Refactor server into submodule

src/openflexure_microscope_server/server/__init__.py

@@ -0,0 +1,43 @@
+from __future__ import annotations
+
+from labthings_fastapi.thing_server import ThingServer
+from labthings_sangaboard import SangaboardThing
+from labthings_picamera2.thing import StreamingPiCamera2
+
+from ..things.autofocus import AutofocusThing
+from ..things.camera_stage_mapping import CameraStageMapper
+from ..things.system_control import SystemControlThing
+from ..things.settings_manager import SettingsManager
+from ..things.auto_recentre_stage import RecentringThing
+from ..things.smart_scan import SmartScanThing, BackgroundDetectThing
+from ..things.test import APITestThing
+from .serve_static_files import add_static_files
+from .legacy_api import add_v2_endpoints
+from ..logging import configure_logging, retrieve_log
+
+configure_logging()
+
+thing_server = ThingServer()
+thing_server.add_thing(StreamingPiCamera2(), "/camera/")
+thing_server.add_thing(SangaboardThing(), "/stage/")
+thing_server.add_thing(RecentringThing(), "/auto_recentre_stage/")
+thing_server.add_thing(AutofocusThing(), "/autofocus/")
+thing_server.add_thing(CameraStageMapper(), "/camera_stage_mapping/")
+thing_server.add_thing(SystemControlThing(), "/system_control/")
+thing_server.add_thing(SettingsManager(), "/settings/")
+thing_server.add_thing(SmartScanThing("application/openflexure-stitching/.venv/bin/openflexure-stitch"), "/smart_scan/")
+thing_server.add_thing(BackgroundDetectThing(), "/background_detect/")
+thing_server.add_thing(APITestThing(), "/api_test/")
+try:
+    add_static_files(thing_server.app)
+except RuntimeError:
+    print("Failed to add static files - you will have to do without them!")
+
+add_v2_endpoints(thing_server)  # Add the v2 endpoints for compatibility with OpenFlexure Connect
+
+# Add an endpoint to get the log
+thing_server.app.get("/log/")(retrieve_log)
+
+
+app = thing_server.app
+