wip - failed pipeline as reference for gitea

.copier-answers.yml

@@ -1,9 +0,0 @@
-# Do not edit this file!
-# 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: v1.2.8
-_src_path: https://github.com/bec-project/plugin_copier_template.git
-make_commit: false
-project_name: phoenix_bec
-widget_plugins_input: []

.gitea/workflows/ci.yml

@@ -1,102 +0,0 @@
-name: CI for phoenix_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: "${{ inputs.PYTHON_VERSION || '3.12' }}"
-
-      - name: Checkout BEC Plugin Repository
-        uses: actions/checkout@v4
-        with:
-          repository: bec/phoenix_bec
-          ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
-          path: ./phoenix_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 ./phoenix_bec
-
-      - name: Run Pytest with Coverage
-        id: coverage
-        run: pytest --random-order --cov=./phoenix_bec --cov-config=./phoenix_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./phoenix_bec/tests/ || test $? -eq 5

.gitea/workflows/create_update_pr.yml

@@ -1,62 +0,0 @@
-name: Create template upgrade PR for phoenix_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: Install tools
-        run: |
-          pip install copier PySide6
-
-      - name: Checkout
-        uses: actions/checkout@v4
-    
-      - name: Perform update
-        run: |
-          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 $branch
-
-          echo "Running copier update..."
-          output="$(copier update --trust --defaults --conflict inline 2>&1)"
-          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\"
-                }"

.gitignore

@@ -7,6 +7,7 @@
 **/.vscode
 **/.pytest_cache
 **/*.egg*
+*.gz
 
 # recovery_config files
 recovery_config_*

.gitlab-ci.yml

@@ -0,0 +1,6 @@
+include:
+- file: /templates/plugin-repo-template.yml
+  inputs:
+    name: phoenix_bec
+    target: phoenix_bec
+  project: bec/awi_utils

LICENSE

@@ -1,7 +1,6 @@
-
 BSD 3-Clause License
 
-Copyright (c) 2025, Paul Scherrer Institute 
+Copyright (c) 2024, Paul Scherrer Institute
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
@@ -26,4 +25,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

bin/.gitignore

@@ -1 +0,0 @@
-# Add anything you don't want to check in to git, e.g. very large files

phoenix_bec/bec_ipython_client/startup/pre_startup.py

@@ -1,14 +1,10 @@
 """
 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.
+is started. It can be used to add additional command line arguments. 
 """
 
-import os
-
 from bec_lib.service_config import ServiceConfig
 
-import phoenix_bec
-
 
 def extend_command_line_args(parser):
     """
@@ -19,13 +15,9 @@ def extend_command_line_args(parser):
 
     return parser
 
-def get_config() -> ServiceConfig:
+
-    """
+# def get_config() -> ServiceConfig:
-    Create and return the ServiceConfig for the plugin repository
+#     """
-    """
+#     Create and return the service configuration.
-    deployment_path = os.path.dirname(os.path.dirname(os.path.dirname(phoenix_bec.__file__)))
+#     """
-    files = os.listdir(deployment_path)
+#     return ServiceConfig(redis={"host": "localhost", "port": 6379})
-    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})

phoenix_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 phoenix_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

phoenix_bec/scans/metadata_schema/metadata_schema_registry.py

@@ -1,12 +0,0 @@
-# from .metadata_schema_template import ExampleSchema
-
-METADATA_SCHEMA_REGISTRY = {
-    # Add models which should be used to validate scan metadata here.
-    # Make a model according to the template, and import it as above
-    # Then associate it with a scan like so:
-    # "example_scan": ExampleSchema
-}
-
-# Define a default schema type which should be used as the fallback for everything:
-
-DEFAULT_SCHEMA = None

phoenix_bec/scans/metadata_schema/metadata_schema_template.py

@@ -1,34 +0,0 @@
-# # By inheriting from BasicScanMetadata you can define a schema by which metadata
-# # supplied to a scan must be validated.
-# # This schema is a Pydantic model: https://docs.pydantic.dev/latest/concepts/models/
-# # but by default it will still allow you to add any arbitrary information to it.
-# # That is to say, when you run a scan with which such a model has been associated in the
-# # metadata_schema_registry, you can supply any python dictionary with strings as keys
-# # and built-in python types (strings, integers, floats) as values, and these will be
-# # added to the experiment metadata, but it *must* contain the keys and values of the
-# # types defined in the schema class.
-# #
-# #
-# # For example, say that you would like to enforce recording information about sample
-# # pretreatment, you could define the following:
-# #
-#
-# from bec_lib.metadata_schema import BasicScanMetadata
-#
-#
-# class ExampleSchema(BasicScanMetadata):
-#    treatment_description: str
-#    treatment_temperature_k: int
-#
-#
-# # If this was used according to the example in metadata_schema_registry.py,
-# # then when calling the scan, the user would need to write something like:
-# >>> scans.example_scan(
-# >>>     motor,
-# >>>     1,
-# >>>     2,
-# >>>     3,
-# >>>     metadata={"treatment_description": "oven overnight", "treatment_temperature_k": 575},
-# >>> )
-#
-# # And the additional metadata would be saved in the HDF5 file created for the scan.

phoenix_bec/scripts/phoenix.py

@@ -32,8 +32,6 @@ logger = bec_logger.logger
 # .. define base path for directory with scripts
 
 
-# next version V2 
-
 class PhoenixBL:
     """
     #

pyproject.toml

@@ -5,8 +5,8 @@ build-backend = "hatchling.build"
 [project]
 name = "phoenix_bec"
 version = "0.0.0"
-description = "A plugin repository for BEC"
+description = "Custom device implementations based on the ophyd hardware abstraction layer"
-requires-python = ">=3.11"
+requires-python = ">=3.10"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
@@ -17,7 +17,6 @@ dependencies = []
 [project.optional-dependencies]
 dev = [
     "black",
-    "copier",
     "isort",
     "coverage",
     "pylint",
@@ -39,15 +38,12 @@ plugin_file_writer = "phoenix_bec.file_writer"
 [project.entry-points."bec.scans"]
 plugin_scans = "phoenix_bec.scans"
 
-[project.entry-points."bec.scans.metadata_schema"]
-plugin_metadata_schema = "phoenix_bec.scans.metadata_schema"
-
 [project.entry-points."bec.ipython_client_startup"]
 plugin_ipython_client_pre = "phoenix_bec.bec_ipython_client.startup.pre_startup"
 plugin_ipython_client_post = "phoenix_bec.bec_ipython_client.startup"
 
 [project.entry-points."bec.widgets.auto_updates"]
-plugin_widgets_update = "phoenix_bec.bec_widgets.auto_updates"
+plugin_widgets_update = "phoenix_bec.bec_widgets.auto_updates:PlotUpdate"
 
 [project.entry-points."bec.widgets.user_widgets"]
 plugin_widgets = "phoenix_bec.bec_widgets.widgets"

tests/tests_bec_ipython_client/README.md

@@ -1,34 +1,31 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be installed via
+It can be install via 
-
+``` bash
-```bash
 pip install pytest
 ```
-
+in your *python environment*. 
-in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
-It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
 
-```bash
+``` bash
 pytest -v --random-order ./tests
 ```
-
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
 
 ## Test examples
 
-Writing tests can be quite specific for the given function.
+Writing tests can be quite specific for the given function. 
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
+

tests/tests_bec_widgets/README.md

@@ -1,34 +1,31 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be installed via
+It can be install via 
-
+``` bash
-```bash
 pip install pytest
 ```
-
+in your *python environment*. 
-in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
-It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
 
-```bash
+``` bash
 pytest -v --random-order ./tests
 ```
-
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
 
 ## Test examples
 
-Writing tests can be quite specific for the given function.
+Writing tests can be quite specific for the given function. 
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
+

tests/tests_dap_services/README.md

@@ -1,34 +1,31 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be installed via
+It can be install via 
-
+``` bash
-```bash
 pip install pytest
 ```
-
+in your *python environment*. 
-in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
-It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
 
-```bash
+``` bash
 pytest -v --random-order ./tests
 ```
-
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
 
 ## Test examples
 
-Writing tests can be quite specific for the given function.
+Writing tests can be quite specific for the given function. 
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
+

tests/tests_devices/README.md

@@ -1,34 +1,31 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be installed via
+It can be install via 
-
+``` bash
-```bash
 pip install pytest
 ```
-
+in your *python environment*. 
-in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
-It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
 
-```bash
+``` bash
 pytest -v --random-order ./tests
 ```
-
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
 
 ## Test examples
 
-Writing tests can be quite specific for the given function.
+Writing tests can be quite specific for the given function. 
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
+

tests/tests_devices/test_phoenix_trigger.py

@@ -16,7 +16,7 @@ def mock_trigger():
     name = "phoenix_trigger"
     prefix = "X07MB-OP2:"
     dm = DMMock()
-    with mock.patch.object(dm, "connector"):
+    with mock.patch.object(dm, "connecto"):
         with (
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"

tests/tests_file_writer/README.md

@@ -1,34 +1,31 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be installed via
+It can be install via 
-
+``` bash
-```bash
 pip install pytest
 ```
-
+in your *python environment*. 
-in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
-It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
 
-```bash
+``` bash
 pytest -v --random-order ./tests
 ```
-
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
 
 ## Test examples
 
-Writing tests can be quite specific for the given function.
+Writing tests can be quite specific for the given function. 
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
+

tests/tests_scans/README.md

@@ -1,34 +1,31 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be installed via
+It can be install via 
-
+``` bash
-```bash
 pip install pytest
 ```
-
+in your *python environment*. 
-in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
-It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
 
-```bash
+``` bash
 pytest -v --random-order ./tests
 ```
-
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
 
 ## Test examples
 
-Writing tests can be quite specific for the given function.
+Writing tests can be quite specific for the given function. 
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
+