Refactors matlab save in "project_to_r1"

Author: DrPaulSharp

RATapi/examples/convert_rascal_project/convert_rascal.py

@@ -26,7 +26,7 @@ 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)
+    project = RAT.utils.convert.r1_to_project(project_path)
 
     # change values if you like, including ones not supported by R1
     project.parameters["Head Thickness"].prior_type = "gaussian"
@@ -35,10 +35,10 @@ def convert_rascal(mat_filename="lipid_bilayer.mat"):
 
     # 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=mat_filename)
+    RAT.utils.convert.project_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)
+    struct = RAT.utils.convert.project_to_r1(lipid_bilayer_project, return_struct=True)
 
     return project, struct
 

RATapi/utils/convert.py

@@ -15,7 +15,7 @@
 from RATapi.utils.enums import Geometries, Languages, LayerModels
 
 
-def r1_to_project_class(filename: Union[str, PathLike]) -> Project:
+def r1_to_project(filename: Union[str, PathLike]) -> Project:
     """Read a RasCAL1 project struct as a Python `Project`.
 
     Parameters
@@ -318,7 +318,7 @@ def fix_invalid_constraints(name: str, constrs: tuple[float, float], value: floa
     return project
 
 
-def project_class_to_r1(
+def project_to_r1(
     project: Project, filename: Union[str, PathLike] = "RAT_project", return_struct: bool = False
 ) -> Union[dict, None]:
     """Convert a RAT Project to a RasCAL1 project struct.
@@ -549,11 +549,10 @@ def convert_parameters(
     # scipy.io.savemat doesn't do cells properly:
     # https://github.com/scipy/scipy/issues/3756
     # rather than fiddling we just use matlab
-    eng = wrappers.start_matlab()
-    if eng is None:
+    loader = wrappers.MatlabWrapper.loader
+    if loader is None:
         raise ImportError("matlabengine is not installed.")
-    eng = eng.result()
+    eng = loader.result()
     eng.workspace["problem"] = r1
     eng.save(str(filename), "problem", nargout=0)
-    eng.exit()
     return None

tests/test_convert.py

@@ -8,7 +8,7 @@
 import pytest
 
 import RATapi
-from RATapi.utils.convert import project_class_to_r1, r1_to_project_class
+from RATapi.utils.convert import project_to_r1, r1_to_project
 
 TEST_DIR_PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)), "test_data")
 
@@ -58,9 +58,9 @@ def dspc_bilayer():
     ],
 )
 @pytest.mark.parametrize("path_type", [os.path.join, pathlib.Path])
-def test_r1_to_project_class(file, project, path_type, request):
+def test_r1_to_project(file, project, path_type, request):
     """Test that R1 to Project class conversion returns the expected Project."""
-    output_project = r1_to_project_class(path_type(TEST_DIR_PATH, file))
+    output_project = r1_to_project(path_type(TEST_DIR_PATH, file))
     expected_project = request.getfixturevalue(project)
 
     # assert statements have to be more careful due to R1 missing features
@@ -83,7 +83,7 @@ def test_r1_to_project_class(file, project, path_type, request):
 def test_r1_involution(project, request, monkeypatch):
     """Test that converting a Project to an R1 struct and back returns the same project."""
     original_project = request.getfixturevalue(project)
-    r1_struct = project_class_to_r1(original_project, return_struct=True)
+    r1_struct = project_to_r1(original_project, return_struct=True)
 
     # rather than writing the struct to a file and reading the file, just directly
     # hand the struct over
@@ -93,7 +93,7 @@ def mock_load(ignored_filename, **ignored_settings):
 
     monkeypatch.setattr("RATapi.utils.convert.loadmat", mock_load, raising=True)
 
-    converted_project = r1_to_project_class(project)
+    converted_project = r1_to_project(project)
 
     for class_list in RATapi.project.class_lists:
         assert getattr(converted_project, class_list) == getattr(original_project, class_list)
@@ -105,7 +105,7 @@ def test_invalid_constraints():
         match=r"The parameter (.+) has invalid constraints,"
         " these have been adjusted to satisfy the current value of the parameter."
     ):
-        output_project = r1_to_project_class(pathlib.Path(TEST_DIR_PATH, "R1DoubleBilayerVolumeModel.mat"))
+        output_project = r1_to_project(pathlib.Path(TEST_DIR_PATH, "R1DoubleBilayerVolumeModel.mat"))
 
     assert output_project.background_parameters[0].min == output_project.background_parameters[0].value
 
@@ -117,7 +117,7 @@ def test_matlab_save(path_type, request):
     project = request.getfixturevalue("r1_default_project")
     with tempfile.TemporaryDirectory() as temp:
         matfile = path_type(temp, "testfile.mat")
-        project_class_to_r1(project, filename=matfile)
-        converted_project = r1_to_project_class(matfile)
+        project_to_r1(project, filename=matfile)
+        converted_project = r1_to_project(matfile)
 
     assert project == converted_project