add Cython profiling option for later use (currently not working)

pyproject.toml

@@ -53,6 +53,7 @@ log_cli = true
 
 [tool.coverage.run]
 relative_files = true
+plugins = ["Cython.Coverage"]
 source = [
     "src/",
     "tests/",

setup.py

@@ -1,3 +1,5 @@
+import os
+
 from Cython.Build import cythonize
 from Cython.Compiler import Options
 from setuptools import setup
@@ -13,8 +15,14 @@ ext_modules = cythonize(
         "language_level": 3,
         "embedsignature": False,
         "annotation_typing": True,
+        "linetrace": True,
     },
 )
 
 
+DEBUG = bool(os.getenv("DOPT_DEBUG", None))
+
+if DEBUG:
+    ext_modules[0].define_macros.append(("CYTHON_TRACE", "1"))
+
 setup(ext_modules=ext_modules)

src/dopt_sensor_anomalies/detection.py

@@ -74,7 +74,7 @@ def measure_length(
 
     cnts = cv2.findContours(edged.copy(), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
     cnts = imutils.grab_contours(cnts)
-    if cnts is None:
+    if cnts is None:  # pragma: no cover
         raise errors.ContourCalculationError(
             "No contours were found in the provided image. Can not continue analysis."
         )
@@ -82,7 +82,7 @@ def measure_length(
     cnts, _ = contours.sort_contours(cnts)
     x_coords = [cv2.boundingRect(c)[0] for c in cnts]
     is_sorted = np.all(x1 <= x2 for x1, x2 in zip(x_coords, x_coords[1:]))  # type: ignore
-    if not is_sorted:
+    if not is_sorted:  # pragma: no cover
         raise errors.ContourCalculationError(
             "Contour detection not valid: contours are not "
             "properly sorted from left to right."
@@ -128,13 +128,13 @@ def measure_length(
             ]
         )
 
-    if not filtered_cnts:
+    if not filtered_cnts:  # pragma: no cover
         raise errors.ContourCalculationError(
             "Contour detection not valid: no contours recognized"
         )
 
     num_contours = len(filtered_cnts)
-    if num_contours != const.NUM_VALID_ELECTRODES:
+    if num_contours != const.NUM_VALID_ELECTRODES:  # pragma: no cover
         raise errors.InvalidElectrodeCount(
             f"Number of counted electrodes does not match the "
             f"expected value: count = {num_contours}, expected = {const.NUM_VALID_ELECTRODES}"