From 24233412af0016c44edd84fca1483d168a9004be Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Wed, 27 Aug 2025 13:21:34 +0100
Subject: [PATCH 1/7] Start adding ANN ruff rules

---
 change_log_helper.py                          |  2 +-
 pyproject.toml                                |  8 +++++-
 src/openflexure_microscope_server/logging.py  |  4 +--
 .../scan_directories.py                       |  2 +-
 .../scan_planners.py                          |  2 +-
 .../stitching.py                              |  2 +-
 .../things/autofocus.py                       |  4 +--
 .../things/camera/__init__.py                 | 10 +++++--
 .../things/camera/opencv.py                   |  8 +++++-
 .../things/camera/picamera.py                 | 24 ++++++++++++----
 .../camera/picamera_recalibrate_utils.py      |  4 ++-
 .../things/camera/simulation.py               |  8 +++++-
 .../things/smart_scan.py                      | 13 ++++++---
 .../things/stage/__init__.py                  |  8 +++---
 .../things/stage/dummy.py                     | 13 +++++++--
 .../things/stage/sangaboard.py                | 14 +++++++---
 src/openflexure_microscope_server/ui.py       | 10 +++++--
 .../utilities.py                              | 28 ++++++++++++++-----
 tests/test_stage.py                           |  5 ++--
 19 files changed, 123 insertions(+), 46 deletions(-)

diff --git a/change_log_helper.py b/change_log_helper.py
index 94202aaf..79296132 100755
--- a/change_log_helper.py
+++ b/change_log_helper.py
@@ -12,7 +12,7 @@ from gitlab.exceptions import GitlabGetError
 PROJECT_ID = 9238334
 
 
-def main(tag, branch: str = "v3"):
+def main(tag: str, branch: str = "v3"):
     """Create a list of the MRs into a given branch after a tag.
 
     :param tag: The tag the mrs should be since.
diff --git a/pyproject.toml b/pyproject.toml
index 746cc24e..b1d8aaa9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -124,8 +124,9 @@ select = [
     "C90", # McCabe complexity!
     "NPY", # Numpy linting
     "N", # PEP8 naming
-    "D", # Docstring checks these may need to be added gradually
+    "D", # Docstring checks
     "ERA001", # Commented out code!
+    "ANN001",
 ]
 
 ignore = [
@@ -140,6 +141,11 @@ ignore = [
 # Tests are currently not fully docstring-ed, we'll ignore this for now.
 "tests/*" = [
     "B018", # Complaining about useless attribute access in tests, but we need them to check errors are raised
+    "ANN", # Tests are not typehinted for fixtures etc
+]
+"hardware-specific-tests/*" = [
+    "B018", # Complaining about useless attribute access in tests, but we need them to check errors are raised
+    "ANN", # Tests are not typehinted for fixtures etc
 ]
 
 [tool.ruff.lint.pydocstyle]
diff --git a/src/openflexure_microscope_server/logging.py b/src/openflexure_microscope_server/logging.py
index 69a03ffc..0df9a60e 100644
--- a/src/openflexure_microscope_server/logging.py
+++ b/src/openflexure_microscope_server/logging.py
@@ -21,7 +21,7 @@ from fastapi import HTTPException
 OFM_LOG_FILE = None
 
 
-def configure_logging(log_folder):
+def configure_logging(log_folder: str):
     """Configure logging for the server while it is running.
 
     This modifies the root logger to have a rotating file handler and
@@ -120,7 +120,7 @@ class OFMLogFileFormatter(logging.Formatter):
 class OFMHandler(logging.Handler):
     """A logging.Handler that stores the most recent logs for access by the server."""
 
-    def __init__(self, level=logging.INFO, max_logs=250):
+    def __init__(self, level: int = logging.INFO, max_logs: int = 250):
         """Initialise the handler with a set logging level and message buffer size.
 
         :param level: The level of logs captured. As standard logs of INFO and above
diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index a6fd124f..cb96bd25 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -551,7 +551,7 @@ class ScanDirectory:
         return zip_fname
 
 
-def get_files_in_zip(zip_path):
+def get_files_in_zip(zip_path: 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()]
diff --git a/src/openflexure_microscope_server/scan_planners.py b/src/openflexure_microscope_server/scan_planners.py
index 065b3258..87f9000b 100644
--- a/src/openflexure_microscope_server/scan_planners.py
+++ b/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):
+        def sort_key(pos: XYPos):
             return (
                 self.moves_between(current_pos, pos),
                 self.moves_between(self._initial_position, pos),
diff --git a/src/openflexure_microscope_server/stitching.py b/src/openflexure_microscope_server/stitching.py
index 1660944e..32a5253e 100644
--- a/src/openflexure_microscope_server/stitching.py
+++ b/src/openflexure_microscope_server/stitching.py
@@ -185,7 +185,7 @@ class FinalStitcher(BaseStitcher):
 
     def __init__(
         self,
-        images_dir,
+        images_dir: str,
         *,
         logger: lt.deps.InvocationLogger,
         overlap: Optional[float] = None,
diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py
index a6c0e92a..e80d1e47 100644
--- a/src/openflexure_microscope_server/things/autofocus.py
+++ b/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):
+    def slice_to_save(self, sharpest_index: int):
         """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(
@@ -401,7 +401,7 @@ class AutofocusThing(lt.Thing):
         self,
         stage: Stage,
         sharpness_monitor: SharpnessMonitorDep,
-        dz=2000,
+        dz: int = 2000,
         start: Literal["centre", "base"] = "centre",
     ):
         """Repeatedly autofocus the stage until it looks focused.
diff --git a/src/openflexure_microscope_server/things/camera/__init__.py b/src/openflexure_microscope_server/things/camera/__init__.py
index abee8f06..94badd0c 100644
--- a/src/openflexure_microscope_server/things/camera/__init__.py
+++ b/src/openflexure_microscope_server/things/camera/__init__.py
@@ -8,6 +8,7 @@ See repository root for licensing information.
 
 from __future__ import annotations
 from typing import Literal, Optional, Tuple, Any
+from types import TracebackType
 import json
 import io
 import time
@@ -185,7 +186,12 @@ class BaseCamera(lt.Thing):
         """Open hardware connection when the Thing context manager is opened."""
         raise NotImplementedError("CameraThings must define their own __enter__ method")
 
-    def __exit__(self, _exc_type, _exc_value, _traceback) -> None:
+    def __exit__(
+        self,
+        _exc_type: type[BaseException],
+        _exc_value: Optional[BaseException],
+        _traceback: Optional[TracebackType],
+    ) -> None:
         """Close hardware connection when the Thing context manager is closed."""
         raise NotImplementedError("CameraThings must define their own __exit__ method")
 
@@ -575,7 +581,7 @@ class BaseCamera(lt.Thing):
         return self.active_detector.status
 
     @lt.thing_action
-    def update_detector_settings(self, data) -> None:
+    def update_detector_settings(self, data: dict[str, Any]) -> None:
         """Update the settings of the current detector.
 
         This is an action not a setting/property as the data model depends on the
diff --git a/src/openflexure_microscope_server/things/camera/opencv.py b/src/openflexure_microscope_server/things/camera/opencv.py
index 5f179301..e87befec 100644
--- a/src/openflexure_microscope_server/things/camera/opencv.py
+++ b/src/openflexure_microscope_server/things/camera/opencv.py
@@ -10,6 +10,7 @@ from __future__ import annotations
 
 import logging
 from typing import Literal, Optional
+from types import TracebackType
 from threading import Thread
 
 import cv2
@@ -42,7 +43,12 @@ class OpenCVCamera(BaseCamera):
         self._capture_thread.start()
         return self
 
-    def __exit__(self, _exc_type, _exc_value, _traceback):
+    def __exit__(
+        self,
+        _exc_type: type[BaseException],
+        _exc_value: Optional[BaseException],
+        _traceback: Optional[TracebackType],
+    ):
         """Release the camera when the Thing context manager is closed.
 
         Before releasing the camera the capture thread is closed.
diff --git a/src/openflexure_microscope_server/things/camera/picamera.py b/src/openflexure_microscope_server/things/camera/picamera.py
index 5e55ea92..25b29a44 100644
--- a/src/openflexure_microscope_server/things/camera/picamera.py
+++ b/src/openflexure_microscope_server/things/camera/picamera.py
@@ -15,7 +15,8 @@ https://datasheets.raspberrypi.com/camera/raspberry-pi-camera-guide.pdf
 """
 
 from __future__ import annotations
-from typing import Annotated, Iterator, Literal, Mapping, Optional, overload
+from typing import Annotated, Iterator, Literal, Mapping, Optional, overload, Any
+from types import TracebackType
 import json
 import logging
 import os
@@ -65,7 +66,12 @@ class PicameraStreamOutput(Output):
         self.portal = portal
 
     def outputframe(
-        self, frame, _keyframe=True, _timestamp=None, _packet=None, _audio=False
+        self,
+        frame: bytes,
+        _keyframe: Optional[bool] = True,
+        _timestamp: Optional[int] = None,
+        _packet: Any = None,
+        _audio: bool = False,
     ):
         """Add a frame to the stream's ringbuffer."""
         self.stream.add_frame(frame, self.portal)
@@ -396,7 +402,7 @@ class StreamingPiCamera2(BaseCamera):
         return self._picamera is not None and self._picamera.started
 
     @contextmanager
-    def _streaming_picamera(self, pause_stream=False) -> Iterator[Picamera2]:
+    def _streaming_picamera(self, pause_stream: bool = False) -> Iterator[Picamera2]:
         """Lock access to picamera and return the underlying ``Picamera2`` instance.
 
         Optionally the stream can be paused to allow updating the camera settings.
@@ -419,7 +425,12 @@ class StreamingPiCamera2(BaseCamera):
                 if pause_stream and already_streaming:
                     self.start_streaming()
 
-    def __exit__(self, exc_type, exc_value, traceback):
+    def __exit__(
+        self,
+        _exc_type: type[BaseException],
+        _exc_value: Optional[BaseException],
+        _traceback: Optional[TracebackType],
+    ):
         """Close the picamera connection when the Thing context manager is closed."""
         self.stop_streaming()
         with self._streaming_picamera() as cam:
@@ -725,7 +736,10 @@ class StreamingPiCamera2(BaseCamera):
         return tuple(recalibrate_utils.get_static_ccm(self.tuning)[0]["ccm"])
 
     @colour_correction_matrix.setter  # type: ignore
-    def colour_correction_matrix(self, value) -> None:
+    def colour_correction_matrix(
+        self,
+        value: tuple[float, float, float, float, float, float, float, float, float],
+    ) -> None:
         recalibrate_utils.set_static_ccm(self.tuning, value)
 
         if self._picamera is not None:
diff --git a/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py b/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py
index fbf827df..44f269f6 100644
--- a/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py
+++ b/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py
@@ -353,7 +353,9 @@ def upsample_channels(grids: np.ndarray, shape: tuple[int]) -> np.ndarray:
     return zoom(grids, zoom_factors, order=1)[:, : shape[0], : shape[1]]
 
 
-def downsampled_channels(channels: np.ndarray, blacklevel=64) -> list[np.ndarray]:
+def downsampled_channels(
+    channels: np.ndarray, blacklevel: int = 64
+) -> list[np.ndarray]:
     """Generate a downsampled, un-normalised image from which to calculate the LST.
 
     TODO: blacklevel probably ought to be determined from the camera...
diff --git a/src/openflexure_microscope_server/things/camera/simulation.py b/src/openflexure_microscope_server/things/camera/simulation.py
index 7c7a856b..31e1c9aa 100644
--- a/src/openflexure_microscope_server/things/camera/simulation.py
+++ b/src/openflexure_microscope_server/things/camera/simulation.py
@@ -9,6 +9,7 @@ See repository root for licensing information.
 from __future__ import annotations
 import logging
 from typing import Literal, Optional
+from types import TracebackType
 from threading import Thread
 import time
 
@@ -212,7 +213,12 @@ class SimulatedCamera(BaseCamera):
         self.start_streaming()
         return self
 
-    def __exit__(self, _exc_type, _exc_value, _traceback):
+    def __exit__(
+        self,
+        _exc_type: type[BaseException],
+        _exc_value: Optional[BaseException],
+        _traceback: Optional[TracebackType],
+    ):
         """Close the capture thread when the Thing context manager is closed."""
         if self.stream_active:
             self._capture_enabled = False
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 9e44a329..a7b70fb8 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -7,7 +7,7 @@ It also controls external processes for live stitching composite images, and
 the creation of the final stitched images.
 """
 
-from typing import Optional
+from typing import Optional, Self, TypeVar, ParamSpec, Callable, Concatenate
 import threading
 import os
 import time
@@ -30,6 +30,9 @@ from .camera_stage_mapping import CameraStageMapper
 from .camera import CameraDependency as CameraClient
 from .stage import StageDependency as StageDep
 
+T = TypeVar("T")
+P = ParamSpec("P")
+
 CSMDep = lt.deps.direct_thing_client_dependency(
     CameraStageMapper, "/camera_stage_mapping/"
 )
@@ -43,7 +46,9 @@ class ScanNotRunningError(RuntimeError):
     """Exception called when scan not running that requires a scan to be running."""
 
 
-def _scan_running(method):
+def _scan_running(
+    method: Callable[Concatenate[Self, P], T],
+) -> Callable[Concatenate[Self, P], T]:
     """Decorate a method so that it will error if a scan is not running.
 
     This decorator is used by all methods in SmartScanThing that are using
@@ -52,7 +57,7 @@ def _scan_running(method):
     the same time and released with the lock
     """
 
-    def scan_running_wrapper(self, *args, **kwargs):
+    def scan_running_wrapper(self: Self, *args: P.args, **kwargs: P.kwargs) -> T:
         # Only start the method is the scan logger is set
         if self._scan_logger is not None:
             return method(self, *args, **kwargs)
@@ -623,7 +628,7 @@ class SmartScanThing(lt.Thing):
             if scan_info.number_of_images == 0:
                 self._delete_scan(scan_info.name, logger)
 
-    def _delete_scan(self, scan_name, logger: lt.deps.InvocationLogger) -> bool:
+    def _delete_scan(self, scan_name: str, logger: lt.deps.InvocationLogger) -> bool:
         """Delete a scan.
 
         This is a wrapper around scan manager's delete_scan that logs to the
diff --git a/src/openflexure_microscope_server/things/stage/__init__.py b/src/openflexure_microscope_server/things/stage/__init__.py
index a57f903d..92bd76d7 100644
--- a/src/openflexure_microscope_server/things/stage/__init__.py
+++ b/src/openflexure_microscope_server/things/stage/__init__.py
@@ -142,7 +142,7 @@ class BaseStage(lt.Thing):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ):
         """Make a relative move. Keyword arguments should be axis names."""
         self._hardware_move_relative(
@@ -155,7 +155,7 @@ class BaseStage(lt.Thing):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ):
         """Make a relative move in the coordinate system used by the physical hardware.
 
@@ -170,7 +170,7 @@ class BaseStage(lt.Thing):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ):
         """Make an absolute move. Keyword arguments should be axis names."""
         self._hardware_move_absolute(
@@ -183,7 +183,7 @@ class BaseStage(lt.Thing):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ):
         """Make a absolute move in the coordinate system used by the physical hardware.
 
diff --git a/src/openflexure_microscope_server/things/stage/dummy.py b/src/openflexure_microscope_server/things/stage/dummy.py
index 8b71f78f..3015b42c 100644
--- a/src/openflexure_microscope_server/things/stage/dummy.py
+++ b/src/openflexure_microscope_server/things/stage/dummy.py
@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+from typing import Optional
+from types import TracebackType
 from collections.abc import Mapping
 import time
 
@@ -33,7 +35,12 @@ class DummyStage(BaseStage):
         """Register the stage position when the Thing context manager is opened."""
         self.instantaneous_position = self._hardware_position
 
-    def __exit__(self, _exc_type, _exc_value, _traceback):
+    def __exit__(
+        self,
+        _exc_type: type[BaseException],
+        _exc_value: Optional[BaseException],
+        _traceback: Optional[TracebackType],
+    ):
         """Nothing to do when the Thing context manager is closed."""
 
     axis_inverted = lt.ThingSetting(
@@ -47,7 +54,7 @@ class DummyStage(BaseStage):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ):
         """Make a relative move. Keyword arguments should be axis names."""
         displacement = [kwargs.get(k, 0) for k in self.axis_names]
@@ -85,7 +92,7 @@ class DummyStage(BaseStage):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ):
         """Make an absolute move. Keyword arguments should be axis names."""
         displacement = {
diff --git a/src/openflexure_microscope_server/things/stage/sangaboard.py b/src/openflexure_microscope_server/things/stage/sangaboard.py
index d6ab3b29..8fea6684 100644
--- a/src/openflexure_microscope_server/things/stage/sangaboard.py
+++ b/src/openflexure_microscope_server/things/stage/sangaboard.py
@@ -5,7 +5,8 @@ import logging
 import threading
 import time
 from copy import copy
-from typing import Iterator, Literal
+from typing import Iterator, Literal, Optional
+from types import TracebackType
 from contextlib import contextmanager
 from collections.abc import Mapping
 
@@ -53,7 +54,12 @@ class SangaboardThing(BaseStage):
             sb.query("blocking_moves false")
         self.update_position()
 
-    def __exit__(self, _exc_type, _exc_value, _traceback):
+    def __exit__(
+        self,
+        _exc_type: type[BaseException],
+        _exc_value: Optional[BaseException],
+        _traceback: Optional[TracebackType],
+    ):
         """Close the sangaboard connection when the Thing context manager is closed."""
         with self.sangaboard() as sb:
             sb.close()
@@ -85,7 +91,7 @@ class SangaboardThing(BaseStage):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ) -> None:
         """Make a relative move in the coordinate system used by the sangaboard."""
         displacement = [kwargs.get(axis, 0) for axis in self.axis_names]
@@ -112,7 +118,7 @@ class SangaboardThing(BaseStage):
         self,
         cancel: lt.deps.CancelHook,
         block_cancellation: bool = False,
-        **kwargs: Mapping[str, int],
+        **kwargs: int,
     ) -> None:
         """Make a absolute move in the coordinate system used by the sangaboard."""
         with self.sangaboard():
diff --git a/src/openflexure_microscope_server/ui.py b/src/openflexure_microscope_server/ui.py
index be2a5c12..7a595dd9 100644
--- a/src/openflexure_microscope_server/ui.py
+++ b/src/openflexure_microscope_server/ui.py
@@ -1,7 +1,11 @@
 """Functionality for communicating the required user interface for a thing."""
 
+from typing import Callable, Any
+
 from pydantic import BaseModel
 
+import labthings_fastapi as lt
+
 
 class ActionButton(BaseModel):
     """The data required for creating an actionButton in Vue.
@@ -43,7 +47,7 @@ class ActionButton(BaseModel):
     """The message to show on successful completion."""
 
 
-def action_button_for(action, **kwargs) -> ActionButton:
+def action_button_for(action: Callable[..., Any], **kwargs: Any) -> ActionButton:
     """Create a ActionButton data for the specified Thing Action.
 
     :param action: The thing action to create a button for.
@@ -80,7 +84,9 @@ class PropertyControl(BaseModel):
     """The delay in ms before reading back the property."""
 
 
-def property_control_for(thing, property_name, **kwargs) -> PropertyControl:
+def property_control_for(
+    thing: lt.Thing, property_name: str, **kwargs: Any
+) -> PropertyControl:
     """Create an PropertyControl data for the specified Thing Property.
 
     :param thing: The instance of the thing that has the property to be controlled.
diff --git a/src/openflexure_microscope_server/utilities.py b/src/openflexure_microscope_server/utilities.py
index bbad56f9..5975ed1e 100644
--- a/src/openflexure_microscope_server/utilities.py
+++ b/src/openflexure_microscope_server/utilities.py
@@ -1,6 +1,6 @@
 """Utility functions and classes."""
 
-from typing import TypeVar, Callable, ParamSpec
+from typing import TypeVar, Callable, ParamSpec, Optional, Any, Concatenate, Self
 import os
 import re
 import sys
@@ -24,7 +24,7 @@ COMMIT_REGEX = re.compile(r"[0-9a-f]{40}")
 REF_REGEX = re.compile(r"^ref:\s(.*)$")
 
 
-def _is_lock_like(obj):
+def _is_lock_like(obj: Any) -> bool:
     """Check if an object is a lock.
 
     Cannot use ``isinstance(obj, threading.RLock)``, may be possible to use
@@ -34,14 +34,16 @@ def _is_lock_like(obj):
     return hasattr(obj, "acquire") and hasattr(obj, "release")
 
 
-def requires_lock(method: Callable[P, T]) -> Callable[P, T]:
+def requires_lock(
+    method: Callable[Concatenate[Self, P], T],
+) -> Callable[Concatenate[Self, P], T]:
     """Decorate a class method so that it requires the class lock to run.
 
     The class should have a reentrant lock with the name ``self._lock``.
     """
 
     @wraps(method)
-    def wrapper(self, *args: P.args, **kwargs: P.kwargs) -> T:
+    def wrapper(self: Self, *args: P.args, **kwargs: P.kwargs) -> T:
         # Confirm the object the method is attached to has a self._lock property
         if not hasattr(self, "_lock"):
             raise AttributeError(f"{self.__class__.__name__} has no '_lock' attribute")
@@ -67,7 +69,16 @@ class ErrorCapturingThread(Thread):
     join is run.
     """
 
-    def __init__(self, group=None, target=None, args=None, kwargs=None, daemon=None):
+    def __init__(
+        self,
+        group: Optional[Any] = None,
+        target: Optional[Callable[..., Any]] = None,
+        name: Optional[str] = None,
+        args: tuple[Any, ...] = (),
+        kwargs: Optional[dict[str, Any]] = None,
+        *,
+        daemon: Optional[bool] = None,
+    ):
         """Initialise with the same arguments as Thread."""
         # As all inputs are keywords we need to set the default values for args and kwargs:
         if args is None:
@@ -88,12 +99,13 @@ class ErrorCapturingThread(Thread):
         super().__init__(
             group=group,
             target=_wrap_and_catch_errors,
+            name=name,
             args=args,
             kwargs=kwargs,
             daemon=daemon,
         )
 
-    def join(self, timeout=None):
+    def join(self, timeout: Optional[float] = None):
         """Join when the thread is complete.
 
         If the thread ended due to an unhandled exception, the exception will be raised
@@ -107,7 +119,9 @@ class ErrorCapturingThread(Thread):
             raise err
 
 
-def _wrap_and_catch_errors(target, error_buffer, *args, **kwargs):
+def _wrap_and_catch_errors(
+    target: Callable[..., Any], error_buffer: list, *args, **kwargs
+):
     """Run target function in a try-except block.
 
     This function is designed only to be used by ErrorCapturingThread.
diff --git a/tests/test_stage.py b/tests/test_stage.py
index c9ae0918..1beebf9b 100644
--- a/tests/test_stage.py
+++ b/tests/test_stage.py
@@ -1,6 +1,5 @@
 """Test the stage without creating a full HTTP server and socket connection."""
 
-from collections.abc import Mapping
 import tempfile
 import itertools
 
@@ -69,7 +68,7 @@ def test_override_base_movement():
             self,
             cancel: lt.deps.CancelHook,
             block_cancellation: bool = False,
-            **kwargs: Mapping[str, int],
+            **kwargs: int,
         ):
             pass
 
@@ -82,7 +81,7 @@ def test_override_base_movement():
             self,
             cancel: lt.deps.CancelHook,
             block_cancellation: bool = False,
-            **kwargs: Mapping[str, int],
+            **kwargs: int,
         ):
             pass
 

From d6731966715e260389bed2d17d9b9f6fcb62370e Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Wed, 27 Aug 2025 13:33:11 +0100
Subject: [PATCH 2/7] Add ANN002, and ANN003 rules

---
 pyproject.toml                                              | 2 +-
 src/openflexure_microscope_server/server/__init__.py        | 6 +++---
 src/openflexure_microscope_server/things/autofocus.py       | 4 ++--
 src/openflexure_microscope_server/things/stage/dummy.py     | 4 ++--
 .../things/stage/sangaboard.py                              | 4 ++--
 src/openflexure_microscope_server/utilities.py              | 2 +-
 6 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b1d8aaa9..58430873 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -126,7 +126,7 @@ select = [
     "N", # PEP8 naming
     "D", # Docstring checks
     "ERA001", # Commented out code!
-    "ANN001",
+    "ANN001", "ANN002", "ANN003",
 ]
 
 ignore = [
diff --git a/src/openflexure_microscope_server/server/__init__.py b/src/openflexure_microscope_server/server/__init__.py
index d5058fe8..e7964da3 100644
--- a/src/openflexure_microscope_server/server/__init__.py
+++ b/src/openflexure_microscope_server/server/__init__.py
@@ -2,13 +2,13 @@
 
 from __future__ import annotations
 
-from typing import Optional, Callable
+from typing import Optional, Callable, Any
 from functools import wraps
 from copy import copy
+import logging
 
 import labthings_fastapi as lt
 import uvicorn
-import logging
 from uvicorn.main import Server
 from .serve_static_files import add_static_files
 from .legacy_api import add_v2_endpoints
@@ -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, **kwargs):
+    def handle_exit(*args: Any, **kwargs: Any):
         shutdown_function()
         original_handler(*args, **kwargs)
 
diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py
index e80d1e47..48c475ac 100644
--- a/src/openflexure_microscope_server/things/autofocus.py
+++ b/src/openflexure_microscope_server/things/autofocus.py
@@ -252,7 +252,7 @@ class JPEGSharpnessMonitor:
         finally:
             self.running = False
 
-    def focus_rel(self, dz: int, **kwargs) -> tuple[int, int]:
+    def focus_rel(self, dz: int, block_cancellation: int = False) -> tuple[int, int]:
         """Move the stage by dz, monitoring the position over time.
 
         This performs exactly one move. Multiple calls of this method
@@ -268,7 +268,7 @@ class JPEGSharpnessMonitor:
         self.stage_positions.append(self.stage.position)
 
         # Main move
-        self.stage.move_relative(z=dz, **kwargs)
+        self.stage.move_relative(z=dz, block_cancellation=block_cancellation)
 
         # Store the end time and position
         self.stage_times.append(time.time())
diff --git a/src/openflexure_microscope_server/things/stage/dummy.py b/src/openflexure_microscope_server/things/stage/dummy.py
index 3015b42c..45f7f38c 100644
--- a/src/openflexure_microscope_server/things/stage/dummy.py
+++ b/src/openflexure_microscope_server/things/stage/dummy.py
@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import Optional
+from typing import Optional, Any
 from types import TracebackType
 from collections.abc import Mapping
 import time
@@ -19,7 +19,7 @@ class DummyStage(BaseStage):
     hardware attached.
     """
 
-    def __init__(self, step_time: float = 0.001, **kwargs):
+    def __init__(self, step_time: float = 0.001, **kwargs: Any):
         """Initialise the Dummy stage, setting the step_time to adjust the speed.
 
         :param step_time: The time in seconds per "motor" step. The default of 0.001
diff --git a/src/openflexure_microscope_server/things/stage/sangaboard.py b/src/openflexure_microscope_server/things/stage/sangaboard.py
index 8fea6684..05fb55a9 100644
--- a/src/openflexure_microscope_server/things/stage/sangaboard.py
+++ b/src/openflexure_microscope_server/things/stage/sangaboard.py
@@ -5,7 +5,7 @@ import logging
 import threading
 import time
 from copy import copy
-from typing import Iterator, Literal, Optional
+from typing import Iterator, Literal, Optional, Any
 from types import TracebackType
 from contextlib import contextmanager
 from collections.abc import Mapping
@@ -25,7 +25,7 @@ class SangaboardThing(BaseStage):
     functionality is accessed by directly querying the serial interface.
     """
 
-    def __init__(self, port: str = None, **kwargs):
+    def __init__(self, port: str = None, **kwargs: Any):
         """Initialise SangaboardThing.
 
         Initialise the "Thing", but do not initialise an underlying
diff --git a/src/openflexure_microscope_server/utilities.py b/src/openflexure_microscope_server/utilities.py
index 5975ed1e..065b2683 100644
--- a/src/openflexure_microscope_server/utilities.py
+++ b/src/openflexure_microscope_server/utilities.py
@@ -120,7 +120,7 @@ class ErrorCapturingThread(Thread):
 
 
 def _wrap_and_catch_errors(
-    target: Callable[..., Any], error_buffer: list, *args, **kwargs
+    target: Callable[..., Any], error_buffer: list, *args: Any, **kwargs: Any
 ):
     """Run target function in a try-except block.
 

From 4c46330959c2a7f1adb9fb9a571f7ad687b7c9c1 Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Wed, 27 Aug 2025 14:00:49 +0100
Subject: [PATCH 3/7] Add ANN20X rules to ruff

---
 change_log_helper.py                          |  2 +-
 pull_webapp.py                                |  2 +-
 pyproject.toml                                |  6 ++--
 src/openflexure_microscope_server/logging.py  | 12 +++----
 .../scan_directories.py                       | 14 ++++----
 .../scan_planners.py                          |  2 +-
 .../server/__init__.py                        | 10 +++---
 .../server/serve_static_files.py              |  4 +--
 .../stitching.py                              |  4 +--
 .../things/autofocus.py                       |  8 ++---
 .../things/camera/__init__.py                 |  4 +--
 .../things/camera/opencv.py                   |  2 +-
 .../things/camera/picamera.py                 | 20 +++++------
 .../things/camera/simulation.py               | 24 +++++++-------
 .../things/camera_stage_mapping.py            |  9 ++---
 .../things/smart_scan.py                      | 33 ++++++++++++-------
 .../things/stage/__init__.py                  | 16 ++++-----
 .../things/stage/dummy.py                     |  6 ++--
 .../things/system.py                          |  2 +-
 .../utilities.py                              |  4 +--
 20 files changed, 98 insertions(+), 86 deletions(-)

diff --git a/change_log_helper.py b/change_log_helper.py
index 79296132..5caaac6a 100755
--- a/change_log_helper.py
+++ b/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.
diff --git a/pull_webapp.py b/pull_webapp.py
index 6584342c..4c8db77a 100755
--- a/pull_webapp.py
+++ b/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.
diff --git a/pyproject.toml b/pyproject.toml
index 58430873..884a32ef 100644
--- a/pyproject.toml
+++ b/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]
diff --git a/src/openflexure_microscope_server/logging.py b/src/openflexure_microscope_server/logging.py
index 0df9a60e..b1b5074b 100644
--- a/src/openflexure_microscope_server/logging.py
+++ b/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")
 
diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index cb96bd25..f34c0836 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/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()]
diff --git a/src/openflexure_microscope_server/scan_planners.py b/src/openflexure_microscope_server/scan_planners.py
index 87f9000b..67efbf65 100644
--- a/src/openflexure_microscope_server/scan_planners.py
+++ b/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),
diff --git a/src/openflexure_microscope_server/server/__init__.py b/src/openflexure_microscope_server/server/__init__.py
index e7964da3..3dfbb721 100644
--- a/src/openflexure_microscope_server/server/__init__.py
+++ b/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()
diff --git a/src/openflexure_microscope_server/server/serve_static_files.py b/src/openflexure_microscope_server/server/serve_static_files.py
index 5defc149..542aa383 100644
--- a/src/openflexure_microscope_server/server/serve_static_files.py
+++ b/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(
diff --git a/src/openflexure_microscope_server/stitching.py b/src/openflexure_microscope_server/stitching.py
index 32a5253e..f8754425 100644
--- a/src/openflexure_microscope_server/stitching.py
+++ b/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)
diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py
index 48c475ac..ca1adfcd 100644
--- a/src/openflexure_microscope_server/things/autofocus.py
+++ b/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
diff --git a/src/openflexure_microscope_server/things/camera/__init__.py b/src/openflexure_microscope_server/things/camera/__init__.py
index 94badd0c..e5e171e0 100644
--- a/src/openflexure_microscope_server/things/camera/__init__.py
+++ b/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
diff --git a/src/openflexure_microscope_server/things/camera/opencv.py b/src/openflexure_microscope_server/things/camera/opencv.py
index e87befec..763096e5 100644
--- a/src/openflexure_microscope_server/things/camera/opencv.py
+++ b/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()
diff --git a/src/openflexure_microscope_server/things/camera/picamera.py b/src/openflexure_microscope_server/things/camera/picamera.py
index 25b29a44..4ff2844d 100644
--- a/src/openflexure_microscope_server/things/camera/picamera.py
+++ b/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
diff --git a/src/openflexure_microscope_server/things/camera/simulation.py b/src/openflexure_microscope_server/things/camera/simulation.py
index 31e1c9aa..2882a216 100644
--- a/src/openflexure_microscope_server/things/camera/simulation.py
+++ b/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.")
diff --git a/src/openflexure_microscope_server/things/camera_stage_mapping.py b/src/openflexure_microscope_server/things/camera_stage_mapping.py
index c74d6c1b..d9281e22 100644
--- a/src/openflexure_microscope_server/things/camera_stage_mapping.py
+++ b/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)
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index a7b70fb8..3e0badba 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/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
diff --git a/src/openflexure_microscope_server/things/stage/__init__.py b/src/openflexure_microscope_server/things/stage/__init__.py
index 92bd76d7..f6a49590 100644
--- a/src/openflexure_microscope_server/things/stage/__init__.py
+++ b/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.
diff --git a/src/openflexure_microscope_server/things/stage/dummy.py b/src/openflexure_microscope_server/things/stage/dummy.py
index 45f7f38c..b238c1c2 100644
--- a/src/openflexure_microscope_server/things/stage/dummy.py
+++ b/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.
diff --git a/src/openflexure_microscope_server/things/system.py b/src/openflexure_microscope_server/things/system.py
index 12aaadf9..48417e31 100644
--- a/src/openflexure_microscope_server/things/system.py
+++ b/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
 
diff --git a/src/openflexure_microscope_server/utilities.py b/src/openflexure_microscope_server/utilities.py
index 065b2683..87503aaa 100644
--- a/src/openflexure_microscope_server/utilities.py
+++ b/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.

From 2ce49088e7575fc9334f931b157cf64491cdbc7d Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Wed, 27 Aug 2025 14:04:25 +0100
Subject: [PATCH 4/7] Add return typehints to magic methods

---
 pyproject.toml                                         |  1 -
 src/openflexure_microscope_server/background_detect.py |  2 +-
 src/openflexure_microscope_server/logging.py           |  2 +-
 src/openflexure_microscope_server/scan_directories.py  |  4 ++--
 src/openflexure_microscope_server/scan_planners.py     |  2 +-
 src/openflexure_microscope_server/stitching.py         | 10 +++++++---
 src/openflexure_microscope_server/things/autofocus.py  |  4 +++-
 .../things/camera/__init__.py                          |  4 ++--
 .../things/camera/opencv.py                            |  6 +++---
 .../things/camera/picamera.py                          | 10 ++++++----
 .../things/camera/simulation.py                        |  6 +++---
 .../things/camera_stage_mapping.py                     |  6 +++---
 src/openflexure_microscope_server/things/smart_scan.py |  2 +-
 .../things/stage/__init__.py                           |  2 +-
 .../things/stage/dummy.py                              |  6 +++---
 .../things/stage/sangaboard.py                         |  6 +++---
 src/openflexure_microscope_server/utilities.py         |  2 +-
 17 files changed, 41 insertions(+), 34 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 884a32ef..9957a3b6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -134,7 +134,6 @@ ignore = [
     "D203",  # incompatible with D204
     "D213",  # incompatible with D212
     "D400",  # A stricter version of #415 that doesn't allow !
-    "ANN204", # Requrite type hints for
     "ANN401", # Disalows Any, Any is needed at times, Once MyPy is running Any will be
               # handled appropriately
 ]
diff --git a/src/openflexure_microscope_server/background_detect.py b/src/openflexure_microscope_server/background_detect.py
index d9e39e15..d9e44cfc 100644
--- a/src/openflexure_microscope_server/background_detect.py
+++ b/src/openflexure_microscope_server/background_detect.py
@@ -55,7 +55,7 @@ class BackgroundDetectAlgorithm:
     settings_data_model: BaseModel = BaseModel
     """The data model of algorithm settings. This must be set by child classes"""
 
-    def __init__(self):
+    def __init__(self) -> None:
         """Initialise the algorithm settings."""
         try:
             self._settings: BaseModel = self.settings_data_model()
diff --git a/src/openflexure_microscope_server/logging.py b/src/openflexure_microscope_server/logging.py
index b1b5074b..0dd3ee12 100644
--- a/src/openflexure_microscope_server/logging.py
+++ b/src/openflexure_microscope_server/logging.py
@@ -120,7 +120,7 @@ class OFMLogFileFormatter(logging.Formatter):
 class OFMHandler(logging.Handler):
     """A logging.Handler that stores the most recent logs for access by the server."""
 
-    def __init__(self, level: int = logging.INFO, max_logs: int = 250):
+    def __init__(self, level: int = logging.INFO, max_logs: int = 250) -> None:
         """Initialise the handler with a set logging level and message buffer size.
 
         :param level: The level of logs captured. As standard logs of INFO and above
diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py
index f34c0836..8256f414 100644
--- a/src/openflexure_microscope_server/scan_directories.py
+++ b/src/openflexure_microscope_server/scan_directories.py
@@ -167,7 +167,7 @@ class ScanDirectoryManager:
 
     _base_scan_dir: str
 
-    def __init__(self, base_scan_dir: str):
+    def __init__(self, base_scan_dir: str) -> None:
         """Initialise the scan directory manager.
 
         :param base_scan_dir: Path of the directory that holds all scans.
@@ -374,7 +374,7 @@ class ScanDirectory:
     _name: str
     _base_scan_dir: str
 
-    def __init__(self, name: str, base_scan_dir: str):
+    def __init__(self, name: str, base_scan_dir: str) -> None:
         """Initialise the scan directory.
 
         :param name: the name of the scan (the scan directory basename).
diff --git a/src/openflexure_microscope_server/scan_planners.py b/src/openflexure_microscope_server/scan_planners.py
index 67efbf65..7682443c 100644
--- a/src/openflexure_microscope_server/scan_planners.py
+++ b/src/openflexure_microscope_server/scan_planners.py
@@ -80,7 +80,7 @@ class ScanPlanner:
 
     def __init__(
         self, initial_position: XYPos, planner_settings: Optional[dict] = None
-    ):
+    ) -> None:
         """Set up lists for the path planning, and scan history."""
         self._initial_position = enforce_xy_tuple(initial_position)
         self._parse(planner_settings)
diff --git a/src/openflexure_microscope_server/stitching.py b/src/openflexure_microscope_server/stitching.py
index f8754425..c81bd34d 100644
--- a/src/openflexure_microscope_server/stitching.py
+++ b/src/openflexure_microscope_server/stitching.py
@@ -59,7 +59,9 @@ class BaseStitcher:
     complete.
     """
 
-    def __init__(self, images_dir: str, *, overlap: float, correlation_resize: float):
+    def __init__(
+        self, images_dir: str, *, overlap: float, correlation_resize: float
+    ) -> None:
         """Initialise a stitcher.
 
         All args except images_dir are positional only.
@@ -128,7 +130,9 @@ class PreviewStitcher(BaseStitcher):
     one preview must finish before another can be started.
     """
 
-    def __init__(self, images_dir: str, *, overlap: float, correlation_resize: float):
+    def __init__(
+        self, images_dir: str, *, overlap: float, correlation_resize: float
+    ) -> None:
         """Initialise a preview stitcher.
 
         All args except images_dir are positional only.
@@ -192,7 +196,7 @@ class FinalStitcher(BaseStitcher):
         correlation_resize: Optional[float] = None,
         stitch_tiff: bool = False,
         scan_data_dict: Optional[dict[str, Any]] = None,
-    ):
+    ) -> None:
         """Initialise a final stitcher, this has more args than the base class.
 
         All args except images_dir are positional only.
diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py
index ca1adfcd..e0b956f1 100644
--- a/src/openflexure_microscope_server/things/autofocus.py
+++ b/src/openflexure_microscope_server/things/autofocus.py
@@ -215,7 +215,9 @@ class JPEGSharpnessMonitor:
     SharpnessMonitorDep as an argument is called.
     """
 
-    def __init__(self, stage: Stage, camera: RawCamera, portal: lt.deps.BlockingPortal):
+    def __init__(
+        self, stage: Stage, camera: RawCamera, portal: lt.deps.BlockingPortal
+    ) -> None:
         """Initialise a new JPEGSharpnessMonitor. The args are injected automatically.
 
         :param stage: A direct_thing_client dependency for the the microscope stage.
diff --git a/src/openflexure_microscope_server/things/camera/__init__.py b/src/openflexure_microscope_server/things/camera/__init__.py
index e5e171e0..ace9d74c 100644
--- a/src/openflexure_microscope_server/things/camera/__init__.py
+++ b/src/openflexure_microscope_server/things/camera/__init__.py
@@ -69,7 +69,7 @@ class CameraMemoryBuffer:
 
     _storage: dict[int, tuple[Any, Optional[dict]]]
 
-    def __init__(self):
+    def __init__(self) -> None:
         """Create the buffer instance."""
         # This dictionary is the main store for data. Dictionaries are ordered since
         # Python 3.6, so the order in the dictionary is the capture order
@@ -170,7 +170,7 @@ class BaseCamera(lt.Thing):
     lores_mjpeg_stream = lt.outputs.MJPEGStreamDescriptor()
     _memory_buffer = CameraMemoryBuffer()
 
-    def __init__(self):
+    def __init__(self) -> None:
         """Initialise the base camera, this creates the background detectors.
 
         This must be run by all child camera classes.
diff --git a/src/openflexure_microscope_server/things/camera/opencv.py b/src/openflexure_microscope_server/things/camera/opencv.py
index 763096e5..c159ce41 100644
--- a/src/openflexure_microscope_server/things/camera/opencv.py
+++ b/src/openflexure_microscope_server/things/camera/opencv.py
@@ -25,7 +25,7 @@ from . import BaseCamera
 class OpenCVCamera(BaseCamera):
     """A Thing that provides and interface to an OpenCV Camera."""
 
-    def __init__(self, camera_index: int = 0):
+    def __init__(self, camera_index: int = 0) -> None:
         """Iniatilise the thing storing the index of the camera to use.
 
         :param camera_index: The index of the camera to use for the microscope.
@@ -35,7 +35,7 @@ class OpenCVCamera(BaseCamera):
         self._capture_thread: Optional[Thread] = None
         self._capture_enabled = False
 
-    def __enter__(self):
+    def __enter__(self) -> None:
         """Start the capture thread when the Thing context manager is opened."""
         self.cap = cv2.VideoCapture(self.camera_index)
         self._capture_enabled = True
@@ -48,7 +48,7 @@ class OpenCVCamera(BaseCamera):
         _exc_type: type[BaseException],
         _exc_value: Optional[BaseException],
         _traceback: Optional[TracebackType],
-    ):
+    ) -> None:
         """Release the camera when the Thing context manager is closed.
 
         Before releasing the camera the capture thread is closed.
diff --git a/src/openflexure_microscope_server/things/camera/picamera.py b/src/openflexure_microscope_server/things/camera/picamera.py
index 4ff2844d..e8ab2e2f 100644
--- a/src/openflexure_microscope_server/things/camera/picamera.py
+++ b/src/openflexure_microscope_server/things/camera/picamera.py
@@ -53,7 +53,9 @@ class MissingCalibrationError(RuntimeError):
 class PicameraStreamOutput(Output):
     """An Output class that sends frames to a stream."""
 
-    def __init__(self, stream: lt.outputs.MJPEGStream, portal: lt.deps.BlockingPortal):
+    def __init__(
+        self, stream: lt.outputs.MJPEGStream, portal: lt.deps.BlockingPortal
+    ) -> None:
         """Create an output that puts frames in an MJPEGStream.
 
         We need to pass the stream object, and also the blocking portal, because
@@ -126,7 +128,7 @@ class StreamingPiCamera2(BaseCamera):
     generalisation.
     """
 
-    def __init__(self, camera_num: int = 0):
+    def __init__(self, camera_num: int = 0) -> None:
         """Initialise the camera with the given camera number.
 
         This makes no connection to the camera (except to get the default tuning file).
@@ -384,7 +386,7 @@ class StreamingPiCamera2(BaseCamera):
             )
         self._picamera_lock = RLock()
 
-    def __enter__(self):
+    def __enter__(self) -> None:
         """Start streaming when the Thing context manager is opened.
 
         This opens the picamera connection, initialises the camera, sets the
@@ -430,7 +432,7 @@ class StreamingPiCamera2(BaseCamera):
         _exc_type: type[BaseException],
         _exc_value: Optional[BaseException],
         _traceback: Optional[TracebackType],
-    ):
+    ) -> None:
         """Close the picamera connection when the Thing context manager is closed."""
         self.stop_streaming()
         with self._streaming_picamera() as cam:
diff --git a/src/openflexure_microscope_server/things/camera/simulation.py b/src/openflexure_microscope_server/things/camera/simulation.py
index 2882a216..80dadb55 100644
--- a/src/openflexure_microscope_server/things/camera/simulation.py
+++ b/src/openflexure_microscope_server/things/camera/simulation.py
@@ -54,7 +54,7 @@ class SimulatedCamera(BaseCamera):
         glyph_shape: tuple[int, int, int] = (91, 91, 3),
         canvas_shape: tuple[int, int, int] = (3000, 4000, 3),
         frame_interval: float = 0.1,
-    ):
+    ) -> None:
         """Initialise the simulated with settings for how images are generated.
 
         :param shape: The shape (size) of the generated image.
@@ -208,7 +208,7 @@ class SimulatedCamera(BaseCamera):
             pos = {"x": 0, "y": 0, "z": 0}
         return self.generate_image((pos["y"], pos["x"], pos["z"]))
 
-    def __enter__(self):
+    def __enter__(self) -> None:
         """Start the capture thread when the Thing context manager is opened."""
         self.start_streaming()
         return self
@@ -218,7 +218,7 @@ class SimulatedCamera(BaseCamera):
         _exc_type: type[BaseException],
         _exc_value: Optional[BaseException],
         _traceback: Optional[TracebackType],
-    ):
+    ) -> None:
         """Close the capture thread when the Thing context manager is closed."""
         if self.stream_active:
             self._capture_enabled = False
diff --git a/src/openflexure_microscope_server/things/camera_stage_mapping.py b/src/openflexure_microscope_server/things/camera_stage_mapping.py
index d9281e22..a05a3385 100644
--- a/src/openflexure_microscope_server/things/camera_stage_mapping.py
+++ b/src/openflexure_microscope_server/things/camera_stage_mapping.py
@@ -62,7 +62,7 @@ class RecordedMove:
     for calibrating the stage as it allows measuring how long moves take.
     """
 
-    def __init__(self, stage: Stage):
+    def __init__(self, stage: Stage) -> None:
         """Set the stage client used for for movement.
 
         :param stage: the stage client to be used. ``stage.move_to_xyz_position`` will
@@ -72,7 +72,7 @@ class RecordedMove:
         self._current_position: Optional[CoordinateType] = None
         self._history: List[Tuple[float, Optional[CoordinateType]]] = []
 
-    def __call__(self, new_position: CoordinateType):
+    def __call__(self, new_position: CoordinateType) -> None:
         """Move to a new position, and record it."""
         self._history.append((time.time(), self._current_position))
         self._stage.move_to_xyz_position(xyz_pos=new_position)
@@ -99,7 +99,7 @@ class CSMUncalibratedError(HTTPException):
     live preview to move, or when performing a scan.
     """
 
-    def __init__(self):
+    def __init__(self) -> None:
         """Customise the default error code and message of HTTPException."""
         HTTPException.__init__(
             self,
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 3e0badba..ae723880 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -85,7 +85,7 @@ class SmartScanThing(lt.Thing):
     past scans.
     """
 
-    def __init__(self, scans_folder: str):
+    def __init__(self, scans_folder: str) -> None:
         """Initialise a SmartScanThing saving to and loading from the input directory.
 
         :param scans_folder: This is the path to the directory where all scans will be
diff --git a/src/openflexure_microscope_server/things/stage/__init__.py b/src/openflexure_microscope_server/things/stage/__init__.py
index f6a49590..4bbcacaf 100644
--- a/src/openflexure_microscope_server/things/stage/__init__.py
+++ b/src/openflexure_microscope_server/things/stage/__init__.py
@@ -45,7 +45,7 @@ class BaseStage(lt.Thing):
 
     _axis_names = ("x", "y", "z")
 
-    def __init__(self):
+    def __init__(self) -> None:
         """Initialise the stage.
 
         :raises RedefinedBaseMovementError: if ``move_relative`` and/or
diff --git a/src/openflexure_microscope_server/things/stage/dummy.py b/src/openflexure_microscope_server/things/stage/dummy.py
index b238c1c2..6758b37a 100644
--- a/src/openflexure_microscope_server/things/stage/dummy.py
+++ b/src/openflexure_microscope_server/things/stage/dummy.py
@@ -19,7 +19,7 @@ class DummyStage(BaseStage):
     hardware attached.
     """
 
-    def __init__(self, step_time: float = 0.001, **kwargs: Any):
+    def __init__(self, step_time: float = 0.001, **kwargs: Any) -> None:
         """Initialise the Dummy stage, setting the step_time to adjust the speed.
 
         :param step_time: The time in seconds per "motor" step. The default of 0.001
@@ -31,7 +31,7 @@ class DummyStage(BaseStage):
         self.step_time = step_time
         self.instantaneous_position = self._hardware_position
 
-    def __enter__(self):
+    def __enter__(self) -> None:
         """Register the stage position when the Thing context manager is opened."""
         self.instantaneous_position = self._hardware_position
 
@@ -40,7 +40,7 @@ class DummyStage(BaseStage):
         _exc_type: type[BaseException],
         _exc_value: Optional[BaseException],
         _traceback: Optional[TracebackType],
-    ):
+    ) -> None:
         """Nothing to do when the Thing context manager is closed."""
 
     axis_inverted = lt.ThingSetting(
diff --git a/src/openflexure_microscope_server/things/stage/sangaboard.py b/src/openflexure_microscope_server/things/stage/sangaboard.py
index 05fb55a9..932fa373 100644
--- a/src/openflexure_microscope_server/things/stage/sangaboard.py
+++ b/src/openflexure_microscope_server/things/stage/sangaboard.py
@@ -25,7 +25,7 @@ class SangaboardThing(BaseStage):
     functionality is accessed by directly querying the serial interface.
     """
 
-    def __init__(self, port: str = None, **kwargs: Any):
+    def __init__(self, port: str = None, **kwargs: Any) -> None:
         """Initialise SangaboardThing.
 
         Initialise the "Thing", but do not initialise an underlying
@@ -42,7 +42,7 @@ class SangaboardThing(BaseStage):
         self.sangaboard_kwargs["port"] = port
         super().__init__(**kwargs)
 
-    def __enter__(self):
+    def __enter__(self) -> None:
         """Connect to the sangaboard when the Thing context manager is opened."""
         self._sangaboard = sangaboard.Sangaboard(**self.sangaboard_kwargs)
         self._sangaboard_lock = threading.RLock()
@@ -59,7 +59,7 @@ class SangaboardThing(BaseStage):
         _exc_type: type[BaseException],
         _exc_value: Optional[BaseException],
         _traceback: Optional[TracebackType],
-    ):
+    ) -> None:
         """Close the sangaboard connection when the Thing context manager is closed."""
         with self.sangaboard() as sb:
             sb.close()
diff --git a/src/openflexure_microscope_server/utilities.py b/src/openflexure_microscope_server/utilities.py
index 87503aaa..d9debd1e 100644
--- a/src/openflexure_microscope_server/utilities.py
+++ b/src/openflexure_microscope_server/utilities.py
@@ -78,7 +78,7 @@ class ErrorCapturingThread(Thread):
         kwargs: Optional[dict[str, Any]] = None,
         *,
         daemon: Optional[bool] = None,
-    ):
+    ) -> None:
         """Initialise with the same arguments as Thread."""
         # As all inputs are keywords we need to set the default values for args and kwargs:
         if args is None:

From 8f78369aaf3d470a5574d23e5717e7732a5d81b0 Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Wed, 27 Aug 2025 14:28:14 +0100
Subject: [PATCH 5/7] fixup! Add ANN20X rules to ruff

---
 src/openflexure_microscope_server/things/system.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/openflexure_microscope_server/things/system.py b/src/openflexure_microscope_server/things/system.py
index 48417e31..d2b022bb 100644
--- a/src/openflexure_microscope_server/things/system.py
+++ b/src/openflexure_microscope_server/things/system.py
@@ -6,7 +6,7 @@ the microscope, server, and thing states to the web API.
 
 from collections.abc import Mapping
 import socket
-from typing import Optional
+from typing import Optional, Any
 from uuid import UUID, uuid4
 import subprocess
 import os
@@ -127,7 +127,7 @@ class OpenFlexureSystem(lt.Thing):
         return metadata_getter()
 
     @property
-    def thing_state(self) -> Mapping:
+    def thing_state(self) -> Mapping[str, Any]:
         """Summary metadata describing the current state of the Thing."""
         return {
             "hostname": self.hostname,

From 8500b479f562dacf9720dbf0155ef8a285ccb1ab Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Thu, 28 Aug 2025 09:13:44 +0100
Subject: [PATCH 6/7] No Never returns from actions in base Thing classes

---
 src/openflexure_microscope_server/things/stage/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/openflexure_microscope_server/things/stage/__init__.py b/src/openflexure_microscope_server/things/stage/__init__.py
index 4bbcacaf..3643fc5d 100644
--- a/src/openflexure_microscope_server/things/stage/__init__.py
+++ b/src/openflexure_microscope_server/things/stage/__init__.py
@@ -194,7 +194,7 @@ class BaseStage(lt.Thing):
         )
 
     @lt.thing_action
-    def set_zero_position(self) -> Never:
+    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.

From 51f0ac3d82b1f5e7c7936fbc52cf6b5716f9991f Mon Sep 17 00:00:00 2001
From: Julian Stirling <julian@julianstirling.co.uk>
Date: Thu, 28 Aug 2025 09:34:30 +0100
Subject: [PATCH 7/7] Update Picamera coverage data

---
 picamera_coverage.zip | Bin 53913 -> 53913 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/picamera_coverage.zip b/picamera_coverage.zip
index eccadaccead003edc27c4e0edec8681f49e0739e..c0370980c9f1901309a9cf162c83d578d03d33c4 100644
GIT binary patch
delta 520
zcmbQalzHY-W}yIYW)=|!5Qy}WiSB>C-eseZN`pW%1OHF{kNng4oB5;pF7Y*Qb`;3v
zo4mcxM9=t#_92#n3ql`Q9^`W#VDV*4Xlh`{;If-jz}3jc#>&Xq#KXqK@bCThgfzyO
zd6Omjbu=ExGBB|IdB1<(gEt>8oBfeuV0a)e&9I=2jo~mGgPk<PKYkt#a|VN5le7E1
z@&s8}7&%o~R`J~4mV2A!z=qrz%#qBjjGT=|%uN5jo1NICW9&SUjbRTX0|SGg1p|-X
z1Em8D91LvDyg3ZV7#{pGVLV{Qc%z-uBY}f~!GMXujE#Z8jp0M1LIcw`Mrnp*o@-fa
z85{ntJIH>R;WW!;#R-xQ93Zb-Khan{+37;MdUC2|in&R$p+Ra&a*|n+MY5r#sbx}<
znW3eHfkBFiMPibrX{x2+<O>&^HBv1SlZ;Z0(#(x5EmJKmj4hH(ObiW-5)&;`(=05^
zQ;iK%4O7f4Ehb;MU^BV=qGY{^Nt%(FWty3Rfu*6jX;NZhvWaQ3fk~oSqDh*8p|P2f
zkx8OOigB`%j)Ib2a(-EAQDS<kUO{GZVs2_tqLP(@QmVO8nxR2rnnkLGp^=$Us+mEm
vMT&`0vSp&Ng{85vX|kc2ablWzl2UDeHzSh>GfLz#x=a?hWP$K+z$H%r){~-8

delta 516
zcmbQalzHY-W}yIYW)=|!5Gd=Cj(+yIV9iD$l?H)!2L7M?ANi;AxAMpGUE^!t>?lyk
zH+gfPiLUU!E(1oHEi5*SKcblo9D^BVC@3(@YT{R)!_>&a#>&Xq#KFeI@b7!H!RCh9
zlSTV=)Za5OXgsL@|CKepeg3wG*BKZX{@-9=Fg0P2Fk|>|li@>sg2N8RhTW4h`@M1m
zSXdZ2l~_(~$i2PImx1SY8)pPFD<fy40W;ITYUz~7X)_mkFf-g^U|?wAkYQjGFA!u_
zV36Q3+rTKn-0=D`3&U-e1bH=uMnwjO0~`!DBp4VZ7!R;FF>u{r&td2>j99&ujp5sF
zHhCUq9pTN26C@otK;AA7(9ECgbRk_mDK*t1&A=?xDB099$uuQ3$<iP(*~~Q6(9p~<
z$uim8+}O}8IW2Yag$vFarm3c;sfm_GX@=%0CKiUtMutX77N*8&$;rkkMrJ0)mdO@o
zi5975lP_GbnOuHRvOX;-&BDk$B`wV&$s{Gs+%nnNFxA2!IVsU7#nLF*GA+^E(!w+`
z$v{a*K}jz;zbv&VF+EkUATv2JH?=5H$x1;f$;jN&BH6$=E!oV_(8$u*(9+V(!oob&
qAlcN+!Yt9iGR@G?G}$y&sW!lykx7IZC1M%ZOcuCgf$(p@B~Ji3v7a^o