Add ANN20X rules to ruff

change_log_helper.py

@@ -12,7 +12,7 @@ from gitlab.exceptions import GitlabGetError
 PROJECT_ID = 9238334
 
 
-def main(tag: str, branch: str = "v3"):
+def main(tag: str, branch: str = "v3") -> None:
     """Create a list of the MRs into a given branch after a tag.
 
     :param tag: The tag the mrs should be since.

pull_webapp.py

@@ -43,7 +43,7 @@ def extract_zip(zip_data: bytes) -> None:
         print(f"Extracted zip to: {THIS_DIR}")
 
 
-def main(branch: str = "v3"):
+def main(branch: str = "v3") -> None:
     """Fetch build artifacts from GitLab for a given branch and unzip.
 
     Clear any existing static directory before extract the new files.

pyproject.toml

@@ -126,7 +126,7 @@ select = [
     "N", # PEP8 naming
     "D", # Docstring checks
     "ERA001", # Commented out code!
-    "ANN001", "ANN002", "ANN003",
+    "ANN",
 ]
 
 ignore = [
@@ -134,7 +134,9 @@ ignore = [
     "D203",  # incompatible with D204
     "D213",  # incompatible with D212
     "D400",  # A stricter version of #415 that doesn't allow !
-    # The checkers below should be turned on as they complain about missing docstrings.
+    "ANN204", # Requrite type hints for
+    "ANN401", # Disalows Any, Any is needed at times, Once MyPy is running Any will be
+              # handled appropriately
 ]
 
 [tool.ruff.lint.per-file-ignores]

src/openflexure_microscope_server/logging.py

@@ -21,7 +21,7 @@ from fastapi import HTTPException
 OFM_LOG_FILE = None
 
 
-def configure_logging(log_folder: str):
+def configure_logging(log_folder: str) -> None:
     """Configure logging for the server while it is running.
 
     This modifies the root logger to have a rotating file handler and
@@ -103,7 +103,7 @@ def retrieve_log_from_file() -> PlainTextResponse:
 class OFMLogFileFormatter(logging.Formatter):
     """The formatter used for the OpenFlexure Microscope Server log file."""
 
-    def format(self, record: logging.LogRecord):
+    def format(self, record: logging.LogRecord) -> str:
         """Adjust the logging formatting for uvicorn logs.
 
         uvicorn has two loggers. Each API access is ``uvicorn.access`` which we filter
@@ -132,7 +132,7 @@ class OFMHandler(logging.Handler):
         self._log = []
         self._max_logs = max_logs
 
-    def append_record(self, record: logging.LogRecord):
+    def append_record(self, record: logging.LogRecord) -> None:
         """Format message and append it to a list of records.
 
         The built in formatter is used to format the record.
@@ -143,7 +143,7 @@ class OFMHandler(logging.Handler):
         while len(self._log) > self._max_logs:
             self._log.pop(0)
 
-    def emit(self, record: logging.LogRecord):
+    def emit(self, record: logging.LogRecord) -> None:
         """Emit will save the logged record to the log."""
         try:
             if record.levelno >= self.level:
@@ -156,7 +156,7 @@ class OFMHandler(logging.Handler):
             self.handleError(record)
 
     @property
-    def log_history(self):
+    def log_history(self) -> str:
         """Return the log history up to the maximum number of logs."""
         return "\n".join(self._log)
 
@@ -164,7 +164,7 @@ class OFMHandler(logging.Handler):
 class UvicornAccessFilter(logging.Filter):
     """A logging filter to filter out "uvicorn.access" messages."""
 
-    def filter(self, record: logging.LogRecord):
+    def filter(self, record: logging.LogRecord) -> bool:
         """Return False if record is from "uvicorn.access"."""
         return not record.name.startswith("uvicorn.access")
 

src/openflexure_microscope_server/scan_directories.py

@@ -105,7 +105,7 @@ class ScanData(BaseModel):
     This should be set with ``set_final_data()`` to ensure duration is set.
     """
 
-    def set_final_data(self, result: str):
+    def set_final_data(self, result: str) -> None:
         """Set the final data for the scan, scan duration is automatically calculated.
 
         :param result: A string describing the result.
@@ -423,13 +423,13 @@ class ScanDirectory:
         """The time the directory was created on disk."""
         return os.path.getctime(self.dir_path)
 
-    def get_scan_files(self):
+    def get_scan_files(self) -> list[str]:
         """Return a list of the files in the images dir."""
         if self.images_dir is None:
             return []
         return os.listdir(self.images_dir)
 
-    def _extract_scan_images(self, file_list: list[str]):
+    def _extract_scan_images(self, file_list: list[str]) -> list[str]:
         """Extract files which match the naming convention for scan images.
 
         :param file_list: The list of files to search. Normally this would be
@@ -439,7 +439,7 @@ class ScanDirectory:
         """
         return [i for i in file_list if IMAGE_REGEX.search(i)]
 
-    def _extract_final_stitches(self, file_list: list[str]):
+    def _extract_final_stitches(self, file_list: list[str]) -> list[str]:
         """Extract files which match the naming convention for final stitches.
 
         :param file_list: The list of files to search.
@@ -448,7 +448,7 @@ class ScanDirectory:
         """
         return [i for i in file_list if STITCH_REGEX.search(i)]
 
-    def _extract_dzi_files(self, file_list: list[str]):
+    def _extract_dzi_files(self, file_list: list[str]) -> list[str]:
         """Extract files which match the naming convention for dzi_files.
 
         :param file_list: The list of files to search.
@@ -509,7 +509,7 @@ class ScanDirectory:
                 files.append(os.path.relpath(full_path, self.dir_path))
         return files
 
-    def save_scan_data(self, scan_data: ScanData):
+    def save_scan_data(self, scan_data: ScanData) -> None:
         """Save the scan data for this scan to disk."""
         if self.scan_data_path is None:
             raise FileNotFoundError(
@@ -551,7 +551,7 @@ class ScanDirectory:
         return zip_fname
 
 
-def get_files_in_zip(zip_path: str):
+def get_files_in_zip(zip_path: str) -> list[str]:
     """List the relative paths of all files and folders in the zip folder specified."""
     scan_zip = zipfile.ZipFile(zip_path)
     return [os.path.normpath(i) for i in scan_zip.namelist()]

src/openflexure_microscope_server/scan_planners.py

@@ -332,7 +332,7 @@ class SmartSpiral(ScanPlanner):
         """Sort the remaining positions based on the current location."""
 
         # Defined rather than use a lambda for readability
-        def sort_key(pos: XYPos):
+        def sort_key(pos: XYPos) -> tuple[float, float, float]:
             return (
                 self.moves_between(current_pos, pos),
                 self.moves_between(self._initial_position, pos),

src/openflexure_microscope_server/server/__init__.py

@@ -15,7 +15,7 @@ from .legacy_api import add_v2_endpoints
 from ..logging import configure_logging, retrieve_log, retrieve_log_from_file
 
 
-def set_shutdown_function(shutdown_function: Callable[[], None]):
+def set_shutdown_function(shutdown_function: Callable[[], None]) -> None:
     """Ensure a function is called before the shutdown.
 
     This monkey patches the Uvicorn Server's handle_exit. This is needed because
@@ -32,7 +32,7 @@ def set_shutdown_function(shutdown_function: Callable[[], None]):
     original_handler = Server.handle_exit
 
     @wraps(Server.handle_exit)
-    def handle_exit(*args: Any, **kwargs: Any):
+    def handle_exit(*args: Any, **kwargs: Any) -> None:
         shutdown_function()
         original_handler(*args, **kwargs)
 
@@ -41,7 +41,7 @@ def set_shutdown_function(shutdown_function: Callable[[], None]):
 
 def customise_server(
     server: lt.ThingServer, log_folder: str, scans_folder: Optional[str]
-):
+) -> None:
     """Customise the server with additional endpoints, etc."""
     configure_logging(log_folder)
     add_v2_endpoints(server)
@@ -66,7 +66,7 @@ def _get_scans_dir(config: dict) -> Optional[str]:
     return None
 
 
-def serve_from_cli(argv: Optional[list[str]] = None):
+def serve_from_cli(argv: Optional[list[str]] = None) -> None:
     """Start the server from the command line."""
     args = lt.cli.parse_args(argv)
 
@@ -85,7 +85,7 @@ def serve_from_cli(argv: Optional[list[str]] = None):
         server = lt.cli.server_from_config(config)
         customise_server(server, log_folder, scans_folder)
 
-        def shutdown_call():
+        def shutdown_call() -> None:
             try:
                 # Kill any mjpeg streams so that StreamingResponses close.
                 server.things["/camera/"].kill_mjpeg_streams()

src/openflexure_microscope_server/server/serve_static_files.py

@@ -50,7 +50,7 @@ def add_static_files(app: FastAPI, scans_folder: Optional[str]) -> None:
     check_static_dir()
 
     @app.get("/", response_class=RedirectResponse)
-    async def redirect_fastapi():
+    async def redirect_fastapi() -> str:
         return "/index.html"
 
     # Mounting the webapp at / file by file to allow other endpoints to be created
@@ -77,7 +77,7 @@ def add_static_files(app: FastAPI, scans_folder: Optional[str]) -> None:
         )
 
 
-def check_static_dir():
+def check_static_dir() -> None:
     """Check that the static dir exists and contains expected files and dirs."""
     if not os.path.isdir(STATIC_PATH):
         raise FileNotFoundError(

src/openflexure_microscope_server/stitching.py

@@ -34,7 +34,7 @@ class StitcherValidationError(RuntimeError):
     """The stitcher received values that it deems unsafe to create a command from."""
 
 
-def validate_command(cmd: list[str]):
+def validate_command(cmd: list[str]) -> None:
     """Validate that the command only characters that are allowed in a path.
 
     The values in the commands should be numbers, commandline flags, paths, and
@@ -340,7 +340,7 @@ class FinalStitcher(BaseStitcher):
         # Print everything in the buffer when program finishes
         self.log_buffer(process.stdout)
 
-    def log_buffer(self, buffer: TextIOWrapper):
+    def log_buffer(self, buffer: TextIOWrapper) -> None:
         """Log everything in the buffer at INFO level."""
         while line := buffer.readline():
             self.logger.info(line)

src/openflexure_microscope_server/things/autofocus.py

@@ -127,7 +127,7 @@ class StackParams:
         """
         return self.min_images_to_test + 15
 
-    def slice_to_save(self, sharpest_index: int):
+    def slice_to_save(self, sharpest_index: int) -> slice:
         """Return the slice of images to save given the index of the sharpest image."""
         images_each_side = (self.images_to_save - 1) // 2
         return slice(
@@ -234,7 +234,7 @@ class JPEGSharpnessMonitor:
 
     running = False
 
-    async def monitor_sharpness(self):
+    async def monitor_sharpness(self) -> None:
         """Start monitoring the frame sizes."""
         self.running = True
         async for frame in self.camera.lores_mjpeg_stream.frame_async_generator():
@@ -244,7 +244,7 @@ class JPEGSharpnessMonitor:
                 break
 
     @contextmanager
-    def run(self):
+    def run(self) -> None:
         """Context manager, during which we will monitor sharpness from the camera."""
         self.portal.start_task_soon(self.monitor_sharpness)
         try:
@@ -403,7 +403,7 @@ class AutofocusThing(lt.Thing):
         sharpness_monitor: SharpnessMonitorDep,
         dz: int = 2000,
         start: Literal["centre", "base"] = "centre",
-    ):
+    ) -> tuple[list[float], list[float]]:
         """Repeatedly autofocus the stage until it looks focused.
 
         This action will run the ``fast_autofocus`` action until it settles on a point

src/openflexure_microscope_server/things/camera/__init__.py

@@ -133,7 +133,7 @@ class CameraMemoryBuffer:
                 "No image with matching id in memory to retrieve."
             ) from e
 
-    def clear(self):
+    def clear(self) -> None:
         """Clear all images from memory."""
         self._storage.clear()
 
@@ -208,7 +208,7 @@ class BaseCamera(lt.Thing):
             "CameraThings must define their own start_streaming method"
         )
 
-    def kill_mjpeg_streams(self):
+    def kill_mjpeg_streams(self) -> None:
         """Kill the streams now as the server is shutting down.
 
         This is called when uvicorn gets the a shutdown signal. As this is called from

src/openflexure_microscope_server/things/camera/opencv.py

@@ -65,7 +65,7 @@ class OpenCVCamera(BaseCamera):
             return self._capture_thread.is_alive()
         return False
 
-    def _capture_frames(self):
+    def _capture_frames(self) -> None:
         portal = lt.get_blocking_portal(self)
         while self._capture_enabled:
             ret, frame = self.cap.read()

src/openflexure_microscope_server/things/camera/picamera.py

@@ -72,7 +72,7 @@ class PicameraStreamOutput(Output):
         _timestamp: Optional[int] = None,
         _packet: Any = None,
         _audio: bool = False,
-    ):
+    ) -> None:
         """Add a frame to the stream's ringbuffer."""
         self.stream.add_frame(frame, self.portal)
 
@@ -173,7 +173,7 @@ class StreamingPiCamera2(BaseCamera):
     )
     """Whether the MJPEG stream is active."""
 
-    def save_settings(self):
+    def save_settings(self) -> None:
         """Override save_settings to ensure that camera properties don't recurse.
 
         This method is run by any Thing when a ThingSetting is saved. However, the
@@ -204,7 +204,7 @@ class StreamingPiCamera2(BaseCamera):
         return self._analogue_gain
 
     @analogue_gain.setter
-    def analogue_gain(self, value: float):
+    def analogue_gain(self, value: float) -> None:
         self._analogue_gain = value
         if self.streaming:
             with self._streaming_picamera() as cam:
@@ -224,7 +224,7 @@ class StreamingPiCamera2(BaseCamera):
         return self._colour_gains
 
     @colour_gains.setter
-    def colour_gains(self, value: tuple[float, float]):
+    def colour_gains(self, value: tuple[float, float]) -> None:
         self._colour_gains = value
         if self.streaming:
             with self._streaming_picamera() as cam:
@@ -248,7 +248,7 @@ class StreamingPiCamera2(BaseCamera):
         return self._exposure_time
 
     @exposure_time.setter
-    def exposure_time(self, value: int):
+    def exposure_time(self, value: int) -> None:
         self._exposure_time = value
         if self.streaming:
             with self._streaming_picamera() as cam:
@@ -292,7 +292,7 @@ class StreamingPiCamera2(BaseCamera):
         return SensorModeSelector(**self._sensor_mode)
 
     @sensor_mode.setter
-    def sensor_mode(self, new_mode: Optional[SensorModeSelector | dict]):
+    def sensor_mode(self, new_mode: Optional[SensorModeSelector | dict]) -> None:
         """Change the sensor mode used."""
         if new_mode is None:
             self._sensor_mode = None
@@ -352,7 +352,7 @@ class StreamingPiCamera2(BaseCamera):
                 ) from e
             return None
 
-    def _initialise_picamera(self):
+    def _initialise_picamera(self) -> None:
         """Acquire the picamera device and store it as ``self._picamera``.
 
         This duplicates logic in ``Picamera2.__init__`` to provide a tuning file that
@@ -646,7 +646,7 @@ class StreamingPiCamera2(BaseCamera):
         self,
         target_white_level: int = 700,
         percentile: float = 99.9,
-    ):
+    ) -> None:
         """Adjust exposure until a the target white level is reached.
 
         Starting from the minimum exposure, gradually increase exposure until
@@ -672,7 +672,7 @@ class StreamingPiCamera2(BaseCamera):
         self,
         method: Literal["percentile", "centre"] = "centre",
         luminance_power: float = 1.0,
-    ):
+    ) -> None:
         """Correct the white balance of the image.
 
         This calibration requires a neutral image, such that the 99th centile
@@ -747,7 +747,7 @@ class StreamingPiCamera2(BaseCamera):
                 self._initialise_picamera()
 
     @lt.thing_action
-    def reset_ccm(self):
+    def reset_ccm(self) -> None:
         """Overwrite the colour correction matrix in camera tuning with default values.
 
         These values are from the Raspberry Pi Camera Algorithm and Tuning Guide, page

src/openflexure_microscope_server/things/camera/simulation.py

@@ -8,7 +8,7 @@ See repository root for licensing information.
 
 from __future__ import annotations
 import logging
-from typing import Literal, Optional
+from typing import Literal, Optional, Mapping
 from types import TracebackType
 from threading import Thread
 import time
@@ -76,7 +76,7 @@ class SimulatedCamera(BaseCamera):
         self.generate_blobs()
         self.generate_canvas()
 
-    def generate_sprites(self):
+    def generate_sprites(self) -> None:
         """Generate sprites to populate the image."""
         sprite_sizes = [5, 7, 10, 21, 36, 40]
         self.sprites = []
@@ -109,7 +109,7 @@ class SimulatedCamera(BaseCamera):
             # Convert to uint8 and append to the list
             self.sprites.append(sprite.astype(np.uint8))
 
-    def generate_blobs(self, n_blobs: int = 1000):
+    def generate_blobs(self, n_blobs: int = 1000) -> None:
         """Generate coordinates of blobs and their sizes.
 
         A 1000x3 array is returned. Each row represents (x,y) coordinate
@@ -125,7 +125,7 @@ class SimulatedCamera(BaseCamera):
         self.blobs[:, 1] = RNG.uniform(w / 2, self.canvas_shape[1] - w / 2, n_blobs)
         self.blobs[:, 2] = RNG.choice(len(self.sprites), n_blobs)
 
-    def generate_canvas(self):
+    def generate_canvas(self) -> None:
         """Generate a canvas.
 
         Canvas is int16 so that random noise can be added to simulation image before
@@ -145,7 +145,7 @@ class SimulatedCamera(BaseCamera):
         self.canvas[self.canvas < 0] = 0
         self.canvas[self.canvas > 255] = 255
 
-    def generate_image(self, pos: tuple[int, int, int]):
+    def generate_image(self, pos: tuple[int, int, int]) -> np.ndarray:
         """Generate an image with blobs based on supplied coordinates."""
         canvas_width, canvas_height, _ = self.canvas_shape
         image_width, image_height, _ = self.shape
@@ -180,16 +180,16 @@ class SimulatedCamera(BaseCamera):
 
     def attach_to_server(
         self, server: lt.ThingServer, path: str, setting_storage_path: str
-    ):
+    ) -> None:
         """Wrap the attach_to_server method so the server instance can be stored.
 
         Direct access to the server instance is needed to get the stage position while
         maintaining the same public API as a real camera that doesn't need this access.
         """
         self._server = server
-        return super().attach_to_server(server, path, setting_storage_path)
+        super().attach_to_server(server, path, setting_storage_path)
 
-    def get_stage_position(self):
+    def get_stage_position(self) -> Mapping[str, int]:
         """Return the stage position.
 
         The simulation camera has access to the stage position so it can generate a
@@ -199,7 +199,7 @@ class SimulatedCamera(BaseCamera):
             self._stage = self._server.things["/stage/"]
         return self._stage.instantaneous_position
 
-    def generate_frame(self):
+    def generate_frame(self) -> np.ndarray:
         """Generate a frame with blobs based on the stage coordinates."""
         try:
             pos = self.get_stage_position()
@@ -256,7 +256,7 @@ class SimulatedCamera(BaseCamera):
 
     noise_level = lt.ThingProperty(float, 2.0)
 
-    def _capture_frames(self):
+    def _capture_frames(self) -> None:
         portal = lt.get_blocking_portal(self)
         while self._capture_enabled:
             time.sleep(self.frame_interval)
@@ -312,14 +312,14 @@ class SimulatedCamera(BaseCamera):
         return Image.fromarray(self.generate_frame())
 
     @lt.thing_action
-    def remove_sample(self):
+    def remove_sample(self) -> None:
         """Show the simulated background with no sample."""
         if not self._show_sample:
             raise RuntimeError("Sample is already removed.")
         self._show_sample = False
 
     @lt.thing_action
-    def load_sample(self):
+    def load_sample(self) -> None:
         """Show the simulated sample."""
         if self._show_sample:
             raise RuntimeError("Sample is already in place.")

src/openflexure_microscope_server/things/camera_stage_mapping.py

@@ -18,6 +18,7 @@ from typing import (
     NamedTuple,
     Optional,
     Tuple,
+    Mapping,
 )
 from fastapi import HTTPException
 
@@ -85,7 +86,7 @@ class RecordedMove:
         positions: List[CoordinateType] = [p for t, p in self._history if p is not None]
         return MoveHistory(times, positions)
 
-    def clear_history(self):
+    def clear_history(self) -> None:
         """Reset our history to be an empty list."""
         self._history = []
 
@@ -241,7 +242,7 @@ class CameraStageMapper(lt.Thing):
             return None
         return self.last_calibration["image_resolution"]
 
-    def assert_calibrated(self):
+    def assert_calibrated(self) -> None:
         """Raise an exception if the image_to_stage_displacement matrix is not set."""
         if self.image_to_stage_displacement_matrix is None:
             # Disable check of no message in raised exception as the message is explicitly
@@ -254,7 +255,7 @@ class CameraStageMapper(lt.Thing):
         stage: Stage,
         x: float,
         y: float,
-    ):
+    ) -> None:
         """Move by a given number of pixels on the camera.
 
         NB x and y here refer to what is usually understood to be the horizontal and
@@ -273,7 +274,7 @@ class CameraStageMapper(lt.Thing):
         stage.move_relative(x=relative_move[0], y=relative_move[1])
 
     @lt.thing_property
-    def thing_state(self) -> dict[str, Any]:
+    def thing_state(self) -> Mapping[str, Any]:
         """Summary metadata describing the current state of the Thing."""
         return {
             k: getattr(self, k)

src/openflexure_microscope_server/things/smart_scan.py

@@ -38,8 +38,17 @@ CSMDep = lt.deps.direct_thing_client_dependency(
 )
 AutofocusDep = lt.deps.direct_thing_client_dependency(AutofocusThing, "/autofocus/")
 
-JPEGBlob = lt.blob.blob_type("image/jpeg")
-ZipBlob = lt.blob.blob_type("application/zip")
+
+class JPEGBlob(lt.blob.Blob):
+    """A class representing a JPEG image as a LabThings FastAPI Blob."""
+
+    media_type: str = "image/jpeg"
+
+
+class ZipBlob(lt.blob.Blob):
+    """A class representing a Zip file as a LabThings FastAPI Blob."""
+
+    media_type: str = "application/zip"
 
 
 class ScanNotRunningError(RuntimeError):
@@ -116,7 +125,7 @@ class SmartScanThing(lt.Thing):
         cam: CameraClient,
         csm: CSMDep,
         scan_name: str = "",
-    ):
+    ) -> None:
         """Move the stage to cover an area, taking images that can be tiled together.
 
         The stage will move in a pattern that grows outwards from the starting point,
@@ -171,7 +180,7 @@ class SmartScanThing(lt.Thing):
             self._preview_stitcher = None
 
     @_scan_running
-    def _check_background_and_csm_set(self):
+    def _check_background_and_csm_set(self) -> None:
         """Before starting a scan, check that background and camera-stage-mapping are set.
 
         Raise error if:
@@ -311,7 +320,7 @@ class SmartScanThing(lt.Thing):
         )
 
     @_scan_running
-    def _save_final_scan_data(self, scan_result: str):
+    def _save_final_scan_data(self, scan_result: str) -> None:
         """Update scan data JSON file with data only known at the end of the scan.
 
         Takes scan_result, a string that is either "success", "cancelled by user",
@@ -321,7 +330,7 @@ class SmartScanThing(lt.Thing):
         self._ongoing_scan.save_scan_data(self._scan_data)
 
     @_scan_running
-    def _manage_stitching_threads(self):
+    def _manage_stitching_threads(self) -> None:
         """Manage the stitching threads, starting them if needed and not already running."""
         # Assume 4 images means at least one offset in x and y, making the stitching
         # well constrained.
@@ -330,7 +339,7 @@ class SmartScanThing(lt.Thing):
                 self._preview_stitcher.start()
 
     @_scan_running
-    def _run_scan(self):
+    def _run_scan(self) -> None:
         """Prepare and run the main scan, and perform final actions on completion.
 
         The result (or exception) from the main scan loop determines whether the
@@ -382,7 +391,7 @@ class SmartScanThing(lt.Thing):
         self.purge_empty_scans(logger=self._scan_logger)
 
     @_scan_running
-    def _main_scan_loop(self):
+    def _main_scan_loop(self) -> None:
         """Run the main loop of the scan.
 
         This loop runs during a scan, until no more scan x,y positions
@@ -449,7 +458,7 @@ class SmartScanThing(lt.Thing):
             self._ongoing_scan.zip_files()
 
     @_scan_running
-    def _return_to_starting_position(self):
+    def _return_to_starting_position(self) -> None:
         """Return to the initial scan position, if set."""
         self._scan_logger.info("Returning to starting position.")
         if self._scan_data is not None:
@@ -458,7 +467,7 @@ class SmartScanThing(lt.Thing):
             )
 
     @_scan_running
-    def _perform_final_stitch(self):
+    def _perform_final_stitch(self) -> None:
         """Update the scan zip and perform final stitch of the data."""
         if self._scan_data.image_count <= 3:
             self._scan_logger.info("Not performing a stitch as 3 or fewer images taken")
@@ -729,7 +738,7 @@ class SmartScanThing(lt.Thing):
     def download_zip(
         self,
         scan_name: str,
-    ):
+    ) -> ZipBlob:
         """Return zip after including any files left until the end.
 
         The zipfile is returned as a Blob.
@@ -740,7 +749,7 @@ class SmartScanThing(lt.Thing):
     @lt.thing_action
     def stitch_all_scans(
         self, logger: lt.deps.InvocationLogger, cancel: lt.deps.CancelHook
-    ):
+    ) -> None:
         """Check the list of scans, and stitch any that don't have a DZI associated with it.
 
         :raises RuntimeError: if the microscope is currently running a scan

src/openflexure_microscope_server/things/stage/__init__.py

@@ -11,7 +11,7 @@ As the object will be used as a context manager create the hardware connection i
 
 from __future__ import annotations
 from collections.abc import Sequence, Mapping
-from typing import Literal
+from typing import Literal, Never, Any
 
 import labthings_fastapi as lt
 
@@ -119,12 +119,12 @@ class BaseStage(lt.Thing):
         )
 
     @property
-    def thing_state(self):
+    def thing_state(self) -> Mapping[str, Any]:
         """Summary metadata describing the current state of the stage."""
         return {"position": self.position}
 
     @lt.thing_action
-    def invert_axis_direction(self, axis: Literal["x", "y", "z"]):
+    def invert_axis_direction(self, axis: Literal["x", "y", "z"]) -> None:
         """Invert the direction setting of the given axis.
 
         :param axis: The axis name (x, y or z) to invert.
@@ -143,7 +143,7 @@ class BaseStage(lt.Thing):
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
         **kwargs: int,
-    ):
+    ) -> None:
         """Make a relative move. Keyword arguments should be axis names."""
         self._hardware_move_relative(
             cancel=cancel,
@@ -156,7 +156,7 @@ class BaseStage(lt.Thing):
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
         **kwargs: int,
-    ):
+    ) -> Never:
         """Make a relative move in the coordinate system used by the physical hardware.
 
         Make sure to use and update ``self._hardware_position`` not ``self.position``.
@@ -171,7 +171,7 @@ class BaseStage(lt.Thing):
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
         **kwargs: int,
-    ):
+    ) -> None:
         """Make an absolute move. Keyword arguments should be axis names."""
         self._hardware_move_absolute(
             cancel=cancel,
@@ -184,7 +184,7 @@ class BaseStage(lt.Thing):
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
         **kwargs: int,
-    ):
+    ) -> Never:
         """Make a absolute move in the coordinate system used by the physical hardware.
 
         Make sure to use and update ``self._hardware_position`` not ``self.position``.
@@ -194,7 +194,7 @@ class BaseStage(lt.Thing):
         )
 
     @lt.thing_action
-    def set_zero_position(self):
+    def set_zero_position(self) -> Never:
         """Make the current position zero in all axes.
 
         This action does not move the stage, but resets the position to zero.

src/openflexure_microscope_server/things/stage/dummy.py

@@ -55,7 +55,7 @@ class DummyStage(BaseStage):
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
         **kwargs: int,
-    ):
+    ) -> None:
         """Make a relative move. Keyword arguments should be axis names."""
         displacement = [kwargs.get(k, 0) for k in self.axis_names]
         self.moving = True
@@ -93,7 +93,7 @@ class DummyStage(BaseStage):
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
         **kwargs: int,
-    ):
+    ) -> None:
         """Make an absolute move. Keyword arguments should be axis names."""
         displacement = {
             axis: int(pos) - self._hardware_position[axis]
@@ -105,7 +105,7 @@ class DummyStage(BaseStage):
         )
 
     @lt.thing_action
-    def set_zero_position(self):
+    def set_zero_position(self) -> None:
         """Make the current position zero in all axes.
 
         This action does not move the stage, but resets the position to zero.

src/openflexure_microscope_server/things/system.py

@@ -51,7 +51,7 @@ class OpenFlexureSystem(lt.Thing):
         return UUID(self._microscope_id)
 
     @microscope_id.setter
-    def microscope_id(self, uuid: UUID):
+    def microscope_id(self, uuid: UUID) -> None:
         # TODO make read only but still settable from disk
         self._microscope_id = uuid
 

src/openflexure_microscope_server/utilities.py

@@ -105,7 +105,7 @@ class ErrorCapturingThread(Thread):
             daemon=daemon,
         )
 
-    def join(self, timeout: Optional[float] = None):
+    def join(self, timeout: Optional[float] = None) -> None:
         """Join when the thread is complete.
 
         If the thread ended due to an unhandled exception, the exception will be raised
@@ -121,7 +121,7 @@ class ErrorCapturingThread(Thread):
 
 def _wrap_and_catch_errors(
     target: Callable[..., Any], error_buffer: list, *args: Any, **kwargs: Any
-):
+) -> None:
     """Run target function in a try-except block.
 
     This function is designed only to be used by ErrorCapturingThread.