Merge branch 'more-checkers' into 'v3'

Enable more lint checkers

See merge request openflexure/openflexure-microscope-server!290

pyproject.toml

@@ -102,22 +102,21 @@ select = [
 #    "PL", # Pylint (a subset of, catches far less than pylint does)
 #    "B", # Flake8 bugbear
     "A", # Flake8 builtins checker
-#    "C", # Flake8 comprehensions
+    "C", # Flake8 comprehensions
 #    "FIX", #TODO/FIXME's in code. These should be added during develoment for ongoing tasks.
            # If they are not fixed before merge they should be converted to GitLab issues
 #    "LOG", # Flake8 logging issues (pedantic logger formatting issues can be added with "G")
 #    "T20", # Warns for print statments, production code should log
 #    "PT", # pytest linting
-#    "RET", # Consistent clear return statments
+    "RET", # Consistent clear return statements
     "RSE", # Raise parentheses
 #    "SIM", # Simplifications detected
-#    "ARG", # unused arguments
+    "ARG", # unused arguments
-#    "C90", # McCabe complexity!
+    "C90", # McCabe complexity!
     "NPY", # Numpy linting
     "N", # PEP8 naming
-#    "DOC", # Enforce argument, return, and raise to be mentioned in docstrings there is
+#    "D", # Docstring checks these may need to be added gradually
-           # also "D" but this even warns about docstring punctuation. Perhaps a step too
+    "ERA001", # Commented out code!
-           # far?
 ]
 
 ignore = [

ruff-increased-checking.toml

@@ -24,16 +24,15 @@ select = [
     "LOG", # Flake8 logging issues (pedantic logger formatting issues can be added with "G")
     "T20", # Warns for print statments, production code should log
     "PT", # pytest linting
-    "RET", # Consistent clear return statments
+    "RET", # Consistent clear return statements
     "RSE", # Raise parentheses
     "SIM", # Simplifications detected
     "ARG", # unused arguments
     "C90", # McCabe complexity!
     "NPY", # Numpy linting
     "N", # PEP8 naming
-    "DOC", # Enforce argument, return, and raise to be mentioned in docstrings there is
+    "D", # Docstring checks these may need to be added gradually
-           # also "D" but this even warns about docstring punctuation. Perhaps a step too
+    "ERA001", # Commented out code!
-           # far?
 ]
 
 # Line length is set to 88 for ruff. This is what the formatter aims for

src/openflexure_microscope_server/things/auto_recentre_stage.py

@@ -118,20 +118,12 @@ class RecentringThing(Thing):
                         logging.info(
                             f"Breaking because the highest point is at {np.argmax(sorted_all_heights)} in the list"
                         )
-                        # plt.plot(sorted_lateral, sorted_all_heights,'.')
+
-                        # plt.plot(sorted_lateral, quad_fit_func(sorted_lateral))
-                        # plt.show()
                         break
-                    else:
+                    if turning_loc < np.min(sorted_lateral):
-                        if turning_loc < np.min(sorted_lateral):
+                        moves = -1
-                            moves = -1
+                    elif turning_loc > np.max(sorted_lateral):
-                        elif turning_loc > np.max(sorted_lateral):
+                        moves = 1
-                            moves = 1
-                        else:
-                            # plt.plot(sorted_lateral, sorted_all_heights,'.')
-                            # plt.plot(sorted_lateral, quad_fit_func(sorted_lateral))
-                            # plt.show()
-                            pass
 
             # Centre value is replaced by the maximum value recorded in that axis
             centre[direction] = focused_pos[direction][np.argmax(all_heights)][

src/openflexure_microscope_server/things/autofocus.py

@@ -105,11 +105,12 @@ class JPEGSharpnessMonitor:
             stop: int = int(np.argmax(jpeg_times > stage_times[1]))
         except ValueError as e:
             if np.sum(jpeg_times > stage_times[0]) == 0:
-                raise ValueError(
+                errmsg = (
-                    "No images were captured during the move of the stage.  Perhaps the camera is not streaming images?"
+                    "No images were captured during the move of the stage. "
-                ) from e
+                    "Perhaps the camera is not streaming images?"
-            else:
+                )
-                raise e
+                raise ValueError(errmsg) from e
+            raise e
         if stop < 1:
             stop = len(jpeg_times)
             logging.debug("changing stop to %s", (stop))

src/openflexure_microscope_server/things/background_detect.py

@@ -23,8 +23,7 @@ class BackgroundDetectThing(Thing):
         bd = self.thing_settings.get("background_distributions", None)
         if bd:
             return ChannelDistributions(**bd)
-        else:
+        return None
-            return None
 
     @background_distributions.setter
     def background_distributions(self, value: Optional[ChannelDistributions]) -> None:

src/openflexure_microscope_server/things/camera/opencv.py

@@ -83,6 +83,7 @@ class OpenCVCamera(BaseCamera):
         It's likely to be highly inefficient - raw and/or uncompressed captures using
         binary image formats will be added in due course.
         """
+        logging.warning(f"OpenCV camera doen't respect {resolution} setting")
         ret, frame = self.cap.read()
         if not ret:
             raise RuntimeError(
@@ -100,6 +101,7 @@ class OpenCVCamera(BaseCamera):
 
         This function will produce a JPEG image.
         """
+        logging.warning(f"OpenCV camera doen't respect {resolution} setting")
         frame = self.capture_array()
         jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
         exif_dict = {

src/openflexure_microscope_server/things/camera/simulation.py

@@ -189,6 +189,7 @@ class SimulatedCamera(BaseCamera):
         It's likely to be highly inefficient - raw and/or uncompressed captures using
         binary image formats will be added in due course.
         """
+        logging.warning(f"Simulation camera doen't respect {resolution} setting")
         return self.generate_frame()
 
     @thing_action
@@ -201,6 +202,7 @@ class SimulatedCamera(BaseCamera):
 
         This function will produce a JPEG image.
         """
+        logging.warning(f"Simulation camera doen't respect {resolution} setting")
         frame = self.capture_array()
         jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
         exif_dict = {

src/openflexure_microscope_server/things/camera_stage_mapping.py

@@ -87,7 +87,7 @@ def make_hardware_interface(
     axes = stage.axis_names
 
     def pos2dict(pos: Sequence[float]) -> Mapping[str, float]:
-        return {k: p for k, p in zip(axes, pos)}
+        return dict(zip(axes, pos))
 
     def dict2pos(posd: Mapping[str, float]) -> Sequence[float]:
         return tuple(posd[k] for k in axes if k in posd)

src/openflexure_microscope_server/things/stage/__init__.py

@@ -80,7 +80,7 @@ class BaseStage(Thing):
 
     position = PropertyDescriptor(
         Mapping[str, int],
-        {k: 0 for k in _axis_names},
+        dict.fromkeys(_axis_names, 0),
         description="Current position of the stage",
         readonly=True,
         observable=True,

src/openflexure_microscope_server/things/stage/dummy.py

@@ -91,5 +91,5 @@ class DummyStage(BaseStage):
         It is intended for use after manually or automatically recentring the
         stage.
         """
-        self.position = {k: 0 for k in self.axis_names}
+        self.position = dict.fromkeys(self.axis_names, 0)
         self.instantaneous_position = self.position

tests/utilities/scan_test_helpers.py

@@ -189,8 +189,7 @@ def get_expected_result_for_example_smart_spiral(
     """
     pkl_fname = os.path.join(THIS_DIR, f"example_smart_spiral_{sample_name}.pkl")
     with open(pkl_fname, "rb") as pkl_file_obj:
-        planner = pickle.load(pkl_file_obj)
+        return pickle.load(pkl_file_obj)
-    return planner
 
 
 def load_sample_points(sample_name: str):