refactor: copier upgrade to v1-2-2

.copier-answers.yml

@@ -2,7 +2,7 @@
 # It is needed to track the repo template version, and editing may break things.
 # This file will be overwritten by copier on template updates.
 
-_commit: v1.1.2
+_commit: v1.2.2
 _src_path: https://github.com/bec-project/plugin_copier_template.git
 make_commit: false
 project_name: csaxs_bec

.gitea/workflows/ci.yml

@@ -0,0 +1,97 @@
+name: CI for csaxs_bec
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      BEC_WIDGETS_BRANCH:
+        description: "Branch of BEC Widgets to install"
+        required: false
+        type: string
+        default: "main"
+      BEC_CORE_BRANCH:
+        description: "Branch of BEC Core to install"
+        required: false
+        type: string
+        default: "main"
+      OPHYD_DEVICES_BRANCH:
+        description: "Branch of Ophyd Devices to install"
+        required: false
+        type: string
+        default: "main"
+      BEC_PLUGIN_REPO_BRANCH:
+        description: "Branch of the BEC Plugin Repository to install"
+        required: false
+        type: string
+        default: "main"
+      PYTHON_VERSION:
+        description: "Python version to use"
+        required: false
+        type: string
+        default: "3.11"
+
+permissions:
+  pull-requests: write
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    env:
+      QTWEBENGINE_DISABLE_SANDBOX: 1
+      QT_QPA_PLATFORM: "offscreen"
+
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "${{ inputs.PYTHON_VERSION || '3.11' }}"
+
+      - name: Checkout BEC Core
+        uses: actions/checkout@v4
+        with:
+          repository: bec/bec
+          ref: "${{ inputs.BEC_CORE_BRANCH || 'main' }}"
+          path: ./bec
+
+      - name: Checkout Ophyd Devices
+        uses: actions/checkout@v4
+        with:
+          repository: bec/ophyd_devices
+          ref: "${{ inputs.OPHYD_DEVICES_BRANCH || 'main' }}"
+          path: ./ophyd_devices
+
+      - name: Checkout BEC Widgets
+        uses: actions/checkout@v4
+        with:
+          repository: bec/bec_widgets
+          ref: "${{ inputs.BEC_WIDGETS_BRANCH || 'main' }}"
+          path: ./bec_widgets
+
+      - name: Checkout BEC Plugin Repository
+        uses: actions/checkout@v4
+        with:
+          repository: bec/csaxs_bec
+          ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
+          path: ./csaxs_bec
+
+      - name: Install dependencies
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgl1 libegl1 x11-utils libxkbcommon-x11-0 libdbus-1-3 xvfb
+          sudo apt-get -y install libnss3 libxdamage1 libasound2t64 libatomic1 libxcursor1
+
+      - name: Install Python dependencies
+        shell: bash
+        run: |
+          pip install uv
+          uv pip install --system -e ./ophyd_devices
+          uv pip install --system -e ./bec/bec_lib[dev]
+          uv pip install --system -e ./bec/bec_ipython_client
+          uv pip install --system -e ./bec/bec_server[dev]
+          uv pip install --system -e ./bec_widgets[dev,pyside6]
+          uv pip install --system -e ./csaxs_bec
+
+      - name: Run Pytest with Coverage
+        id: coverage
+        run: pytest --random-order --cov=./csaxs_bec --cov-config=./csaxs_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./csaxs_bec/tests/ || test $? -eq 5

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -416,7 +416,7 @@ class FlomniSampleTransferMixin:
     def laser_tracker_on(self):
         dev.rtx.controller.laser_tracker_on()
         time.sleep(0.2)
-        self._laser_tracker_check_signalstrength()
+        dev.rtx.controller.laser_tracker_check_signalstrength()
 
     def laser_tracker_off(self):
         dev.rtx.controller.laser_tracker_off()
@@ -429,11 +429,11 @@ class FlomniSampleTransferMixin:
 
     def feedback_enable_with_reset(self):
         self.device_manager.devices.rtx.controller.feedback_enable_with_reset()
-        self.rt_feedback_status()
+        self.feedback_status()
 
     def feedback_enable_without_reset(self):
         self.device_manager.devices.rtx.controller.feedback_enable_without_reset()
-        self.rt_feedback_status()
+        self.feedback_status()
 
     def feedback_status(self):
         feedback_status = self.device_manager.devices.rtx.controller.feedback_is_running()

csaxs_bec/bec_widgets/widgets/omny_alignment/omny_alignment.py

@@ -63,6 +63,8 @@ class OmnyAlignment(BECWidget, QWidget):
 
         self.ui.liveViewSwitch.enabled.connect(self.on_live_view_enabled)
 
+        self.ui.moveUpButton.clicked.connect(self.on_move_up)
+
 
     @property
     def enable_live_view(self):
@@ -102,7 +104,6 @@ class OmnyAlignment(BECWidget, QWidget):
         image.disconnect_monitor("cam200")
 
 
-
     @property
     def enable_move_buttons(self):
         move_up:QPushButton = self.ui.moveUpButton

csaxs_bec/macros/README.md

@@ -0,0 +1,6 @@
+# Macros
+
+This directory is intended to store macros which will be loaded automatically when starting BEC.
+Macros are small functions to make repetitive tasks easier. Functions defined in python files in this directory will be accessible from the BEC console.
+Please do not put any code outside of function definitions here. If you wish for code to be automatically run when starting BEC, see the startup script at csaxs_bec/bec_ipython_client/startup/post_startup.py
+For a guide on writing macros, please see: https://bec.readthedocs.io/en/latest/user/command_line_interface.html#how-to-write-a-macro

csaxs_bec/scans/flomni_fermat_scan.py

@@ -172,7 +172,7 @@ class FlomniFermatScan(SyncFlyScanBase):
             self.device_manager.connector.raise_alarm(
                 severity=0,
                 alarm_type="LaserTrackerSignalStrength",
-                source="rtx",
+                source={"device": "rtx", "reason": "low signal strength", "method": "_prepare_setup_part2"},
                 metadata={},
                 msg="Signal strength of the laser tracker is low, sufficient to continue. Realignment recommended!",
             )
@@ -295,9 +295,10 @@ class FlomniFermatScan(SyncFlyScanBase):
             logger.debug("reading monitors")
         # yield from self.device_rpc("rtx", "controller.kickoff")
 
-    def return_to_start(self):
+    def move_to_start(self):
         """return to the start position"""
-        # in flomni, we need to move to the start position of the next scan
+        # in flomni, we need to move to the start position of the next scan, which is the end position of the current scan
+        # this method is called in finalize and overwrites the default move_to_start()
         if isinstance(self.positions, np.ndarray) and len(self.positions[-1]) == 3:
             yield from self.stubs.set(device=["rtx", "rty", "rtz"], value=self.positions[-1])
             return

csaxs_bec/scans/omny_fermat_scan.py

@@ -280,9 +280,10 @@ class OMNYFermatScan(SyncFlyScanBase):
             logger.debug("reading monitors")
         # yield from self.device_rpc("rtx", "controller.kickoff")
 
-    def return_to_start(self):
+    def move_to_start(self):
         """return to the start position"""
-        # in omny, we need to move to the start position of the next scan
+        # in omny, we need to move to the start position of the next scan, which is the end position of the current scan
+        # this method is called in finalize and overwrites the default move_to_start()
         if isinstance(self.positions, np.ndarray) and len(self.positions[-1]) == 3:
             yield from self.stubs.set(device=["rtx", "rty", "rtz"], value=self.positions[-1])
             return

docs/user/ptychography/flomni.md

@@ -147,8 +147,14 @@ Following functions exist to move the optics in and out, with self-explaining na
 
 The position feedback in flOMNI is controlled in closed loop to an interferometric position measurement. To show the signal of the interferometers:
 `flomni.show_signal_strength_interferometer()`  
-Typical values with proper alignment, sample stage at the measurement position and laser tracker running are  
-_TODO_
+Typical values with proper alignment, sample stage at the measurement position and laser tracker running are in the range of
+|    Axis   |       Value        |
+| --- | --- |
+|     0     |      13681.0       |
+|     1     |      12383.0       |
+|     2     |      10716.0       |
+|     3     |      11032.0       |
+
 
 #### Laser tracker commands
 
@@ -162,10 +168,10 @@ The horizontal interferometer is built according to the [tracking interferometer
 #### Interferometer feedback commands
 
 The closed loop control of the Piezo stages can be controlled by  
-- `flomni.rt_feedback_enable_with_reset()`.  
+- `flomni.feedback_feedback_enable_with_reset()`.  
 _There is also an enable without reset, which is used during tomography scans, when using coarse stages to increase the scan range. It should not be required to use manually._  
-- `flomni.rt_feedback_disable()`
-- `flomni.rt_feedback_status()`
+- `flomni.feedback_disable()`
+- `flomni.feedback_status()`
 
 ### Scanning in 2D and sample alignment