectivity.DSPC_function_background import DSPC_function_background
+from RATapi.examples.normal_reflectivity.DSPC_standard_layers import DSPC_standard_layers
 
 __all__ = [
     "absorption",

RATapi/examples/convert_rascal_project/convert_rascal.py

@@ -5,7 +5,7 @@
 
 
 # convert R1 project to Project class
-def convert_rascal():
+def convert_rascal(mat_filename="lipid_bilayer.mat"):
     project_path = pathlib.Path(__file__).parent / "R1monolayerVolumeModel.mat"
     project = RAT.utils.convert.r1_to_project_class(project_path)
 
@@ -16,7 +16,7 @@ def convert_rascal():
 
     # convert DSPC standard layers example to a struct and save as file
     lipid_bilayer_project = RAT.examples.DSPC_standard_layers()[0]
-    RAT.utils.convert.project_class_to_r1(lipid_bilayer_project, filename="lipid_bilayer.mat")
+    RAT.utils.convert.project_class_to_r1(lipid_bilayer_project, filename=mat_filename)
 
     # convert and return as a Python dictionary
     struct = RAT.utils.convert.project_class_to_r1(lipid_bilayer_project, return_struct=True)

RATapi/examples/non_polarised/backgroundFunction.m

@@ -142,11 +142,10 @@ def DSPC_function_background():
     )
     problem.backgrounds.append(name="SMW Background", type="constant", source="Background parameter SMW")
 
-    # FIXME: replace this with a Python custom file when Python backgrounds are added!
     problem.custom_files.append(
         name="D2O Background Function",
-        filename="backgroundFunction.m",
-        language="matlab",
+        filename="background_function.py",
+        language="python",
         path=pathlib.Path(__file__).parent.resolve(),
     )