Update to version 0.3.1

CHANGELOG.md

@@ -1,4 +1,11 @@
 # Changelog
+## 0.3.1 (2026-04-29)
+- **DAQ/Server**:
+    - Improved baton exchange logic with automatic timeout and Redis-backed state.
+- **GUI**:
+    - Updated about dialog with correct version and copyright.
+    - Improved layout persistence and state management.
+
 ## 0.3.0 (2026-04-24)
 - Merge three repos into one, remove Ultralytics as dependency
 - **Testing & CI/CD**:
@@ -6,6 +13,7 @@
     - Integrated `pytest-cov` and `pytest-mock` into the testing workflow with 100% coverage on core modules like `coordinate` and `exception_handler`.
     - Added automated testing stage to Gitea workflow (`.gitea/workflows/action.yaml`) ensuring tests pass before build and documentation updates.
     - Added `pytest-qt` support for GUI testing.
+    - Added tests for `aerotech`, `models`, `autofocus`, `automation`, `beamline`, `diffraction_geometry`, `enum_pv`, `face_detection`, `jfjoch_client`, `mlbox`, `my_motor`, `spreadsheet_updater`, and `workflows`.
 - **DAQ/Server**:
     - Added lifespan function for one-time initialization of core objects (devices, daq, config) on startup, reducing conflicting Redis and device connections.
     - Big Aerotech upgrade: transitioned to Aerotech API with ported coordinate functions.
@@ -27,6 +35,8 @@
     - Updated `server_exception_handler.py` and `error_codes.py` to cover all custom exceptions.
     - Added `auto_exposure` endpoint and improved `autofocus` logic.
     - Fixed multiple bugs in raster scan positioning and state transitions.
+    - Refactored `MLBOX` and `LOOP_CENTERING` types; loop centering now avoids moving if only non-crystal classes (pin, ice, needle) are found.
+    - Split `LOOP_CENTERING` from main DAQ script for better maintainability.
 - **Baton & Sessions**:
     - Major rework of the baton exchange procedure and session management.
     - Added `NOT_BATON_HOLDER` error code and specialized handling for baton requests.
@@ -51,6 +61,7 @@
     - Added automation progress panel and wired it to the persistent Redis backend.
     - Improved prediction subscriber performance and target stability visualization.
     - Added shortcuts and improved user feedback in the status bar using `BeamlineStateEnum` display names.
+    - Improved prediction subscriber and metrics panel performance.
 - **TELL & Infrastructure**:
     - Added mTLS certificate authentication for `aaredb`, `tellupdater`, and `spreadsheetupdater`.
     - Improved SSE client resilience in `tellupdater` with retry mechanisms and enhanced error logging.
@@ -62,6 +73,7 @@
     - Added control for pin blower and annealing (in/out) to `TellClient`.
     - Improved TELL HTTP communication handling to prevent swallowed errors.
     - Added magnet position sensor state checks and exception handling.
+    - Improved Gitea workflows with better dependency management and testing steps.
 - **Common & Devices**:
     - Added BEC worker and Aerotech controller initialization in `devices.py`.
     - Added magnet position sensor functions and centralized transmission settings.
@@ -75,10 +87,7 @@
     - Added `display_name` to `BeamlineStateEnum` for consistent UI strings.
     - Refactored `SampleShortInfo` handling across DAQ and database modules.
     - Multiple bug fixes in ML box prediction logic and coordinate transformations.
-- **Infrastructure**:
-    - Updated dependencies (added `pshell`) and improved documentation autodeployment workflows.
-    - Refactored package structure and imports.
-    - Fixed `logger_config` file path expansion.
+    - `JFJOCH` wrapper: Added retries for image retrieval and new `wait_till_running` method.
 
 ### 0.2.69
 - check beamline state before running raster, rotation and automation

README.md

@@ -1,4 +1,6 @@
-# Readme
+# AareDAQ (v0.3.1)
+
+AareDAQ is the Data Acquisition system for MX beamlines at PSI.
 
 ## GUI Controls Cheat Sheet
 

VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

docs/conf.py

@@ -16,7 +16,7 @@ sys.path.insert(0, os.path.abspath('../src/aare/gui'))
 project = 'AareDAQ'
 copyright = '2026, Paul Scherrer Institute'
 author = 'Martin Appleby, Guillaume Gotthard, Filip Leonarski and Dawn (Jiaxin) Daun'
-release = '0.3.0'
+release = '0.3.1'
 master_doc = 'index'
 root_doc = 'index'
 
@@ -109,6 +109,13 @@ html_theme_options = {
     "site_url": "https://gitea.psi.ch/mx/aaredaq",
     "repo_url": "https://gitea.psi.ch/mx/aaredaq",
     "repo_name": "AareDAQ",
+    "social": [
+        {
+            "icon": "fontawesome/brands/github",
+            "link": "https://gitea.psi.ch/mx/aaredaq",
+            "name": "AareDAQ on Gitea",
+        },
+    ],
     "palette": [
         {
             "media": "(prefers-color-scheme: light)",
@@ -137,8 +144,17 @@ html_theme_options = {
         "navigation.top",
         "search.share",
         "toc.follow",
+        "navigation.instant",
+        "content.tabs.link",
+        "content.code.annotate",
+        "content.code.copy",
     ],
     "globaltoc_collapse": False,
+    "toc_title": "On this page",
+    "toc_title_container": True,
+    "font": {
+        "code": "JetBrains Mono",
+    },
 }
 html_theme_options["google_fonts"] = []
 html_sidebars = {
@@ -154,4 +170,5 @@ autodoc_default_options = {
     'members': True,
     'undoc-members': True,
     'show-inheritance': True,
+    'member-order': 'bysource',
 }

docs/index.rst

@@ -3,22 +3,33 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to the AareDAQ Documentation
-=====================
+Welcome to AareDAQ
+=================
+
+AareDAQ is the Data Acquisition system for MX beamlines at the Paul Scherrer Institute (PSI). 
+It provides a robust backend for orchestrating beamline devices and a user-friendly GUI for data collection.
+
+Overview
+--------
+
+* :doc:`User Guide <readme>`: New to AareDAQ? Check out the overview and cheat sheet.
+* :doc:`Changelog <changelog>`: See what's new in the latest version.
+* :doc:`API Reference <api/aare>`: Detailed documentation for all AareDAQ modules and classes.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
-   :glob:
+   :caption: Documentation
+   :hidden:
 
-   ../README
-   ../CHANGELOG
+   README <readme>
+   CHANGELOG <changelog>
 
 .. toctree::
    :maxdepth: 2
-   :caption: API Reference
+   :caption: Development
+   :hidden:
 
-   api/aare
+   API Reference <api/aare>
 
 Indices and tables
 ==================

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aaredaq"
-version = "0.3.0"
+version = "0.3.1"
 description = "AareDAQ (with GUI)"
 readme = "README.md"
 requires-python = ">=3.11"

src/aare/daq/daq.py

@@ -74,6 +74,12 @@ from aare.devices.tell_client import TellEventValueEnum
 logger = setup_logger("aareDAQ")
 #TODO tidy up DAQ - migrate functions itno different scripts, to reduce size?
 class AareDAQ:
+    """
+    Main Data Acquisition class for the Aare system.
+    
+    This class orchestrates interactions between various beamline devices,
+    the Aare database, ML services, and data collection workflows.
+    """
 
     MIN_SPOTS_LOW_RES_THRESHOLD = 10.0
 

src/aare/gui/gui.py

@@ -17,7 +17,7 @@ def main():
     try:
         app = QApplication(sys.argv)
         app.setApplicationName("AareGUI")
-        app.setApplicationVersion("0.1.0")
+        app.setApplicationVersion("0.3.1")
         app.setOrganizationName("PSI")
         app.setOrganizationDomain("psi.ch")
 

src/aare/gui/main_window.py

@@ -1016,7 +1016,7 @@ class MainWindow(QMainWindow):
         QMessageBox.about(
             self,
             "About",
-            "Aare Macromolecular Crystallography GUI\nVersion: 1.0\nCopyright: Paul Scherrer Institute 2024-2025",
+            "Aare Macromolecular Crystallography GUI\nVersion: 0.3.1\nCopyright: Paul Scherrer Institute 2024-2026",
         )
 
     def show_controls_help(self) -> None: