Autofix import order

src/openflexure_microscope_server/background_detect.py

@@ -5,11 +5,13 @@ for analysis. Information from these images is used to detect whether an image f
 current camera field of view contains sample.
 """
 
-from typing import Optional, Any
+from typing import Any, Optional
+
 import cv2
 import numpy as np
-from pydantic import BaseModel, Field, ConfigDict
+from pydantic import BaseModel, ConfigDict, Field
 from pydantic.errors import PydanticUserError
+
 from labthings_fastapi.thing_description import type_to_dataschema
 
 

src/openflexure_microscope_server/logging.py

@@ -12,11 +12,11 @@ output to STDOUT/STDERR are captured by ``systemd``. These can be viewed by usin
 """
 
 import logging
-from logging.handlers import RotatingFileHandler
 import os
+from logging.handlers import RotatingFileHandler
 
-from fastapi.responses import PlainTextResponse
 from fastapi import HTTPException
+from fastapi.responses import PlainTextResponse
 
 LOGGER = logging.getLogger(__name__)
 OFM_LOG_FILE = None

src/openflexure_microscope_server/scan_directories.py

@@ -1,25 +1,24 @@
 """Functionality to manage file system operations for scan directories."""
 
-from typing import Optional, Any, Mapping
+import json
+import logging
 import os
 import re
 import shutil
-import zipfile
 import threading
-import json
+import zipfile
 from datetime import datetime, timedelta
-import logging
+from typing import Any, Mapping, Optional
 
 from pydantic import (
     BaseModel,
-    field_validator,
-    field_serializer,
     ConfigDict,
     ValidationError,
+    field_serializer,
+    field_validator,
 )
 
-from openflexure_microscope_server.utilities import requires_lock
-from openflexure_microscope_server.utilities import make_name_safe
+from openflexure_microscope_server.utilities import make_name_safe, requires_lock
 
 LOGGER = logging.getLogger(__name__)
 

src/openflexure_microscope_server/scan_planners.py

@@ -9,9 +9,9 @@ subclassing the ScanPlanner
 # would be to import Union and use a string.
 from __future__ import annotations
 
-from typing import TypeAlias, Optional, Any
 import logging
 from copy import copy
+from typing import Any, Optional, TypeAlias
 
 import numpy as np
 

src/openflexure_microscope_server/server/__init__.py

@@ -2,20 +2,22 @@
 
 from __future__ import annotations
 
-from typing import Optional, Callable, Any
-from functools import wraps
-from copy import copy
 import logging
 from argparse import Namespace
+from copy import copy
+from functools import wraps
+from typing import Any, Callable, Optional
 
-import labthings_fastapi as lt
 import uvicorn
 from uvicorn.main import Server
 
+import labthings_fastapi as lt
+
 from openflexure_microscope_server.utilities import load_patched_config
-from .serve_static_files import add_static_files
-from .legacy_api import add_v2_endpoints
+
 from ..logging import configure_logging, retrieve_log, retrieve_log_from_file
+from .legacy_api import add_v2_endpoints
+from .serve_static_files import add_static_files
 
 LOGGER = logging.getLogger(__name__)
 

src/openflexure_microscope_server/server/legacy_api.py

@@ -1,9 +1,11 @@
 """Provide endpoints that mimic the v2 API for OpenFlexure Connect discoverability."""
 
-import labthings_fastapi as lt
-from fastapi import Response
 from socket import gethostname
 
+from fastapi import Response
+
+import labthings_fastapi as lt
+
 FAKE_ROUTES = [
     "/api/v2/",
     "/api/v2/streams/snapshot",

src/openflexure_microscope_server/server/serve_static_files.py

@@ -3,9 +3,9 @@
 import os
 from typing import Optional
 
+from fastapi import FastAPI
 from fastapi.responses import FileResponse, RedirectResponse
 from fastapi.staticfiles import StaticFiles
-from fastapi import FastAPI
 
 THIS_DIR = os.path.dirname(os.path.abspath(__file__))
 STATIC_PATH = os.path.normpath(os.path.join(THIS_DIR, "..", "static"))

src/openflexure_microscope_server/stitching.py

@@ -6,13 +6,13 @@ CPU intensity of stitching causing scanning problems due to the Python Global
 Interpreter Lock (GIL). May be possible to shift to multiprocessing in the future.
 """
 
-from typing import Optional, Any
-import threading
-import subprocess
-import signal
 import os
-from io import TextIOWrapper
 import shlex
+import signal
+import subprocess
+import threading
+from io import TextIOWrapper
+from typing import Any, Optional
 
 import labthings_fastapi as lt
 

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
 

src/openflexure_microscope_server/ui.py

@@ -1,6 +1,6 @@
 """Functionality for communicating the required user interface for a thing."""
 
-from typing import Callable, Any
+from typing import Any, Callable
 
 from pydantic import BaseModel
 

src/openflexure_microscope_server/utilities.py

@@ -1,26 +1,26 @@
 """Utility functions and classes."""
 
-from typing import (
-    TypeVar,
-    Callable,
-    ParamSpec,
-    Optional,
-    Any,
-    Concatenate,
-    Self,
-    overload,
-    TypeAlias,
-    Literal,
-)
+import json
+import logging
 import os
 import re
 import sys
-from threading import Thread
-import logging
-from importlib.metadata import version
 import tomllib
 from functools import wraps
-import json
+from importlib.metadata import version
+from threading import Thread
+from typing import (
+    Any,
+    Callable,
+    Concatenate,
+    Literal,
+    Optional,
+    ParamSpec,
+    Self,
+    TypeAlias,
+    TypeVar,
+    overload,
+)
 
 from pydantic import BaseModel