refactor: upgrade to copier v1

.copier-answers.yml

@@ -0,0 +1,9 @@
+# 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: v1.0.0
+_src_path: https://gitea.psi.ch/bec/bec_plugin_copier_template.git
+make_commit: false
+project_name: phoenix_bec
+widget_plugins_input: []

.gitignore

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

.gitlab-ci.yml

@@ -3,4 +3,5 @@ include:
   inputs:
     name: phoenix_bec
     target: phoenix_bec
+    branch: $CHILD_PIPELINE_BRANCH
   project: bec/awi_utils

LICENSE

@@ -1,6 +1,7 @@
+
 BSD 3-Clause License
 
-Copyright (c) 2024, Paul Scherrer Institute
+Copyright (c) 2025, Paul Scherrer Institute 
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

bin/.gitignore

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

phoenix_bec/scans/metadata_schema/metadata_schema_registry.py

@@ -0,0 +1,12 @@
+# 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

@@ -0,0 +1,34 @@
+# # 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.

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "phoenix_bec"
 version = "0.0.0"
-description = "Custom device implementations based on the ophyd hardware abstraction layer"
+description = "The Phoenix plugin repository for BEC"
 requires-python = ">=3.10"
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -17,6 +17,7 @@ dependencies = []
 [project.optional-dependencies]
 dev = [
     "black",
+    "copier",
     "isort",
     "coverage",
     "pylint",
@@ -38,12 +39,15 @@ 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:PlotUpdate"
+plugin_widgets_update = "phoenix_bec.bec_widgets.auto_updates"
 
 [project.entry-points."bec.widgets.user_widgets"]
 plugin_widgets = "phoenix_bec.bec_widgets.widgets"

tests/tests_bec_ipython_client/README.md

@@ -1,23 +1,27 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
-It can be install via 
+It can be installed 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
 
-``` 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.
@@ -28,4 +32,3 @@ 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

@@ -1,23 +1,27 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
-It can be install via 
+It can be installed 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
 
-``` 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.
@@ -28,4 +32,3 @@ 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

@@ -1,23 +1,27 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
-It can be install via 
+It can be installed 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
 
-``` 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.
@@ -28,4 +32,3 @@ 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

@@ -1,23 +1,27 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
-It can be install via 
+It can be installed 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
 
-``` 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.
@@ -28,4 +32,3 @@ 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

@@ -6,7 +6,6 @@ import numpy as np
 import ophyd
 import pytest
 from bec_server.device_server.tests.utils import DMMock
-from ophyd_devices.interfaces.base_classes.psi_detector_base import DeviceTimeoutError
 from ophyd_devices.tests.utils import MockPV, patch_dual_pvs
 
 from phoenix_bec.devices.phoenix_trigger import SAMPLING, PhoenixTrigger
@@ -20,7 +19,7 @@ def mock_trigger():
     with mock.patch.object(dm, "connector"):
         with (
             mock.patch(
-                "ophyd_devices.interfaces.base_classes.psi_detector_base.FileWriter"
+                "ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"
             ) as filemixin,
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.psi_detector_base.PSIDetectorBase._update_service_config"

tests/tests_file_writer/README.md

@@ -1,23 +1,27 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
-It can be install via 
+It can be installed 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
 
-``` 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.
@@ -28,4 +32,3 @@ 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

@@ -1,23 +1,27 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
-It can be install via 
+It can be installed 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
 
-``` 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.
@@ -28,4 +32,3 @@ 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).
-