Add module level docstrings.

src/openflexure_microscope_server/logging.py

@@ -1,3 +1,16 @@
+"""Configure logging for the OpenFlexure Server.
+
+A module containing a custom logging handler and helper function for
+the OpenFlexure server. These handle formatting logs, ensuring that logs
+are logged both to a file and to the terminal (see note below!). Functionality
+is also provided for retrieving logs for to send over HTTP.
+
+Note that when running in production OpenFlexure Microscope the server is run via
+``systemd``. As such, the logs that are sent to the terminal (STDERR) or any other
+output to STDOUT/STDERR are captured by ``systemd``. These can be viewed by using
+``journalctl`` or the ``ofm journal`` command.
+"""
+
 import logging
 from logging.handlers import RotatingFileHandler
 import os

src/openflexure_microscope_server/server/legacy_api.py

@@ -1,3 +1,5 @@
+"""Provide endpoints that mimic the v2 API for OpenFlexure Connect discoverability."""
+
 import labthings_fastapi as lt
 from fastapi import Response
 from socket import gethostname

src/openflexure_microscope_server/server/serve_static_files.py

@@ -1,3 +1,5 @@
+"""Add endpoints for static files to the underlying FastAPI server."""
+
 import os
 from typing import Optional
 

src/openflexure_microscope_server/things/auto_recentre_stage.py

@@ -1,3 +1,5 @@
+"""Provide functionality for automatically recentring the Stage."""
+
 import numpy as np
 import logging
 

src/openflexure_microscope_server/things/background_detect.py

@@ -1,3 +1,10 @@
+"""Provide functionality to detect if the camera is imaging sample or background.
+
+An example background image must be captured and analysed by BackgroundDetectThing,
+information from this images is used to detect whether the current camera field of
+view contains sample.
+"""
+
 from typing import Mapping, Optional
 import cv2
 import numpy as np

src/openflexure_microscope_server/things/smart_scan.py

@@ -1,3 +1,12 @@
+"""The core sample scanning functionality for the OpenFlexure Microscope.
+
+SmartScan provides sample scanning functionality including automatic background
+dectection (via the `BackgroundDetectThing`) and automatic path planning via
+`scan_planners`. It manages the directories of past scans via `scan_directories`.
+It also controls external processes for live stitching composite images, and
+the creation of the final stitched images.
+"""
+
 from typing import Optional, Mapping
 import threading
 import os

src/openflexure_microscope_server/things/stage/dummy.py

@@ -1,3 +1,5 @@
+"""Functionality for mimicking a stage during simulation and testing."""
+
 from __future__ import annotations
 
 from collections.abc import Mapping

src/openflexure_microscope_server/things/stage/sangaboard.py

@@ -1,3 +1,5 @@
+"""Provide a LabThings-FastAPI interface to the Sangaboard motor controller."""
+
 from __future__ import annotations
 import logging
 import threading