Autofix import order

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)