Merge branch 'isort' into 'v3'

Formalise import sorting rules and enforce

See merge request openflexure/openflexure-microscope-server!438

change_log_helper.py

@@ -2,11 +2,10 @@
 
 """Create a list of the MRs into v3 (unless specified) since the last release."""
 
-import sys
 import argparse
+import sys
 
 import gitlab
-
 from gitlab.exceptions import GitlabGetError
 
 PROJECT_ID = 9238334

check_version_sync.py

@@ -2,8 +2,8 @@
 """Check that the npm version string matches the Python version string exactly."""
 
 import json
-import tomllib
 import os
+import tomllib
 
 with open("pyproject.toml", "rb") as toml_f:
     pyproject_data = tomllib.load(toml_f)

hardware-specific-tests/picamera2/cam_test_utils/__init__.py

@@ -1,8 +1,8 @@
 """Utilities to help with testing the camera."""
 
-from typing import Optional
 import tempfile
 from contextlib import contextmanager
+from typing import Optional
 
 from fastapi.testclient import TestClient
 

hardware-specific-tests/picamera2/test_acquisition.py

@@ -1,7 +1,7 @@
 """Test data collection from the Raspberry Picamera."""
 
-from PIL import Image
 import numpy as np
+from PIL import Image
 
 
 def test_jpeg_and_array(picamera_client):

hardware-specific-tests/picamera2/test_calibration.py

@@ -1,7 +1,7 @@
 """Test data collection from the Raspberry Picamera."""
 
-from copy import deepcopy
 import tempfile
+from copy import deepcopy
 
 from .cam_test_utils import camera_test_client
 

hardware-specific-tests/picamera2/test_exposure_time_drift.py

@@ -4,13 +4,12 @@ This can get very tedious. Recommend running pytest with -s option
 to monitor progress.
 """
 
-from typing import Any
-import logging
-import time
-import tempfile
-import os
 import json
-
+import logging
+import os
+import tempfile
+import time
+from typing import Any
 
 from .cam_test_utils import camera_test_client
 

hardware-specific-tests/picamera2/test_tuning.py

@@ -10,7 +10,6 @@ from openflexure_microscope_server.things.camera import (
     picamera_tuning_file_utils as tf_utils,
 )
 
-
 MODEL = Picamera2.global_camera_info()[0]["Model"]
 
 

integration-tests/testfile.py

@@ -7,11 +7,11 @@ For now, this file should be run directly rather than through a test framework.
 They are designed to run on CI and should work on Linux or WSL for local debugging.
 """
 
-from typing import Optional
-import subprocess
 import os
 import shutil
+import subprocess
 from time import sleep, time
+from typing import Optional
 
 from PIL import Image
 

picamera_tests.py

@@ -1,12 +1,12 @@
 #! /usr/bin/env python3
 """Run the Piamera tests and archive the results in the git repository."""
 
-import subprocess
-import shutil
-import os
-import posixpath
 import argparse
 import json
+import os
+import posixpath
+import shutil
+import subprocess
 import sys
 import zipfile
 

pull_webapp.py

@@ -10,15 +10,14 @@ If the static directory already exists and contains data, it will be removed bef
 extraction.
 """
 
-import zipfile
+import argparse
 import io
-import sys
 import os
 import shutil
-import argparse
+import sys
+import zipfile
 
 import gitlab
-
 from gitlab.exceptions import GitlabGetError
 
 THIS_DIR = os.path.dirname(os.path.abspath(__file__))

pyproject.toml

@@ -124,7 +124,8 @@ select = [
     "D", # Docstring checks
     "ERA001", # Commented out code!
     "S101",# No asserts!
-    "ANN",
+    "ANN", # Type annotations
+    "I", # Import sorting
 ]
 
 ignore = [
@@ -163,4 +164,16 @@ property-decorators = ["labthings_fastapi.thing_property", "labthings_fastapi.th
 
 [tool.ruff.lint.pylint]
 max-args = 7
-max-positional-args = 5
+max-positional-args = 5
+
+
+[tool.ruff.lint.isort]
+section-order = ["future", "standard-library", "third-party", "ours", "first-party", "local-folder"]
+
+[tool.ruff.lint.isort.sections]
+ours = [
+    "camera_stage_mapping",
+    "openflexure_stitching",
+    "sangaboard",
+    "labthings_fastapi",
+]

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
 

tests/mock_things/mock_camera.py

@@ -7,11 +7,12 @@ The mocks do not subclass Things. Instead, they return predefined
 answers to functions.
 """
 
+from unittest.mock import Mock, PropertyMock
+
 from openflexure_microscope_server.background_detect import (
     BackgroundDetectorStatus,
     ColourChannelDetectSettings,
 )
-from unittest.mock import Mock, PropertyMock
 
 
 class MockCameraThing(Mock):

tests/test_autofocus.py

@@ -3,8 +3,8 @@
 This doesn't check the behaviour of the JPEG shaprness monitor.
 """
 
-import pytest
 import numpy as np
+import pytest
 
 from openflexure_microscope_server.things.autofocus import (
     AutofocusThing,

tests/test_background_detectors.py

@@ -5,19 +5,19 @@ This tests both the base class an individual algorithms.
 
 import re
 
+import numpy as np
 import pytest
 from pydantic import BaseModel
-import numpy as np
 
 from openflexure_microscope_server.background_detect import (
-    MissingBackgroundDataError,
     BackgroundDetectAlgorithm,
-    ChannelDistributions,
-    ColourChannelDetectSettings,
-    ColourChannelDetectLUV,
-    _chunked_stds,
-    ChannelDeviationLUV,
     ChannelBlankError,
+    ChannelDeviationLUV,
+    ChannelDistributions,
+    ColourChannelDetectLUV,
+    ColourChannelDetectSettings,
+    MissingBackgroundDataError,
+    _chunked_stds,
 )
 
 RNG = np.random.default_rng()

tests/test_camera.py

@@ -3,9 +3,9 @@
 import tempfile
 from contextlib import contextmanager
 
+import numpy as np
 import pytest
 from fastapi.testclient import TestClient
-import numpy as np
 from PIL import Image
 
 import labthings_fastapi as lt

tests/test_camera_buffer.py

@@ -3,9 +3,8 @@
 from random import randint
 
 import numpy as np
-from PIL import Image
 import pytest
-
+from PIL import Image
 
 from openflexure_microscope_server.things.camera import (
     CameraMemoryBuffer,

tests/test_cameras.py

@@ -7,8 +7,8 @@ on camera functionality using the simulation camera are in "test_camera".
 import pytest
 
 from openflexure_microscope_server.things.camera import BaseCamera
-from openflexure_microscope_server.things.camera.simulation import SimulatedCamera
 from openflexure_microscope_server.things.camera.opencv import OpenCVCamera
+from openflexure_microscope_server.things.camera.simulation import SimulatedCamera
 
 
 @pytest.fixture

tests/test_config_utilities.py

@@ -1,10 +1,11 @@
 """Test the configuration handling functions in utilities."""
 
-import pytest
-import os
 import json
+import os
 from json import JSONDecodeError
 
+import pytest
+
 from openflexure_microscope_server import utilities
 
 

tests/test_dummy_server.py

@@ -12,18 +12,18 @@ import json
 import os
 import tempfile
 
-from fastapi.testclient import TestClient
-from PIL import Image
 import numpy as np
 import piexif
 import pytest
+from fastapi.testclient import TestClient
+from PIL import Image
 
 import labthings_fastapi as lt
 
-from openflexure_microscope_server.things.camera.simulation import SimulatedCamera
-from openflexure_microscope_server.things.stage.dummy import DummyStage
 from openflexure_microscope_server.things.autofocus import AutofocusThing
+from openflexure_microscope_server.things.camera.simulation import SimulatedCamera
 from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
+from openflexure_microscope_server.things.stage.dummy import DummyStage
 
 
 @pytest.fixture

tests/test_legacy_api.py

@@ -1,7 +1,7 @@
 """Test server booting and shut down."""
 
-from socket import gethostname
 import asyncio
+from socket import gethostname
 
 # Import as ofm server to attempt to minimise confusion with server as a var in other
 # functions and also FastAPI `Server`.

tests/test_logging.py

@@ -1,12 +1,12 @@
 """Test the server's logging configuration and handling."""
 
+import logging
 import os
 import tempfile
-import logging
 
-from fastapi.responses import PlainTextResponse
-from fastapi import HTTPException
 import pytest
+from fastapi import HTTPException
+from fastapi.responses import PlainTextResponse
 
 from openflexure_microscope_server import logging as ofm_logging
 

tests/test_picamera_tuning_files.py

@@ -2,9 +2,8 @@
 
 from copy import deepcopy
 
-import pytest
 import numpy as np
-
+import pytest
 
 from openflexure_microscope_server.things.camera import (
     picamera_tuning_file_utils as tf_utils,

tests/test_sangaboard.py

@@ -5,9 +5,9 @@ import logging
 import pytest
 
 from openflexure_microscope_server.things.stage.sangaboard import (
-    SangaboardThing,
-    REQUIRED_VERSION,
     RECOMMENDED_VERSION,
+    REQUIRED_VERSION,
+    SangaboardThing,
 )
 
 

tests/test_scan_data.py

@@ -1,8 +1,8 @@
 """Test the functionality in the scan_directories module."""
 
-from datetime import datetime, timedelta
-from copy import copy
 import json
+from copy import copy
+from datetime import datetime, timedelta
 from math import floor
 
 from openflexure_microscope_server.scan_directories import ScanData

tests/test_scan_directories.py

@@ -1,24 +1,24 @@
 """Test the functionality in the scan_directories module."""
 
-import tempfile
-import os
-import math
-import shutil
-import logging
-import random
-import time
 import json
+import logging
+import math
+import os
+import random
+import shutil
+import tempfile
+import time
 from collections import namedtuple
 
 import pytest
 
 from openflexure_microscope_server.scan_directories import (
-    ScanDirectoryManager,
+    SCAN_DATA_FILENAME,
+    NotEnoughFreeSpaceError,
     ScanDirectory,
+    ScanDirectoryManager,
     ScanInfo,
     get_files_in_zip,
-    NotEnoughFreeSpaceError,
-    SCAN_DATA_FILENAME,
 )
 
 from .test_scan_data import _fake_scan_data

tests/test_scan_planners.py

@@ -4,10 +4,12 @@ As well as low level function by function tests, this test suite also provides t
 that simulate scanning a sample, checking that the expected path is followed.
 """
 
-import pytest
 from copy import copy
 
+import pytest
+
 from openflexure_microscope_server import scan_planners
+
 from .utilities import scan_test_helpers
 
 

tests/test_serve_static_files.py

@@ -1,9 +1,9 @@
 """Test the code that mounts static files to the server, without creating a server."""
 
+import asyncio
 import os
 import shutil
 import tempfile
-import asyncio
 
 import pytest
 from starlette.responses import FileResponse, RedirectResponse

tests/test_server_config.py

@@ -1,7 +1,7 @@
 """Test server booting and shut down."""
 
-import os
 import json
+import os
 from copy import deepcopy
 
 import pytest

tests/test_smart_scan.py

@@ -13,31 +13,31 @@ For these tests to reliably represent real behaviour the mock Things will need t
 be tested for matching signatures with dynamically generated clients.
 """
 
-from typing import Callable, Optional
-import tempfile
+import logging
 import os
 import shutil
-import logging
+import tempfile
 from datetime import datetime
+from typing import Callable, Optional
 
-from fastapi import HTTPException
 import pytest
+from fastapi import HTTPException
 
 from labthings_fastapi.exceptions import InvocationCancelledError
 
-from openflexure_microscope_server.things.smart_scan import (
-    SmartScanThing,
-    ScanNotRunningError,
-)
 from openflexure_microscope_server.scan_directories import (
-    ScanData,
     NotEnoughFreeSpaceError,
+    ScanData,
+)
+from openflexure_microscope_server.things.smart_scan import (
+    ScanNotRunningError,
+    SmartScanThing,
 )
 
-from .mock_things.mock_csm import MockCSMThing
 from .mock_things.mock_autofocus import MockAutoFocusThing
-from .mock_things.mock_stage import MockStageThing
 from .mock_things.mock_camera import MockCameraThing
+from .mock_things.mock_csm import MockCSMThing
+from .mock_things.mock_stage import MockStageThing
 
 # A global logger to pass in as an Invocation Logger
 LOGGER = logging.getLogger("mock-invocation_logger")

tests/test_stack.py

@@ -1,31 +1,32 @@
 """Tests for the smart and fast stacking."""
 
-from typing import Optional
+import logging
 import tempfile
 from random import randint
-import logging
+from typing import Optional
 
-import pytest
 import numpy as np
-from hypothesis import given, strategies as st
+import pytest
 from fastapi.testclient import TestClient
+from hypothesis import given
+from hypothesis import strategies as st
 
 import labthings_fastapi as lt
 
+from openflexure_microscope_server.scan_directories import IMAGE_REGEX
 from openflexure_microscope_server.things.autofocus import (
-    AutofocusThing,
-    StackParams,
-    CaptureInfo,
-    MIN_TEST_IMAGE_COUNT,
+    EXTRA_STACK_CAPTURES,
     MAX_TEST_IMAGE_COUNT,
+    MIN_TEST_IMAGE_COUNT,
+    AutofocusThing,
+    CaptureInfo,
+    NotAPeakError,
+    StackParams,
+    _count_turning_points,
     _get_capture_by_id,
     _get_capture_index_by_id,
-    EXTRA_STACK_CAPTURES,
-    NotAPeakError,
     _get_peak_turning_point,
-    _count_turning_points,
 )
-from openflexure_microscope_server.scan_directories import IMAGE_REGEX
 
 LOGGER = logging.getLogger("mock-invocation_logger")
 RANDOM_GENERATOR = np.random.default_rng()

tests/test_stage.py

@@ -1,12 +1,13 @@
 """Test the stage without creating a full HTTP server and socket connection."""
 
-import tempfile
 import itertools
+import tempfile
 
-from fastapi.testclient import TestClient
 import pytest
+from fastapi.testclient import TestClient
 from httpx import HTTPStatusError
-from hypothesis import given, settings, HealthCheck, strategies as st
+from hypothesis import HealthCheck, given, settings
+from hypothesis import strategies as st
 
 import labthings_fastapi as lt
 from labthings_fastapi.exceptions import NotConnectedToServerError
@@ -17,7 +18,6 @@ from openflexure_microscope_server.things.stage import (
 )
 from openflexure_microscope_server.things.stage.dummy import DummyStage
 
-
 from .mock_things.mock_cancel import MockCancel
 
 # Keep the size and number of moves fairly small or the tests can take forever

tests/test_stage_measure.py

@@ -1,13 +1,13 @@
 """File contains unit tests for stage_measure."""
 
-from copy import copy
-import logging
 import dataclasses
+import logging
 import tempfile
+from copy import copy
 
-from fastapi.testclient import TestClient
 import numpy as np
 import pytest
+from fastapi.testclient import TestClient
 
 import labthings_fastapi as lt
 

tests/test_stitching.py

@@ -6,20 +6,20 @@ generated, and the subprocess calling works as expected.
 
 import logging
 import os
-from copy import copy
-import uuid
 import threading
 import time
+import uuid
+from copy import copy
 
 import pytest
 
 import labthings_fastapi as lt
 
 from openflexure_microscope_server.stitching import (
-    BaseStitcher,
-    PreviewStitcher,
-    FinalStitcher,
     STITCHING_RESOLUTION,
+    BaseStitcher,
+    FinalStitcher,
+    PreviewStitcher,
     StitcherValidationError,
 )
 

tests/test_version_strings.py

@@ -1,16 +1,16 @@
 """Tests that version strings can be produced reliably."""
 
-import subprocess
+import logging
 import os
 import re
-import tempfile
 import shutil
+import subprocess
+import tempfile
 import warnings
-import logging
 
+import pytest
 from hypothesis import strategies as st
 from hypothesis.errors import NonInteractiveExampleWarning
-import pytest
 
 from openflexure_microscope_server import utilities
 

tests/utilities/__init__.py

@@ -4,8 +4,8 @@ At the top level are some basic testing functions. More specific testing utiliti
 provided by modules inside the package.
 """
 
-from typing import Protocol, Iterable
 from collections.abc import Hashable
+from typing import Iterable, Protocol
 
 
 class SizedIterableHashable(Iterable[Hashable], Protocol):

tests/utilities/scan_test_helpers.py

@@ -11,11 +11,11 @@ import os
 import pickle
 
 import numpy as np
-from scipy import interpolate
 from matplotlib import pyplot as plt
-from matplotlib.path import Path as MatPath
-from matplotlib.patches import PathPatch
 from matplotlib.figure import Figure
+from matplotlib.patches import PathPatch
+from matplotlib.path import Path as MatPath
+from scipy import interpolate
 
 from openflexure_microscope_server import scan_planners
 
@@ -145,8 +145,8 @@ def example_smart_spiral(
 
 def profile_example_smart_spiral():
     """Profile running an example scan and print the cumulative profile stats."""
-    import pstats
     import cProfile
+    import pstats
 
     profiler = cProfile.Profile()
     profiler.runcall(example_smart_spiral)