diff --git a/.git_hooks/post-commit b/.git_hooks/post-commit new file mode 100644 index 0000000..3fe80fe --- /dev/null +++ b/.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__ \ No newline at end of file diff --git a/.git_hooks/pre-commit b/.git_hooks/pre-commit new file mode 100644 index 0000000..392493b --- /dev/null +++ b/.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 $(git diff --cached --name-only --diff-filter=ACM -- '*.py') diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..f4c73aa --- /dev/null +++ b/.gitignore @@ -0,0 +1,180 @@ +**/*_venv +**/.idea +*.log +**/__pycache__ +**/.DS_Store +**/out +**/.vscode +**/.pytest_cache +**/*.egg* + +# recovery_config files +recovery_config_* + +# file writer data +**.h5 + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$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/ diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000..34cc148 --- /dev/null +++ b/.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 diff --git a/phoenix_bec/__init__.py b/phoenix_bec/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/bec_ipython_client/__init__.py b/phoenix_bec/bec_ipython_client/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/bec_ipython_client/high_level_interface/__init__.py b/phoenix_bec/bec_ipython_client/high_level_interface/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/bec_ipython_client/plugins/__init__.py b/phoenix_bec/bec_ipython_client/plugins/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/bec_ipython_client/startup/__init__.py b/phoenix_bec/bec_ipython_client/startup/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/bec_ipython_client/startup/post_startup.py b/phoenix_bec/bec_ipython_client/startup/post_startup.py new file mode 100644 index 0000000..07d6da4 --- /dev/null +++ b/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 diff --git a/phoenix_bec/bec_ipython_client/startup/pre_startup.py b/phoenix_bec/bec_ipython_client/startup/pre_startup.py new file mode 100644 index 0000000..e22e554 --- /dev/null +++ b/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}) diff --git a/phoenix_bec/bec_widgets/__init__.py b/phoenix_bec/bec_widgets/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/bec_widgets/widgets/__init__.py b/phoenix_bec/bec_widgets/widgets/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/deployments/__init__.py b/phoenix_bec/deployments/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/deployments/device_server/__init__.py b/phoenix_bec/deployments/device_server/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/deployments/device_server/startup.py b/phoenix_bec/deployments/device_server/startup.py new file mode 100644 index 0000000..c4b1f88 --- /dev/null +++ b/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() diff --git a/phoenix_bec/device_configs/__init__.py b/phoenix_bec/device_configs/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/devices/__init__.py b/phoenix_bec/devices/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/file_writer/__init__.py b/phoenix_bec/file_writer/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/scans/__init__.py b/phoenix_bec/scans/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/scans/scan_plugin_template.py b/phoenix_bec/scans/scan_plugin_template.py new file mode 100644 index 0000000..29e0d2b --- /dev/null +++ b/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 diff --git a/phoenix_bec/services/__init__.py b/phoenix_bec/services/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..f3dee8d --- /dev/null +++ b/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.*", +] diff --git a/tests/tests_bec_ipython_client/README.md b/tests/tests_bec_ipython_client/README.md new file mode 100644 index 0000000..5762245 --- /dev/null +++ b/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 ``. + +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). + diff --git a/tests/tests_bec_widgets/README.md b/tests/tests_bec_widgets/README.md new file mode 100644 index 0000000..5762245 --- /dev/null +++ b/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 ``. + +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). + diff --git a/tests/tests_dap_services/README.md b/tests/tests_dap_services/README.md new file mode 100644 index 0000000..5762245 --- /dev/null +++ b/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 ``. + +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). + diff --git a/tests/tests_devices/README.md b/tests/tests_devices/README.md new file mode 100644 index 0000000..5762245 --- /dev/null +++ b/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 ``. + +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). + diff --git a/tests/tests_file_writer/README.md b/tests/tests_file_writer/README.md new file mode 100644 index 0000000..5762245 --- /dev/null +++ b/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 ``. + +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). + diff --git a/tests/tests_scans/README.md b/tests/tests_scans/README.md new file mode 100644 index 0000000..5762245 --- /dev/null +++ b/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 ``. + +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). +