replace sub_process with interpreter

Author: SarahAlidoost

PyStemmusScope/stemmus_scope.py

@@ -32,10 +32,10 @@ def _is_model_src_exe(model_src_path: Path):
     raise ValueError(msg)
 
 
-def _check_sub_process(sub_process: str):
-    if sub_process not in {"Octave" , "Matlab"}:
+def _check_interpreter(interpreter: str):
+    if interpreter not in {"Octave" , "Matlab"}:
         msg = (
-            "Set `sub_process` as Octave or Matlab to run the model using source codes."
+            "Set `interpreter` as Octave or Matlab to run the model using source codes."
             "Otherwise set `model_src_path` to the model executable file, "
             "see the documentaion.")
         raise ValueError(msg)
@@ -77,15 +77,15 @@ class StemmusScope():
         repository <https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing>`_
         model_src_path(str): path to Stemmus_Scope executable file or to a
         directory containing model source codes.
-        sub_process(str, optional): use `Matlab` or `Octave`. It is optional if
+        interpreter(str, optional): use `Matlab` or `Octave`. It is optional if
         `model_src_path` is a path to Stemmus_Scope executable file.
 
     Example:
         See notebooks/run_model_in_notebook.ipynb in `STEMMUS_SCOPE_Processing
         repository <https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing>`_
     """
 
-    def __init__(self, config_file: str, model_src_path: str, sub_process: str = None):
+    def __init__(self, config_file: str, model_src_path: str, interpreter: str = None):
         # make sure paths are abolute and path objects
         config_file = utils.to_absolute_path(config_file)
         model_src_path = utils.to_absolute_path(model_src_path)
@@ -95,10 +95,10 @@ def __init__(self, config_file: str, model_src_path: str, sub_process: str = Non
         if _is_model_src_exe(model_src_path):
             self.exe_file = model_src_path
         else:
-            _check_sub_process(sub_process)
+            _check_interpreter(interpreter)
 
         self.model_src = model_src_path
-        self.sub_process = sub_process
+        self.interpreter = interpreter
 
         # read config template
         self._config = config_io.read_config(config_file)
@@ -163,7 +163,7 @@ def run(self) -> str:
             # set matlab log dir
             os.environ['MATLAB_LOG_DIR'] = str(self._config["InputPath"])
             result = _run_sub_process(args, None)
-        if self.sub_process=="Matlab":
+        if self.interpreter=="Matlab":
             # set Matlab arguments
             path_to_config = f"'{self.cfg_file}'"
             eval_code= f'STEMMUS_SCOPE_exe({path_to_config});exit;'
@@ -172,7 +172,7 @@ def run(self) -> str:
             if utils.os_name() !="nt":
                 args = shlex.join(args)
             result = _run_sub_process(args, self.model_src)
-        if self.sub_process=="Octave":
+        if self.interpreter=="Octave":
             # set Octave arguments
             # use subprocess instead of oct2py,
             # see issue STEMMUS_SCOPE_Processing/issues/46

notebooks/run_model_in_notebook.ipynb

@@ -182,7 +182,7 @@
    "outputs": [],
    "source": [
     "# create an an instance of the model\n",
-    "model = StemmusScope(config_file=path_to_config_file, model_src_path=path_to_model_src, sub_process=\"Matlab\")"
+    "model = StemmusScope(config_file=path_to_config_file, model_src_path=path_to_model_src, interpreter=\"Matlab\")"
    ]
   },
   {
@@ -286,7 +286,7 @@
    "outputs": [],
    "source": [
     "# create an an instance of the model\n",
-    "model = StemmusScope(config_file=path_to_config_file, model_src_path=path_to_model_src, sub_process=\"Octave\")"
+    "model = StemmusScope(config_file=path_to_config_file, model_src_path=path_to_model_src, interpreter=\"Octave\")"
    ]
   },
   {
@@ -374,7 +374,7 @@
    "hash": "28b136f154b3384fcb2854e5626613232692c304dbc5315064ef4c9363104a2c"
   },
   "kernelspec": {
-   "display_name": "Python",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -388,7 +388,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,

tests/test_stemmus_scope.py

@@ -24,17 +24,17 @@ def test_model_without_src(self):
             StemmusScope(config_file, model_src_path="src")
         assert "Provide a valid path to an executable file" in str(excinfo.value)
 
-    def test_model_without_subprocess(self, tmp_path):
+    def test_model_without_interpreter(self, tmp_path):
         config_file = str(data_folder / "config_file_test.txt")
         with pytest.raises(ValueError) as excinfo:
             StemmusScope(config_file, model_src_path=tmp_path)
-        assert "Set `sub_process` as Octave or Matlab" in str(excinfo.value)
+        assert "Set `interpreter` as Octave or Matlab" in str(excinfo.value)
 
-    def test_model_wrong_subprocess(self, tmp_path):
+    def test_model_wrong_interpreter(self, tmp_path):
         config_file = str(data_folder / "config_file_test.txt")
         with pytest.raises(ValueError) as excinfo:
-            StemmusScope(config_file, model_src_path=tmp_path, sub_process="Nothing")
-        assert "Set `sub_process` as Octave or Matlab" in str(excinfo.value)
+            StemmusScope(config_file, model_src_path=tmp_path, interpreter="Nothing")
+        assert "Set `interpreter` as Octave or Matlab" in str(excinfo.value)
 
 
 class TestWithDefaults:
@@ -174,7 +174,7 @@ class TestWithMatlab:
     @pytest.fixture
     def model(self, tmp_path):
         config_file = str(data_folder / "config_file_test.txt")
-        yield StemmusScope(config_file, model_src_path=tmp_path, sub_process="Matlab")
+        yield StemmusScope(config_file, model_src_path=tmp_path, interpreter="Matlab")
 
     @pytest.fixture
     def model_with_setup(self, model):
@@ -226,7 +226,7 @@ class TestWithOctave:
     @pytest.fixture
     def model(self, tmp_path):
         config_file = str(data_folder / "config_file_test.txt")
-        yield StemmusScope(config_file, model_src_path=tmp_path, sub_process="Octave")
+        yield StemmusScope(config_file, model_src_path=tmp_path, interpreter="Octave")
 
     @pytest.fixture
     def model_with_setup(self, model):