as

Author: StephenNneji

.github/workflows/run_tests.yml

@@ -1,3 +1,4 @@
+
 name: Run Unit Tests
 
 on:
@@ -11,8 +12,11 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  run_ruff:
+    uses: ./.github/workflows/run_ruff.yml
 
   test:
+    needs: [run_ruff]
     strategy:
       fail-fast: false
       matrix:
@@ -47,12 +51,8 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt install libomp-dev
-      - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v2
-        with:
-          release: R2024a
       - name: Install and Test with pytest
         run: |
           export PATH="$pythonLocation:$PATH"
           python -m pip install -e .[Dev,Orso]
-          python RATapi/examples/normal_reflectivity/DSPC_custom_layers.py
+          pytest tests/ --cov=RATapi --cov-report=term

RATapi/inputs.py

@@ -8,7 +8,6 @@
 import numpy as np
 
 import RATapi
-import RATapi.controls
 import RATapi.wrappers
 from RATapi.rat_core import Checks, Control, NameStore, ProblemDefinition
 from RATapi.utils.enums import Calculations, Languages, LayerModels, TypeOptions

RATapi/wrappers.py

@@ -1,80 +1,107 @@
 """Wrappers for the interface between RATapi and MATLAB custom files."""
-from contextlib import contextmanager
+
 import os
 import pathlib
 import platform
 import shutil
 import subprocess
+from contextlib import contextmanager
 from typing import Callable
 
-import numpy as np
 from numpy.typing import ArrayLike
 
 import RATapi.rat_core
 
-
 MATLAB_PATH_FILE = os.path.join(os.path.dirname(os.path.realpath(__file__)), "matlab.txt")
 
 
 @contextmanager
-def cd(newdir):
+def cd(new_dir):
+    """Context manager to change to a given directory and return to current directory on exit.
+
+    Parameters
+    ----------
+    new_dir : string
+        The path to change to
+    """
     prev_dir = os.getcwd()
-    os.chdir(os.path.expanduser(newdir))
+    os.chdir(os.path.expanduser(new_dir))
     try:
         yield
     finally:
         os.chdir(prev_dir)
 
 
-def set_matlab_path(matlab_path):
-    if not matlab_path:
-        return 
-    
-    if platform.system() == "Windows": 
-        process = subprocess.Popen(f'"{matlab_path}" -batch "comserver(\'register\')"')
+def set_matlab_path(matlab_exe_path):
+    """Set the path of MATLAB to use for custom functions.
+
+    This will also register the MATLAB COM server on Windows OS which could be slow.
+
+    Parameters
+    ----------
+    matlab_path : string
+        The full path of the MATLAB executable
+    """
+    if not matlab_exe_path:
+        return
+
+    if platform.system() == "Windows":
+        process = subprocess.Popen(f'"{matlab_exe_path}" -batch "comserver(\'register\')"')
         process.wait()
-        
 
     with open(MATLAB_PATH_FILE, "w") as path_file:
-        path_file.write(matlab_path)
+        path_file.write(matlab_exe_path)
+
 
+def get_matlab_paths(matlab_exe_path):
+    """Return paths for loading MATLAB engine C interface dynamic libraries.
 
-def get_matlab_paths(exe_path):
-    if not exe_path:
+    Parameters
+    ----------
+    matlab_exe_path : string
+        The full path of the MATLAB executable
+
+    Returns
+    -------
+    paths : Tuple[string, string]
+        The path of the MATLAB bin and the DLL location
+    """
+    if not matlab_exe_path:
         raise FileNotFoundError()
-    
-    bin_path = pathlib.Path(exe_path).parent
-    if bin_path.stem != 'bin':
+
+    bin_path = pathlib.Path(matlab_exe_path).parent
+    if bin_path.stem != "bin":
         raise FileNotFoundError()
-    
-    if platform.system() == "Windows": 
-        arch  = "win64"
-    elif  platform.system() == "Darwin":
-        arch = "maca64" if platform.mac_ver()[-1] == 'arm64' else "maci64"
-    else: 
+
+    if platform.system() == "Windows":
+        arch = "win64"
+    elif platform.system() == "Darwin":
+        arch = "maca64" if platform.mac_ver()[-1] == "arm64" else "maci64"
+    else:
         arch = "glnxa64"
-    
+
     dll_path = bin_path / arch
     if not dll_path.exists():
         raise FileNotFoundError(f"The expected MATLAB folders were in found at the path: {dll_path}")
-    
-    return f'{bin_path.as_posix()}/' , f'{dll_path.as_posix()}/'
+
+    return f"{bin_path.as_posix()}/", f"{dll_path.as_posix()}/"
+
 
 def start_matlab():
-    """Start MATLAB asynchronously and returns a future to retrieve the engine later.
+    """Load MATLAB engine dynamic libraries and creates wrapper object.
 
     Returns
     -------
-    future : RATapi.rat_core.MatlabEngine
-        A custom matlab engine wrapper.
+    engine : Optional[RATapi.rat_core.MatlabEngine]
+        A matlab engine object
 
     """
     try:
         with open(MATLAB_PATH_FILE) as path_file:
             matlab_path = path_file.read()
     except FileNotFoundError:
         matlab_path = ""
-    
+
     if not matlab_path:
         matlab_path = shutil.which("matlab")
         if matlab_path is None:
@@ -85,17 +112,16 @@ def start_matlab():
             if temp.is_symlink():
                 matlab_path = temp.readlink().as_posix()
             set_matlab_path(matlab_path)
-    
+
     if matlab_path:
         bin_path, dll_path = get_matlab_paths(matlab_path)
         os.environ["MATLAB_DLL_PATH"] = dll_path
-        print(bin_path, dll_path)
-        if platform.system() == "Windows": 
+        if platform.system() == "Windows":
             os.environ["PATH"] = dll_path + os.pathsep + os.environ["PATH"]
-        
+
         with cd(bin_path):
             engine = RATapi.rat_core.MatlabEngine()
-        
+
         return engine
 
 
@@ -107,12 +133,15 @@ class MatlabWrapper:
     filename : string
         The path of the file containing MATLAB function
     """
+
     engine = start_matlab()
-    
+
     def __init__(self, filename) -> None:
         if self.engine is None:
-            raise ValueError("MATLAB is not found. Please use `set_matlab_path` to set the location of your MATLAB installation") from None
-        
+            raise ValueError(
+                "MATLAB is not found. Please use `set_matlab_path` to set the location of your MATLAB installation"
+            ) from None
+
         path = pathlib.Path(filename)
         self.engine.cd(str(path.parent))
         self.engine.setFunction(path.stem)
@@ -133,7 +162,6 @@ def handle(*args):
         return handle
 
 
-
 class DylibWrapper:
     """Creates a python callback for a function in dynamic library.
 

cpp/rat.cpp

@@ -54,7 +54,6 @@ class MatlabEngine
     std::function<int(Engine *, const char *)> engEvalString;
 
     std::function<double(const mxArray *)> mxGetScalar;
-    // std::function<const mwSize *(const mxArray *)> mxGetDimensions;
     std::function<void *(const mxArray *)> mxGetData;
     std::function<mxArray *(double)> mxCreateDoubleScalar;
     std::function<mxArray *(mwSize, mwSize, mxComplexity)> mxCreateDoubleMatrix;

setup.py

@@ -1,8 +1,5 @@
-import os
 import platform
-import shutil
 import sys
-import warnings
 from glob import glob
 from pathlib import Path
 
@@ -105,13 +102,15 @@ def run(self):
 
         if self.inplace:
             obj_name = get_shared_object_name(libevent[0])
-            build_py.copy_file(f"{build_py.build_lib}/{PACKAGE_NAME}/{obj_name}", 
-                               f"{build_py.get_package_dir(PACKAGE_NAME)}/{obj_name}")
-                
-            open(f"{build_py.get_package_dir(PACKAGE_NAME)}/matlab.txt", 'w').close()
-                
+            build_py.copy_file(
+                f"{build_py.build_lib}/{PACKAGE_NAME}/{obj_name}",
+                f"{build_py.get_package_dir(PACKAGE_NAME)}/{obj_name}",
+            )
+
+            open(f"{build_py.get_package_dir(PACKAGE_NAME)}/matlab.txt", "w").close()
 
-class BuildClib(build_clib):   
+
+class BuildClib(build_clib):
     def initialize_options(self):
         super().initialize_options()
         build_py = self.get_finalized_command("build_py")
@@ -153,6 +152,7 @@ def build_libraries(self, libraries):
 
         super().build_libraries(libraries)
 
+
 setup(
     name=PACKAGE_NAME,
     version=__version__,
@@ -165,8 +165,8 @@ def build_libraries(self, libraries):
     packages=find_packages(),
     include_package_data=True,
     package_data={"": ["matlab.txt", get_shared_object_name(libevent[0])], "RATapi.examples": ["data/*.dat"]},
-    cmdclass={"build_clib": BuildClib,  "build_ext": BuildExt},
-    libraries=[libevent], 
+    cmdclass={"build_clib": BuildClib, "build_ext": BuildExt},
+    libraries=[libevent],
     ext_modules=ext_modules,
     python_requires=">=3.10",
     install_requires=[