# Changelog

## Hand-written changelog is now superseded by the generated one in CHANGELOG.md; preserved for posterity.

## 0.3.2 (unreleased)
- **Authentication & Sessions**:
    - Migrated DAQ server URLs to HTTPS with per-beamline configurable certificate paths (cacert) and mTLS; GUI now validates certificates and handles self-signed certs / SSL errors in `DAQWorker` and `SSEClient`.
    - Reworked authentication around Kerberos/SPNEGO token negotiation (via `curl`) behind an Apache/HTTPS proxy; removed the direct `gssapi` dependency and simplified proxy-header handling.
    - GUI session management: track active GUIs in Redis, show the current baton holder, let staff force-close erroneous sessions, and auto-close idle GUIs after a grace period.
- **Operations refactor (major)**:
    - Standardised every multi-step procedure under `aare/daq/operations/<name>/` as a `*Service` with constructor-injected context (`deps`, `runtime` providers, `services` protocols, `settings`); added the `rotation` operation and `screenshot`/common helpers.
    - Major refactor of the mounting service, plus loop-centering, face-detection and raster services, with runtime-state providers/protocols and updated unit tests.
- **Exception model (major refactor)**:
    - Reworked the exception hierarchy into `AareException` with a load-bearing `critical` flag, routing roots (`AutomationError`/`AareUserError`/`AareAuthError`), empty device-family bases for `isinstance` grouping, and centralised `AareErrorCode`s served through FastAPI handlers; the GUI reads `body.critical` to pause/halt automation.
    - Added `StateTransitionFailed`, `MaintenanceStateException`, `BECCommunicationError`, `BeamlineBusyTimeoutException`, `AutoRasterSampleSkipped` and improved `TransformationInvalidException` handling; moved excessive logging out of the exception classes themselves.
- **DAQ/Server**:
    - Converted the in-use EPICS devices to BEC (ring current, energy, front/back light, zoom, transmission, fast shutter, detector Z), and cached BEC device handles as variables for a large speed-up (~6 µs vs ~200 ms per read).
    - Store detector metadata and TELL events in Redis so `/status` polling stays fast; moved detector-Z soft-limit checks into the device with a `detector_limit_modifier` to avoid hitting limits.
    - Added a TELL state handler that derives activity/phase from the TELL SSE stream and surfaces the current robot action in the GUI BUSY label, status bar and recovery panel.
    - Critical detector faults now halt automation (and surface during manual collection); added blower-on for every mount, anneal in/out, `change_energy` and `mono_pitch_scan` controls.
    - Scaling/skip handling for over-large raster grids (Jungfrau buffer limit), with a longer busy timeout and busy-timeout exceptions.
- **GUI**:
    - Added portrait mode, a compact automation view with mode-switching buttons, a Redis-backed automation progress panel, a beamline-state panel, a shared busy-overlay widget, and a splash screen / app banner / icon.
    - Added a local-contact panel that restarts backend device connections (JFJoch, TELL, Aerotech, Smargon), reinitialises BEC macros/devices and opens beamline web helpers.
    - Performance: raster grid manager now renders a single bitmap to remove lag on large grids; added a Database/User-values toggle to data-collection settings.
- **Common, Devices & Config**:
    - Moved all hardware URLs (GUI, JFJoch, Aerotech, BEC, Smargon, TELL) into per-beamline YAML read via `cfg_get`; added `lens_magnification`, `maximum_flux`, `detector_distance_minimum`, `detector_limit_modifier`, beamline-specific transmission PVs and cryojet temperature PVs; removed unused EPICS devices.
- **Workflows**:
    - Added `maintenance2sa`/`maintenance2se` transitions, a safe detector-Z position check, explicit per-transition error messages, and switched to `ABR_POS`/`ABR_OMEGA` mount positions; removed the unused `ws` mode.
- **Hutch safety & error pop-ups** (in progress):
    - Re-wired the GUI pop-up path: failed user operations (mount/unmount) now raise a modal dialog (e.g. *Mounting Failed: No Pin in Gripper*) and background/polling errors a non-modal banner — previously the `http_error` signal was emitted but never connected, so these were silently dropped. Blocking-but-benign errors (e.g. "Beamline is busy" from acting mid-operation) are surfaced quietly in the log/status bar instead of a modal.
    - Added a `PssState` device reading the hutch personnel-safety system (`…-EH1-PSYS:PROHIBITED-STATE` / `:ALARM-STATE`); mounts are blocked (critical `DoorSafetyError`, automation queue paused) when the hutch is not in the prohibited state or a safety alarm is active, and an active alarm also raises a non-modal warning banner via `/status`.
    - `/status` now publishes `pss_prohibited`/`pss_alarm`; the GUI blocks manual mount/unmount and the automation Run button immediately (with a pop-up) when the hutch door is open, instead of letting the robot fail to move server-side.
    - Centralised the per-action precondition checks (ring current, safety shutter, hutch door) into one combined "continue?" dialog used by all data-collection buttons (Evaluate grid, X-ray centering, Run screening/rotation/fluorescence, simple rotation), with a session-global "Don't ask me again for 1 hour" snooze.
    - Live automation now pauses and auto-resumes when the beam, experiment shutter, hutch door or robot (TELL) are not ready (with Continue-now / Stop overrides), gated by a "Pause on bad conditions" checkbox (default on) that replaces the dead `CHECK_ENABLED` constant.
    - Restored "No Pin in Gripper" detection: a mount that returns on the intermediate TELL "Busy" state event now verifies the robot's `get_mounted_sample()` after the command completes, so an empty-gripper mount surfaces `MountingFailed` (and the GUI pop-up) instead of silently reporting success.

## 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**:
    - Implemented comprehensive `pytest` infrastructure for unit and integration tests.
    - 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.
    - Re-enabled and updated automation workflow 2.0 with new backend endpoints.
    - Added `park_and_dry` functionality for repeated mount failures.
    - Workflow assertions to ensure scintillator is down when possible.
    - Improved aerotech movement and position calculations.
    - Implementation of camera auto-exposure and zoom-dependent settings.
    - Added SAS-TT school demo temporary raster function.
    - Enhanced status polling with robust error handling for `Tell`, `Smargon`, and `Aerotech` communication.
    - `ml_box` updated with beamline-specific URLs, model class types, and new YOLO26 engine.
    - Added separate authentication pathway for staff-only beamline recovery operations.
    - Improved database message limits for omega (to 2 decimal places).
    - Added screenshot to database from GUI; face detection sequence and beamline recovery updates.
    - Throttled `UserRightsException` logging to reduce log noise.
    - Implemented persistent automation progress tracking using Redis across multiple workers.
    - Added automation progress panel to the GUI for real-time monitoring.
    - Improved raster and rotation scan error handling and centralized database message handling.
    - 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.
    - Integrated baton status messages into the camera image display and status bar.
    - Improved session state transitions with new `Pending` states and P-group selection logic.
- **GUI**:
    - Added `ui_state_manager` to handle `QSettings` for persistent UI state.
    - Major rework of `predict_subscriber` and prediction stream updates; corrected default ZMQ stream for ML box.
    - Added FPS counter and sharpness monitoring for sample camera.
    - Improved camera thread performance and authentication failure handling.
    - Added X10SA specific camera and prediction configurations.
    - New `display_status` for user-facing connection/error messages.
    - Integrated `dev_help` panel with logs and error code search.
    - Added framework for building GUI tutorials with first draft of X10SA tutorial.
    - Added alert banner for critical disconnection issues (server/Tell/Aerotech).
    - New screenshot button and controls in sample camera GUI.
    - Added SSE support for face detection panel updates during automation.
    - Integrated sample position resync in recovery panel to reduce Tell polling.
    - Fixed matplotlib warnings in face detection panel and improved layout persistence. 
    - Added `beamline_state_panel` with station widgets for improved state management and visibility.
    - Performance optimizations: throttled raster grid drawing to 25Hz and improved dense heat map rendering.
    - 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.
    - Major refactor: removed redundant code and added simulated client.
    - Converted wait functions to use inbuilt pshell functionality.
    - Added error handling and proxy support for connection failures.
    - Fixed event names for mounting, and added missing events for gripper detection and motion sync.
    - Refactored SSE connection handling for simplicity and robustness.
    - 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.
    - Added centralized `error_codes` and refactored exception handling to use FastAPI handlers.
    - Expanded device support with new PVs (beamstop, scintillator, collimator, cryojet, etc.).
    - Cleaned up `mx_lib` wait functions and `my_motor` class; added `clean_filename` helper.
    - Improved Smargon connection exception handling.
    - Updated ABR_POS_HOME configuration and added comments for cryo positions.
    - Added image upload comments and improved authentication error messaging.
    - Centralized custom exceptions in `aare.common.exception_handler`.
    - 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.
    - `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
- lowered polling rate of daq status to improve GUI performance
- robot drys then parks after repeated mount failures
### 0.2.68:
- added check box to numberlineedits to switch between user input and spreadsheet
- re-enabled MLprediction
- fixed bug in gui where manual sample couldnt be created when run nubmer was negative.
- Combined beamline view now split vertically not horizontally
- New error handling in DAQ for robot mounting errors
- Error box pop ups in GUI when sample gripper detection error occurs
- Automation queue pauses if sample gripper detection error occurs multiple times to allow robot dry, if continues stops and wiats for user interverntion
- added ingest_scan to send rotation and screening result to db

### 0.2.67:
- added run number to sampleshortinfo
- ingest raster result, including beam center to database
- aerotech goes to mount postion for manual mount
- logger config correctly expands file path for logger location.
- smart_rotiation_panel fix - but will be mvoed to DAQ in future update
- Fluoresence scan can be saved to CSV with right click
- Wait for ready before sending Tell to dry

### 0.2.66:
- moved rastergridingestmodel and centreofmassmodel from models to raster_grid.py
- after raster load closest image to new centre