init repo

.git_hooks/post-commit

@@ -0,0 +1,3 @@
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+semantic-release changelog -D version_variable=$SCRIPT_DIR/../../semantic_release/__init__.py:__version__
+semantic-release version -D version_variable=$SCRIPT_DIR/../../semantic_release/__init__.py:__version__

.git_hooks/pre-commit

@@ -0,0 +1,3 @@
+black --line-length=100 $(git diff --cached --name-only --diff-filter=ACM -- '*.py')
+isort --line-length=100 --profile=black --multi-line=3 --trailing-comma $(git diff --cached --name-only --diff-filter=ACM -- '*.py')
+git add $(git diff --cached --name-only --diff-filter=ACM -- '*.py')

.gitignore

@@ -0,0 +1,180 @@
+**/*_venv
+**/.idea
+*.log
+**/__pycache__
+**/.DS_Store
+**/out
+**/.vscode
+**/.pytest_cache
+**/*.egg*
+
+# recovery_config files
+recovery_config_*
+
+# file writer data
+**.h5
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/**/_build/
+docs/**/autodoc/
+docs/**/_autosummary/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+**.prof
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.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

phoenix_bec/bec_ipython_client/startup/post_startup.py

@@ -0,0 +1,36 @@
+"""
+Post startup script for the BEC client. This script is executed after the
+IPython shell is started. It is used to load the beamline specific
+information and to setup the prompts.
+
+The script is executed in the global namespace of the IPython shell. This
+means that all variables defined here are available in the shell.
+
+While command-line arguments have to be set in the pre-startup script, the
+post-startup script can be used to load beamline specific information and
+to setup the prompts.
+
+    from bec_lib.logger import bec_logger
+
+    logger = bec_logger.logger
+
+    # pylint: disable=import-error
+    _args = _main_dict["args"]
+
+    _session_name = "cSAXS"
+    if _args.session.lower() == "lamni":
+        from csaxs_bec.bec_ipython_client.plugins.cSAXS import *
+        from csaxs_bec.bec_ipython_client.plugins.LamNI import *
+
+        _session_name = "LamNI"
+        lamni = LamNI(bec)
+        logger.success("LamNI session loaded.")
+
+    elif _args.session.lower() == "csaxs":
+        print("Loading cSAXS session")
+        from csaxs_bec.bec_ipython_client.plugins.cSAXS import *
+
+        logger.success("cSAXS session loaded.")
+"""
+
+# pylint: disable=invalid-name, unused-import, import-error, undefined-variable, unused-variable, unused-argument, no-name-in-module

phoenix_bec/bec_ipython_client/startup/pre_startup.py

@@ -0,0 +1,23 @@
+"""
+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. 
+"""
+
+from bec_lib.service_config import ServiceConfig
+
+
+def extend_command_line_args(parser):
+    """
+    Extend the command line arguments of the BEC client.
+    """
+
+    # parser.add_argument("--session", help="Session name", type=str, default="cSAXS")
+
+    return parser
+
+
+# def get_config() -> ServiceConfig:
+#     """
+#     Create and return the service configuration.
+#     """
+#     return ServiceConfig(redis={"host": "localhost", "port": 6379})

phoenix_bec/deployments/device_server/startup.py

@@ -0,0 +1,11 @@
+import os
+
+
+def setup_epics_ca():
+    # os.environ["EPICS_CA_AUTO_ADDR_LIST"] = "NO"
+    # os.environ["EPICS_CA_ADDR_LIST"] = "129.129.122.255 sls-x12sa-cagw.psi.ch:5836"
+    os.environ["PYTHONIOENCODING"] = "latin1"
+
+
+def run():
+    setup_epics_ca()

phoenix_bec/scans/scan_plugin_template.py

@@ -0,0 +1,34 @@
+"""
+SCAN PLUGINS
+
+All new scans should be derived from ScanBase. ScanBase provides various methods that can be customized and overriden
+but they are executed in a specific order:
+
+- self.initialize                        # initialize the class if needed
+- self.read_scan_motors                  # used to retrieve the start position (and the relative position shift if needed)
+- self.prepare_positions                 # prepare the positions for the scan. The preparation is split into multiple sub fuctions:
+    - self._calculate_positions          # calculate the positions
+    - self._set_positions_offset         # apply the previously retrieved scan position shift (if needed)
+    - self._check_limits                 # tests to ensure the limits won't be reached
+- self.open_scan                         # send an open_scan message including the scan name, the number of points and the scan motor names
+- self.stage                             # stage all devices for the upcoming acquisiton
+- self.run_baseline_readings             # read all devices to get a baseline for the upcoming scan
+- self.pre_scan                          # perform additional actions before the scan starts
+- self.scan_core                         # run a loop over all position
+    - self._at_each_point(ind, pos)      # called at each position with the current index and the target positions as arguments
+- self.finalize                          # clean up the scan, e.g. move back to the start position; wait everything to finish
+- self.unstage                           # unstage all devices that have been staged before
+- self.cleanup                           # send a close scan message and perform additional cleanups if needed
+"""
+
+# import time
+
+# import numpy as np
+
+# from bec_lib.endpoints import MessageEndpoints
+# from bec_lib.logger import bec_logger
+# from bec_lib import messages
+# from bec_server.scan_server.errors import ScanAbortion
+# from bec_server.scan_server.scans import FlyScanBase, RequestBase, ScanArgType, ScanBase
+
+# logger = bec_logger.logger

pyproject.toml

@@ -0,0 +1,74 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "phoenix_bec"
+version = "0.0.0"
+description = "Custom device implementations based on the ophyd hardware abstraction layer"
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = []
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "isort",
+    "coverage",
+    "pylint",
+    "pytest",
+    "pytest-random-order",
+    "ophyd_devices",
+    "bec_server",
+]
+
+[project.entry-points."bec"]
+plugin_bec = "phoenix_bec"
+
+[project.entry-points."bec.deployment.device_server"]
+plugin_ds_startup = "phoenix_bec.deployments.device_server.startup:run"
+
+[project.entry-points."bec.file_writer"]
+plugin_file_writer = "phoenix_bec.file_writer"
+
+[project.entry-points."bec.scans"]
+plugin_scans = "phoenix_bec.scans"
+
+[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"
+
+[project.entry-points."bec.widgets.user_widgets"]
+plugin_widgets = "phoenix_bec.bec_widgets.widgets"
+
+[tool.hatch.build.targets.wheel]
+include = ["*"]
+
+[tool.isort]
+profile = "black"
+line_length = 100
+multi_line_output = 3
+include_trailing_comma = true
+
+[tool.black]
+line-length = 100
+skip-magic-trailing-comma = true
+
+[tool.pylint.basic]
+# Good variable names regexes, separated by a comma. If names match any regex,
+# they will always be accepted
+good-names-rgxs = [
+    ".*scanID.*",
+    ".*RID.*",
+    ".*pointID.*",
+    ".*ID.*",
+    ".*_2D.*",
+    ".*_1D.*",
+]

tests/tests_bec_ipython_client/README.md

@@ -0,0 +1,31 @@
+# Getting Started with Testing using pytest
+
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+It can be install via 
+``` bash
+pip install pytest
+```
+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>`.
+
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+
+``` 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. 
+
+## Test examples
+
+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

@@ -0,0 +1,31 @@
+# Getting Started with Testing using pytest
+
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+It can be install via 
+``` bash
+pip install pytest
+```
+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>`.
+
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+
+``` 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. 
+
+## Test examples
+
+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

@@ -0,0 +1,31 @@
+# Getting Started with Testing using pytest
+
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+It can be install via 
+``` bash
+pip install pytest
+```
+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>`.
+
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+
+``` 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. 
+
+## Test examples
+
+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

@@ -0,0 +1,31 @@
+# Getting Started with Testing using pytest
+
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+It can be install via 
+``` bash
+pip install pytest
+```
+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>`.
+
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+
+``` 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. 
+
+## Test examples
+
+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_file_writer/README.md

@@ -0,0 +1,31 @@
+# Getting Started with Testing using pytest
+
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+It can be install via 
+``` bash
+pip install pytest
+```
+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>`.
+
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+
+``` 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. 
+
+## Test examples
+
+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

@@ -0,0 +1,31 @@
+# Getting Started with Testing using pytest
+
+BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
+It can be install via 
+``` bash
+pip install pytest
+```
+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>`.
+
+To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+
+``` 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. 
+
+## Test examples
+
+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).
+