test(live_processing): change test mode to something more unlikely to be implemented

.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: v1.4.0
+_commit: v1.0.0
 _src_path: https://github.com/bec-project/plugin_copier_template.git
 make_commit: false
 project_name: tomcat_bec

.gitea/workflows/ci.yml

@@ -1,102 +0,0 @@
-name: CI for tomcat_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: "3.12"
-
-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: "${{ inputs.PYTHON_VERSION || '3.12' }}"
-
-      - name: Checkout BEC Plugin Repository
-        uses: actions/checkout@v4
-        with:
-          repository: bec/tomcat_bec
-          ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
-          path: ./tomcat_bec
-
-      - name: Lint for merge conflicts from template updates
-        shell: bash
-        # Find all Copier conflicts except this line
-        run: '! grep -r "<<<<<<< before updating" | grep -v "grep -r \"<<<<<<< before updating"'
-
-      - 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: 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 ./tomcat_bec[dev]
-
-      - name: Run Pytest with Coverage
-        id: coverage
-        run: pytest --random-order --cov=./tomcat_bec --cov-config=./tomcat_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./tomcat_bec/tests/ || test $? -eq 5

.gitea/workflows/create_update_pr.yml

@@ -1,70 +0,0 @@
-name: Create template upgrade PR for tomcat_bec
-on:
-  workflow_dispatch:
-
-permissions:
-  pull-requests: write
-
-jobs:
-  create_update_branch_and_pr:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-      pull-requests: write
-
-    steps:
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Create virtualenv
-	    run: |
-	      python -m virtualenv .venv
-
-      - name: Install tools
-        run: |
-          source .venv/bin/activate
-          pip install copier PySide6 bec_lib
-
-      - name: Perform update
-        run: |
-          source .venv/bin/activate
-          git config --global user.email "bec_ci_staging@psi.ch"
-          git config --global user.name "BEC automated CI"
-
-          branch="chore/update-template-$(python -m uuid)"
-          echo "switching to branch $branch"
-          git checkout -b $branch
-
-          echo "Running copier update..."
-          copier update --trust --defaults --conflict inline 2>&1 | tee copier.log
-          status=${PIPESTATUS[0]}
-          output="$(cat copier.log)"
-          echo $output
-          msg="$(printf '%s\n' "$output" | head -n 1)"
-
-          if ! grep -q "make_commit: true" .copier-answers.yml ; then
-            echo "Autocommit not made, committing..."
-            git add -A
-            git commit -a -m "$msg"
-          fi
-
-          if diff-index --quiet HEAD ; then
-            echo "No changes detected"
-            exit 0
-          fi
-
-          git push -u origin $branch
-          curl -X POST "https://gitea.psi.ch/api/v1/repos/${{ gitea.repository }}/pulls" \
-            -H "Authorization: token ${{ secrets.CI_REPO_WRITE }}" \
-            -H "Content-Type: application/json" \
-            -d "{
-                  \"title\": \"Template: $(echo $msg)\",
-                  \"body\": \"This PR was created by Gitea Actions\",
-                  \"head\": \"$(echo $branch)\",
-                  \"base\": \"main\"
-                }"

.gitlab-ci.yml

@@ -0,0 +1,7 @@
+include:
+- file: /templates/plugin-repo-template.yml
+  inputs:
+    name: tomcat_bec
+    target: tomcat_bec
+    branch: $CHILD_PIPELINE_BRANCH
+  project: bec/awi_utils

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "tomcat_bec"
 version = "0.0.0"
 description = "The TOMCAT plugin repository for BEC"
-requires-python = ">=3.11"
+requires-python = ">=3.10"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
@@ -48,9 +48,6 @@ plugin_file_writer = "tomcat_bec.file_writer"
 [project.entry-points."bec.scans"]
 plugin_scans = "tomcat_bec.scans"
 
-[project.entry-points."bec.scans.scan_modifier"]
-plugin_scan_modifier = "tomcat_bec.scans.scan_customization.scan_modifier"
-
 [project.entry-points."bec.scans.metadata_schema"]
 plugin_metadata_schema = "tomcat_bec.scans.metadata_schema"
 

tests/tests_devices/test_std_daq_live_processing.py

@@ -11,7 +11,7 @@ from typeguard import TypeCheckError
 from tomcat_bec.devices.std_daq.std_daq_live_processing import StdDaqLiveProcessing
 
 
-def fake_redis_server(host, port, **kwargs):
+def fake_redis_server(host, port):
     redis = fakeredis.FakeRedis()
     return redis
 
@@ -53,7 +53,7 @@ def test_std_daq_live_processing_set_mode(std_daq_live_processing):
     std_daq_live_processing.set_mode("sum")
     assert std_daq_live_processing.get_mode() == "sum"
     with pytest.raises(TypeCheckError):
-        std_daq_live_processing.set_mode("average")
+        std_daq_live_processing.set_mode("mode_that_does_not_exist")
     with pytest.raises(TypeCheckError):
         std_daq_live_processing.set_mode(123)
 

tomcat_bec/bec_ipython_client/startup/pre_startup.py

@@ -3,12 +3,8 @@ Pre-startup script for BEC client. This script is executed before the BEC client
 is started. It can be used to add additional command line arguments.
 """
 
-import os
-
 from bec_lib.service_config import ServiceConfig
 
-import tomcat_bec
-
 
 def extend_command_line_args(parser):
     """
@@ -20,13 +16,8 @@ def extend_command_line_args(parser):
     return parser
 
 
-def get_config() -> ServiceConfig:
-    """
-    Create and return the ServiceConfig for the plugin repository
-    """
-    deployment_path = os.path.dirname(os.path.dirname(os.path.dirname(tomcat_bec.__file__)))
-    files = os.listdir(deployment_path)
-    if "bec_config.yaml" in files:
-        return ServiceConfig(config_path=os.path.join(deployment_path, "bec_config.yaml"))
-    else:
-        return ServiceConfig(redis={"host": "localhost", "port": 6379})
+# def get_config() -> ServiceConfig:
+#     """
+#     Create and return the service configuration.
+#     """
+#     return ServiceConfig(redis={"host": "localhost", "port": 6379})

tomcat_bec/devices/std_daq/std_daq_client.py

@@ -468,15 +468,11 @@ class StdDaqClient:
         Run the count callbacks with the given count.
         The callbacks will be called with the count as argument.
         """
-        callbacks_ids = list(self._count_callbacks.keys())
-        for cb_id in callbacks_ids:
-            if cb_id not in self._count_callbacks:
-                continue
-            cb = self._count_callbacks[cb_id]
+        for cb in self._count_callbacks.values():
             try:
                 cb(count)
             except Exception as exc:
-                logger.error(f"Error in StdDAQ count callback with ID {cb_id}: {exc}")
+                logger.error(f"Error in StdDAQ count callback: {exc}")
 
     def _run_status_callbacks(self):
         """
@@ -485,25 +481,19 @@ class StdDaqClient:
         or exception, respectively and removed from the list of callbacks.
         """
         status = self._status
-
-        status_callbacks_ids = list(self._status_callbacks.keys())
-        for status_id in status_callbacks_ids:
-            dev_status, success, error = self._status_callbacks.get(status_id, (None, [], []))
-            if dev_status is None:
-                continue
-
+        completed_callbacks = []
+        for dev_status, success, error in self._status_callbacks.values():
             if dev_status.done:
-                logger.info("Status object already resolved. Skipping StdDaq callback.")
-                self._status_callbacks.pop(status_id)
+                logger.warning("Status object already resolved. Skipping StdDaq callback.")
                 continue
-
             if status in success:
                 dev_status.set_finished()
                 logger.info(f"StdDaq status is {status}")
-                self._status_callbacks.pop(status_id)
-                continue
-
-            if status in error:
+                completed_callbacks.append(dev_status)
+            elif status in error:
                 logger.warning(f"StdDaq status is {status}")
                 dev_status.set_exception(StdDaqError(f"StdDaq status is {status}"))
-                self._status_callbacks.pop(status_id)
+                completed_callbacks.append(dev_status)
+
+        for cb in completed_callbacks:
+            self._status_callbacks.pop(id(cb))

tomcat_bec/devices/std_daq/std_daq_live_processing.py

@@ -45,14 +45,14 @@ class StdDaqLiveProcessing:
         return self._mode
 
     @typechecked
-    def set_mode(self, mode: Literal["sum"]):
+    def set_mode(self, mode: Literal["sum", "average"]):
         """
         Set the processing mode.
         Args:
-            mode (str): Processing mode, currently only "sum" is supported.
+            mode (str): Processing mode, currently only "sum" and "average" are supported.
         """
-        if mode not in ["sum"]:
-            raise ValueError("Unsupported mode. Only 'sum' is currently supported.")
+        if mode not in ["sum", "average"]:
+            raise ValueError("Unsupported mode. Only 'sum' and 'average' are currently supported.")
         self._mode = mode
 
     def set_enabled(self, value: bool):
@@ -83,6 +83,8 @@ class StdDaqLiveProcessing:
         match self._mode:
             case "sum":
                 self.process_sum(data)
+            case "average":
+                self.process_average(data)
             case _:
                 raise ValueError(f"Unknown mode: {self._mode}")
 
@@ -98,6 +100,18 @@ class StdDaqLiveProcessing:
         summed_data = np.sum(np.sum(data))
         self.signal.put(summed_data)
 
+    def process_average(self, data: np.ndarray):
+        """
+        Process data by averaging it.
+        Args:
+            data (np.ndarray): Data to average.
+        """
+        if not isinstance(data, np.ndarray):
+            raise ValueError("Data must be a numpy array.")
+
+        averaged_data = np.mean(data)
+        self.signal.put(averaged_data)
+
     ########################################
     ## Flat and Dark Field References ######
     ########################################

tomcat_bec/macros/README.md

@@ -1,6 +0,0 @@
-# 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 tomcat_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

tomcat_bec/scans/scan_customization/scan_components.py

@@ -1,12 +0,0 @@
-"""
-Scan components for tomcat_bec.
-
-The scan components module allows you to define custom components that can be used in your scans.
-These components can be used to encapsulate reusable logic, interact with devices, or perform specific actions during the scan lifecycle.
-"""
-
-from bec_server.scan_server.scans.scan_components import ScanComponents
-
-
-class TomcatBecScanComponents(ScanComponents):
-    """Scan components for tomcat_bec."""

tomcat_bec/scans/scan_customization/scan_modifier.py

@@ -1,33 +0,0 @@
-"""
-Scan modifier plugin for tomcat_bec.
-
-The scan modifier allows you to modify the scan lifecycle and run custom actions before or after the scan hook or replace the scan hook entirely.
-Note that the scan_modifier module must be registered as a plugin in the pyproject.toml file for it to be recognized by the BEC framework and that
-there can only be one scan_modifier plugin registered at a time. If you need to run multiple scan modifiers, you can create a single scan
-modifier plugin that runs multiple actions in sequence with conditional logic to determine which actions to run based on the scan context.
-"""
-
-from bec_server.scan_server.scans.scan_modifier import ScanModifier, scan_hook_impl
-
-
-class TomcatBecScanModifier(ScanModifier):
-    """
-    Scan modifier for tomcat_bec.
-    
-    By inheriting from the ScanModifier base class, you get access to currently running scan (self.scan), the devices (self.dev), the scan info (self.scan_info),
-    the scan components (self.components) and the scan actions (self.actions).
-    """
-
-    def __init__(self, **kwargs):
-        """Initialize the scan modifier."""
-        super().__init__(**kwargs)
-
-    # Example of running code before the scan stage for a specific scan
-    # @scan_hook_impl("stage", "before")
-    # def before_stage(self):
-    #     """Run before the stage hook."""
-    #     self.actions.send_client_info("Custom stage logic executed by ScanModifier.")
-    #     if self.scan_info.scan_name == "example_scan":
-    #         self.dev.samx.set(20)
-
-