Autofix import order

src/openflexure_microscope_server/things/autofocus.py

@@ -7,22 +7,22 @@ of images (a 'z-stack').
 See repository root for licensing information.
 """
 
-from contextlib import contextmanager
 import logging
-import time
-from typing import Annotated, Mapping, Optional, Sequence, Literal
 import os
+import time
+from contextlib import contextmanager
 from dataclasses import dataclass
+from typing import Annotated, Literal, Mapping, Optional, Sequence
 
-from fastapi import Depends
 import numpy as np
-from pydantic import BaseModel, field_validator, computed_field, model_validator
+from fastapi import Depends
+from pydantic import BaseModel, computed_field, field_validator, model_validator
 
 import labthings_fastapi as lt
 from labthings_fastapi.types.numpy import NDArray
 
-from .camera import RawCameraDependency as RawCamera
 from .camera import CameraDependency as CameraClient
+from .camera import RawCameraDependency as RawCamera
 from .stage import StageDependency as Stage
 
 LOGGER = logging.getLogger(__name__)

src/openflexure_microscope_server/things/camera/__init__.py

@@ -7,31 +7,32 @@ See repository root for licensing information.
 """
 
 from __future__ import annotations
-from typing import Literal, Optional, Tuple, Any, Mapping
-from types import TracebackType
-import json
+
 import io
-import time
+import json
 import logging
-from datetime import datetime
-import tempfile
 import os
+import tempfile
+import time
+from datetime import datetime
+from types import TracebackType
+from typing import Any, Literal, Mapping, Optional, Tuple
 
 import numpy as np
-from pydantic import RootModel
-from PIL import Image
 import piexif
+from PIL import Image
+from pydantic import RootModel
 
 import labthings_fastapi as lt
 from labthings_fastapi.types.numpy import NDArray
 
-from openflexure_microscope_server.ui import ActionButton, PropertyControl
 from openflexure_microscope_server.background_detect import (
-    ColourChannelDetectLUV,
-    ChannelDeviationLUV,
     BackgroundDetectAlgorithm,
     BackgroundDetectorStatus,
+    ChannelDeviationLUV,
+    ColourChannelDetectLUV,
 )
+from openflexure_microscope_server.ui import ActionButton, PropertyControl
 
 LOGGER = logging.getLogger(__name__)
 

src/openflexure_microscope_server/things/camera/opencv.py

@@ -9,9 +9,9 @@ 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
+from types import TracebackType
+from typing import Literal, Optional
 
 import cv2
 from PIL import Image

src/openflexure_microscope_server/things/camera/picamera.py

@@ -15,39 +15,40 @@ https://datasheets.raspberrypi.com/camera/raspberry-pi-camera-guide.pdf
 """
 
 from __future__ import annotations
-from typing import Annotated, Iterator, Literal, Mapping, Optional, Any
-from types import TracebackType
+
+import copy
 import json
 import logging
 import os
-import copy
 import tempfile
 import time
 from contextlib import contextmanager
 from threading import RLock
+from types import TracebackType
+from typing import Annotated, Any, Iterator, Literal, Mapping, Optional
 
-from pydantic import BaseModel, BeforeValidator
 import numpy as np
-from PIL import Image
 from picamera2 import Picamera2
 from picamera2.encoders import MJPEGEncoder
 from picamera2.outputs import Output
+from PIL import Image
+from pydantic import BaseModel, BeforeValidator
 
 import labthings_fastapi as lt
 from labthings_fastapi.exceptions import NotConnectedToServerError
 
+from openflexure_microscope_server.background_detect import ChannelBlankError
 from openflexure_microscope_server.ui import (
     ActionButton,
     PropertyControl,
     action_button_for,
     property_control_for,
 )
-from openflexure_microscope_server.background_detect import ChannelBlankError
+
+from . import ArrayModel, BaseCamera
 from . import picamera_recalibrate_utils as recalibrate_utils
 from . import picamera_tuning_file_utils as tf_utils
 
-from . import BaseCamera, ArrayModel
-
 LOGGER = logging.getLogger(__name__)
 
 SUPPORTED_CAMS_SENSOR_INFO = {

src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py

@@ -41,16 +41,17 @@ reliable.  The three steps above can be accomplished by:
 # ruff: noqa: N806 N803
 
 from __future__ import annotations
+
 import gc
 import logging
 import time
 from typing import List, Tuple
-from pydantic import BaseModel
-import numpy as np
-from scipy.ndimage import zoom
 
-from picamera2 import Picamera2
+import numpy as np
 import picamera2
+from picamera2 import Picamera2
+from pydantic import BaseModel
+from scipy.ndimage import zoom
 
 LOGGER = logging.getLogger(__name__)
 

src/openflexure_microscope_server/things/camera/picamera_tuning_file_utils.py

@@ -3,14 +3,13 @@
 The functions that edit the tuning files return a new dictionary that is updated.
 """
 
-from typing import Any, Optional
-from copy import deepcopy
-import os
 import json
+import os
+from copy import deepcopy
+from typing import Any, Optional
 
-from pydantic import BaseModel
 import numpy as np
-
+from pydantic import BaseModel
 
 THIS_DIR = os.path.dirname(os.path.abspath(__file__))
 

src/openflexure_microscope_server/things/camera/simulation.py

@@ -7,12 +7,13 @@ See repository root for licensing information.
 """
 
 from __future__ import annotations
-import logging
-from typing import Literal, Optional, Mapping
-from types import TracebackType
-from threading import Thread
-import time
+
 import io
+import logging
+import time
+from threading import Thread
+from types import TracebackType
+from typing import Literal, Mapping, Optional
 
 import numpy as np
 from PIL import Image, ImageFilter
@@ -26,8 +27,8 @@ from openflexure_microscope_server.ui import (
     property_control_for,
 )
 
-from . import BaseCamera, ArrayModel
 from ..stage import BaseStage
+from . import ArrayModel, BaseCamera
 
 LOGGER = logging.getLogger(__name__)
 

src/openflexure_microscope_server/things/camera_stage_mapping.py

@@ -15,23 +15,23 @@ from typing import (
     Any,
     Dict,
     List,
+    Mapping,
     NamedTuple,
     Optional,
     Tuple,
-    Mapping,
 )
-from fastapi import HTTPException
 
 import numpy as np
+from fastapi import HTTPException
+
+import labthings_fastapi as lt
 from camera_stage_mapping.camera_stage_calibration_1d import (
     calibrate_backlash_1d,
     image_to_stage_displacement_from_1d,
 )
-from camera_stage_mapping.exceptions import MappingError
-
-import labthings_fastapi as lt
-from labthings_fastapi.types.numpy import DenumpifyingDict
 from camera_stage_mapping.camera_stage_tracker import Tracker
+from camera_stage_mapping.exceptions import MappingError
+from labthings_fastapi.types.numpy import DenumpifyingDict
 
 from .camera import CameraDependency as CameraClient
 from .stage import StageDependency as Stage

src/openflexure_microscope_server/things/smart_scan.py

@@ -7,37 +7,35 @@ It also controls external processes for live stitching composite images, and
 the creation of the final stitched images.
 """
 
-from typing import (
-    Optional,
-    Self,
-    TypeVar,
-    ParamSpec,
-    Callable,
-    Concatenate,
-    Mapping,
-    Any,
-)
-import threading
 import os
+import threading
 import time
 from datetime import datetime
 from subprocess import SubprocessError
+from typing import (
+    Any,
+    Callable,
+    Concatenate,
+    Mapping,
+    Optional,
+    ParamSpec,
+    Self,
+    TypeVar,
+)
 
+import numpy as np
 from fastapi import HTTPException
 from fastapi.responses import FileResponse
-import numpy as np
 from pydantic import BaseModel
 
 import labthings_fastapi as lt
 
-from openflexure_microscope_server import scan_directories
-from openflexure_microscope_server import scan_planners
-from openflexure_microscope_server import stitching
+from openflexure_microscope_server import scan_directories, scan_planners, stitching
 
 # Things
 from .autofocus import AutofocusThing, StackParams
-from .camera_stage_mapping import CameraStageMapper
 from .camera import CameraDependency as CameraClient
+from .camera_stage_mapping import CameraStageMapper
 from .stage import StageDependency as StageDep
 
 T = TypeVar("T")

src/openflexure_microscope_server/things/stage/__init__.py

@@ -10,8 +10,9 @@ 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, Never, Any
+
+from collections.abc import Mapping, Sequence
+from typing import Any, Literal, Never
 
 import labthings_fastapi as lt
 

src/openflexure_microscope_server/things/stage/dummy.py

@@ -2,10 +2,10 @@
 
 from __future__ import annotations
 
-from typing import Optional, Any
-from types import TracebackType
-from collections.abc import Mapping
 import time
+from collections.abc import Mapping
+from types import TracebackType
+from typing import Any, Optional
 
 import labthings_fastapi as lt
 

src/openflexure_microscope_server/things/stage/sangaboard.py

@@ -1,18 +1,20 @@
 """Provide a LabThings-FastAPI interface to the Sangaboard motor controller."""
 
 from __future__ import annotations
+
 import logging
 import threading
 import time
-from copy import copy
-from typing import Iterator, Literal, Optional, Any
-from types import TracebackType
-from contextlib import contextmanager
 from collections.abc import Mapping
+from contextlib import contextmanager
+from copy import copy
+from types import TracebackType
+from typing import Any, Iterator, Literal, Optional
 
 import semver
-import sangaboard
+
 import labthings_fastapi as lt
+import sangaboard
 
 from . import BaseStage
 

src/openflexure_microscope_server/things/stage_measure.py

@@ -13,20 +13,20 @@ is tracked and an error is raised if it exceeds a minimum amount. Currently
 this is 10% of the expected motion is the measured axis.
 """
 
-from typing import Literal, Any, Optional, overload
 import time
 from dataclasses import dataclass
 from threading import Lock
+from typing import Any, Literal, Optional, overload
 
 import numpy as np
 
-from camera_stage_mapping import fft_image_tracking
 import labthings_fastapi as lt
+from camera_stage_mapping import fft_image_tracking
 
 # Things
 from .autofocus import AutofocusThing
-from .camera_stage_mapping import CameraStageMapper
 from .camera import CameraDependency as CamDep
+from .camera_stage_mapping import CameraStageMapper
 from .stage import StageDependency as StageDep
 
 CSMDep = lt.deps.direct_thing_client_dependency(

src/openflexure_microscope_server/things/system.py

@@ -4,14 +4,14 @@ A module to control the underlying microscope system and to expose information a
 the microscope, server, and thing states to the web API.
 """
 
-from collections.abc import Mapping
-import socket
-from typing import Optional, Any
-from uuid import UUID, uuid4
-import subprocess
 import os
-from signal import SIGTERM
+import socket
+import subprocess
 import time
+from collections.abc import Mapping
+from signal import SIGTERM
+from typing import Any, Optional
+from uuid import UUID, uuid4
 
 from pydantic import BaseModel