Add more tests, speed up dummy stage

I've sped up the stage motion, to run tests in a more reasonable time.

CSM doesn't yet calibrate in the test - I suspect debugging of capture_array
is needed.

pyproject.toml

@@ -58,49 +58,13 @@ build-backend = "setuptools.build_meta"
 # don't believe it's critical at present, because we don't use 
 # the Python package - we distribute a tarball directly.
 
-[tool.black]
-exclude = '(\.eggs|\.git|\.venv|\venv|node_modules/)'
-
-[tool.isort]
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-ensure_newline_before_comments = true
-line_length = 88
-
-[tool.pylint.'MESSAGES CONTROL']
-# W1203 warns about using f strings in logging statements.
-# I'm really not concerned about the performance implications of this,
-# particularly as we often have the log level set quite high.  I think
-# for our current purposes, using f strings in logging statements is
-# more readable and thus a good idea in many places - I've disabled
-# this warning code globally for that reason.
-disable = "fixme,C,R,W1203"
-max-line-length = 88
-
 [tool.mypy]
 plugins = ["pydantic.mypy"]
 
 [tool.ruff]
 target-version = "py39"
 
-[tool.poe.executor]
-type = "virtualenv"
-location = ".venv"
-
-[tool.poe.tasks]
-black = "black ."
-black_check = "black --check ."
-ruff = "ruff . --fix"
-ruff_check = "ruff ."
-isort = "isort openflexure_microscope"
-pylint = "pylint openflexure_microscope"
-mypy = "mypy --cobertura-xml-report openflexure_microscope openflexure_microscope"
-test = "pytest . --junitxml=pytest_report.xml"
-serve = "python -m openflexure_microscope.api.app"
-
-format = ["black", "isort", "ruff"]
-lint = ["ruff_check", "pylint", "mypy"]
-
-check = ["format", "lint", "test"]
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]

src/openflexure_microscope_server/things/stage/dummy.py

@@ -13,6 +13,9 @@ class DummyStage(BaseStage):
     This stage should work similarly to a Sangaboard stage, but without any
     hardware attached.
     """
+    def __init__(self, step_time: float=0.001, **kwargs):
+        super().__init__(**kwargs)
+        self.step_time = step_time
 
     def __enter__(self):
         self.instantaneous_position = self.position
@@ -27,7 +30,7 @@ class DummyStage(BaseStage):
         self.moving = True
         try:
             fraction_complete = 0.0
-            dt = 0.001
+            dt = self.step_time
             max_displacement = max(abs(v) for v in displacement)
             start_time = time.time()
             while time.time() - start_time < dt * max_displacement:

tests/test_dummy_server.py

@@ -1,4 +1,5 @@
 import json
+import os
 import tempfile
 
 from fastapi import Depends, FastAPI
@@ -6,49 +7,70 @@ from fastapi.testclient import TestClient
 from labthings_fastapi.client import ThingClient
 from PIL import Image
 import piexif
+import pytest
 
 from openflexure_microscope_server.server import ThingServer
 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_stage_mapping import CameraStageMapper
 
-temp_folder = tempfile.TemporaryDirectory()
-server = ThingServer(temp_folder.name)
-server.add_thing(SimulatedCamera(), "/camera/")
-server.add_thing(DummyStage(), "/stage/")
-server.add_thing(AutofocusThing(), "/autofocus/")
+@pytest.fixture
+def thing_server():
+    temp_folder = tempfile.TemporaryDirectory()
+    server = ThingServer(settings_folder=temp_folder.name)
+    server.add_thing(SimulatedCamera(), "/camera/")
+    server.add_thing(DummyStage(step_time=0.000001), "/stage/")
+    server.add_thing(AutofocusThing(), "/autofocus/")
+    server.add_thing(CameraStageMapper(), "/camera_stage_mapping/")
+    assert os.path.exists(os.path.join(temp_folder.name, "camera/"))
+    # NB yield is important: otherwise, the temp folder gets deleted before the test runs
+    yield server
 
-def test_autofocus():
-    with TestClient(server.app) as client:
-        autofocus = ThingClient.from_url("/autofocus/", client)
-        _ = autofocus.fast_autofocus()
+@pytest.fixture
+def client(thing_server):
+    with TestClient(thing_server.app) as client:
+        yield client
 
-def test_grab_jpeg():
-    with TestClient(server.app) as client:
-        camera = ThingClient.from_url("/camera/", client)
-        blob = camera.grab_jpeg()
-        _image = Image.open(blob.open())
+@pytest.fixture
+def slower_client(thing_server):
+    thing_server.things["/stage/"].step_time = 0.0002
+    with TestClient(thing_server.app) as client:
+        yield client
 
-def test_capture_jpeg_metadata():
-    with TestClient(server.app) as client:
-        camera = ThingClient.from_url("/camera/", client)
-        blob = camera.capture_jpeg()
-        image = Image.open(blob.open())
-        exif_dict = piexif.load(image.info["exif"])
-        encoded_metadata = exif_dict["Exif"][piexif.ExifIFD.UserComment]
-        metadata = json.loads(encoded_metadata)
-        assert "position" in metadata["/stage/"]
+def test_autofocus(slower_client):
+    client = slower_client
+    autofocus = ThingClient.from_url("/autofocus/", client)
+    _ = autofocus.fast_autofocus()
 
-def test_stage():
-    with TestClient(server.app) as client:
-        stage = ThingClient.from_url("/stage/", client)
-        start = stage.position
-        move = {"x": 1, "y": 2, "z": 3}
-        stage.move_relative(**move)
-        pos = stage.position
-        for s, m, p in zip(start.values(), move.values(), pos.values()):
-            assert s + m == p
-        stage.move_relative(**{k: -v for k, v in move.items()})
-        pos = stage.position
-        for s, p in zip(start.values(), pos.values()):
-            assert s == p
+def test_grab_jpeg(client):
+    camera = ThingClient.from_url("/camera/", client)
+    blob = camera.grab_jpeg()
+    _image = Image.open(blob.open())
+
+def test_capture_jpeg_metadata(client):
+    camera = ThingClient.from_url("/camera/", client)
+    blob = camera.capture_jpeg()
+    image = Image.open(blob.open())
+    exif_dict = piexif.load(image.info["exif"])
+    encoded_metadata = exif_dict["Exif"][piexif.ExifIFD.UserComment]
+    metadata = json.loads(encoded_metadata)
+    assert "position" in metadata["/stage/"]
+
+def test_stage(client):
+    stage = ThingClient.from_url("/stage/", client)
+    start = stage.position
+    move = {"x": 1, "y": 2, "z": 3}
+    stage.move_relative(**move)
+    pos = stage.position
+    for s, m, p in zip(start.values(), move.values(), pos.values()):
+        assert s + m == p
+    stage.move_relative(**{k: -v for k, v in move.items()})
+    pos = stage.position
+    for s, p in zip(start.values(), pos.values()):
+        assert s == p
+
+# Currently this fails, not yet sure why.
+#def test_camera_stage_mapping_calibration(client):
+#    camera_stage_mapping = ThingClient.from_url("/camera_stage_mapping/", client)
+#    camera_stage_mapping.calibrate_xy()