converter now works with pathlib and fixed example (RascalSoftware#108)

Author: alexhroom

RATapi/examples/convert_rascal_project/convert_rascal.py

@@ -1,11 +1,13 @@
+import pathlib
 from pprint import pp
 
 import RATapi as RAT
 
 
 # convert R1 project to Project class
 def convert_rascal():
-    project = RAT.utils.convert.r1_to_project_class("R1monolayerVolumeModel.mat")
+    project_path = pathlib.Path(__file__).parent / "R1monolayerVolumeModel.mat"
+    project = RAT.utils.convert.r1_to_project_class(project_path)
 
     # change values if you like, including ones not supported by R1
     project.parameters["Head Thickness"].prior_type = "gaussian"

RATapi/utils/convert.py

@@ -2,6 +2,7 @@
 
 import json
 from collections.abc import Iterable
+from os import PathLike
 from pathlib import Path
 from typing import Union
 
@@ -14,12 +15,12 @@
 from RATapi.utils.enums import Geometries, Languages, LayerModels
 
 
-def r1_to_project_class(filename: str) -> Project:
+def r1_to_project_class(filename: Union[str, PathLike]) -> Project:
     """Read a RasCAL1 project struct as a Python `Project`.
 
     Parameters
     ----------
-    filename : str
+    filename : str, PathLike
         The path to a .mat file containing project data.
 
     Returns
@@ -28,7 +29,7 @@ def r1_to_project_class(filename: str) -> Project:
         A RAT `Project` equivalent to the RasCAL1 project struct.
 
     """
-    mat_project = loadmat(filename, simplify_cells=True)["problem"]
+    mat_project = loadmat(str(filename), simplify_cells=True)["problem"]
 
     mat_module = mat_project["module"]
     if mat_module["experiment_type"] == "Air / Liquid (or solid)":
@@ -271,15 +272,15 @@ def read_param(names, constrs, values, fits):
 
 
 def project_class_to_r1(
-    project: Project, filename: str = "RAT_project", return_struct: bool = False
+    project: Project, filename: Union[str, PathLike] = "RAT_project", return_struct: bool = False
 ) -> Union[dict, None]:
     """Convert a RAT Project to a RasCAL1 project struct.
 
     Parameters
     ----------
     project : Project
         The RAT Project to convert.
-    filename : str, default "RAT_project"
+    filename : str or PathLike, default "RAT_project"
         If given, saves as a .mat file with the given filename.
     return_struct : bool, default False
         If True, do not save and instead return the R1 struct.
@@ -503,7 +504,7 @@ def convert_parameters(
     if eng is None:
         raise ImportError("matlabengine is not installed.")
     eng.workspace["problem"] = r1
-    eng.save(filename, "problem", nargout=0)
+    eng.save(str(filename), "problem", nargout=0)
     eng.exit()
     return None
 

tests/test_convert.py

@@ -2,6 +2,7 @@
 
 import importlib
 import os
+import pathlib
 import tempfile
 
 import pytest
@@ -56,9 +57,10 @@ def dspc_bilayer():
         ["R1motofitBenchMark.mat", "r1_motofit_bench_mark"],
     ],
 )
-def test_r1_to_project_class(file, project, request):
+@pytest.mark.parametrize("path_type", [os.path.join, pathlib.Path])
+def test_r1_to_project_class(file, project, path_type, request):
     """Test that R1 to Project class conversion returns the expected Project."""
-    output_project = r1_to_project_class(os.path.join(TEST_DIR_PATH, file))
+    output_project = r1_to_project_class(path_type(TEST_DIR_PATH, file))
     expected_project = request.getfixturevalue(project)
 
     # assert statements have to be more careful due to R1 missing features
@@ -127,11 +129,12 @@ def test_json_involution(project, request):
 
 
 @pytest.mark.skipif(importlib.util.find_spec("matlab") is None, reason="Matlab not installed")
-def test_matlab_save(request):
+@pytest.mark.parametrize("path_type", [os.path.join, pathlib.Path])
+def test_matlab_save(path_type, request):
     """Test that MATLAB correctly saves the .mat file."""
     project = request.getfixturevalue("r1_default_project")
     with tempfile.TemporaryDirectory() as temp:
-        matfile = os.path.join(temp, "testfile.mat")
+        matfile = path_type(temp, "testfile.mat")
         project_class_to_r1(project, filename=matfile)
         converted_project = r1_to_project_class(matfile)