Addresses review comments

Author: DrPaulSharp

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/normal_reflectivity/DSPC_function_background.py

@@ -142,10 +142,9 @@ 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.py",
+        filename="background_function.py",
         language="python",
         path=pathlib.Path(__file__).parent.resolve(),
     )

…ormal_reflectivity/backgroundFunction.py …rmal_reflectivity/background_function.pyRATapi/examples/normal_reflectivity/backgroundFunction.py renamed to RATapi/examples/normal_reflectivity/background_function.py RATapi/examples/normal_reflectivity/backgroundFunction.py renamed to RATapi/examples/normal_reflectivity/background_function.py

@@ -280,10 +280,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
         resolution = project.resolutions[contrast.resolution]
         contrast_resolution_types.append(resolution.type)
         contrast_resolution_param = []
-        if resolution.type == TypeOptions.Data:
-            # The source field is empty for a data resolution
-            pass
-        elif resolution.type == TypeOptions.Function:
+        if resolution.type == TypeOptions.Function:
             contrast_resolution_param.append(project.custom_files.index(resolution.source, True))
             contrast_resolution_param.extend(
                 [
@@ -299,7 +296,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
                 ]
             )
 
-        else:
+        elif resolution.type == TypeOptions.Constant:
             contrast_resolution_param.append(project.resolution_parameters.index(resolution.source, True))
 
         contrast_resolution_params.append(contrast_resolution_param)

RATapi/inputs.py

@@ -1,3 +1,5 @@
+import shutil
+import tempfile
 from pathlib import Path
 
 import numpy as np
@@ -9,6 +11,13 @@
 import RATapi.rat_core
 
 
+@pytest.fixture
+def temp_dir():
+    path = tempfile.mkdtemp()
+    yield path
+    shutil.rmtree(path)
+
+
 @pytest.fixture
 def input_project():
     """A cut-down version of the input Project object for a reflectivity calculation set out in

tests/conftest.py

@@ -1,6 +1,7 @@
 """Test the RAT examples."""
 
 import importlib
+from pathlib import Path
 
 import pytest
 
@@ -31,12 +32,25 @@ def test_rat_examples(example_name):
     "example_name",
     [
         "DSPC_function_background",
-        "convert_rascal",
     ],
 )
 @pytest.mark.skipif(importlib.util.find_spec("matlab") is None, reason="Matlab not installed")
-def test_matlab_examples(example_name):
+def test_function_background(example_name):
     """Test examples which rely on MATLAB engine being installed."""
     p, r = getattr(examples, example_name)()
     assert p is not None
     assert r is not None
+
+
+@pytest.mark.parametrize(
+    "example_name",
+    [
+        "convert_rascal",
+    ],
+)
+@pytest.mark.skipif(importlib.util.find_spec("matlab") is None, reason="Matlab not installed")
+def test_matlab_examples(example_name, temp_dir):
+    """Test convert_rascal example, directing the output to a temporary directory."""
+    p, r = examples.convert_rascal(Path(temp_dir, "lipid_bilayer.mat"))
+    assert p is not None
+    assert r is not None

tests/test_examples.py

@@ -1,8 +1,6 @@
 """Test the project module."""
 
 import copy
-import shutil
-import tempfile
 from pathlib import Path
 from typing import Callable
 
@@ -136,13 +134,6 @@ def default_project_str():
     )
 
 
-@pytest.fixture
-def temp_dir():
-    path = tempfile.mkdtemp()
-    yield path
-    shutil.rmtree(path)
-
-
 def test_classlists(test_project) -> None:
     """The ClassLists in the "Project" model should contain instances of the models given by the dictionary
     "model_in_classlist".