FIRST COMMIT: plugin repo copy, minus entry points and unshared components
This commit is contained in:
@@ -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: v1.5.0
|
||||
_src_path: https://github.com/bec-project/plugin_copier_template.git
|
||||
make_commit: false
|
||||
project_name: mx_bec
|
||||
widget_plugins_input: []
|
||||
@@ -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__
|
||||
@@ -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 $(git diff --cached --name-only --diff-filter=ACM -- '*.py')
|
||||
@@ -0,0 +1,102 @@
|
||||
name: CI for mx_bec
|
||||
on:
|
||||
push:
|
||||
pull_request:
|
||||
workflow_dispatch:
|
||||
inputs:
|
||||
BEC_WIDGETS_BRANCH:
|
||||
description: "Branch of BEC Widgets to install"
|
||||
required: false
|
||||
type: string
|
||||
default: "main"
|
||||
BEC_CORE_BRANCH:
|
||||
description: "Branch of BEC Core to install"
|
||||
required: false
|
||||
type: string
|
||||
default: "main"
|
||||
OPHYD_DEVICES_BRANCH:
|
||||
description: "Branch of Ophyd Devices to install"
|
||||
required: false
|
||||
type: string
|
||||
default: "main"
|
||||
BEC_PLUGIN_REPO_BRANCH:
|
||||
description: "Branch of the BEC Plugin Repository to install"
|
||||
required: false
|
||||
type: string
|
||||
default: "main"
|
||||
PYTHON_VERSION:
|
||||
description: "Python version to use"
|
||||
required: false
|
||||
type: string
|
||||
default: "3.12"
|
||||
|
||||
permissions:
|
||||
pull-requests: write
|
||||
|
||||
jobs:
|
||||
test:
|
||||
runs-on: ubuntu-latest
|
||||
env:
|
||||
QTWEBENGINE_DISABLE_SANDBOX: 1
|
||||
QT_QPA_PLATFORM: "offscreen"
|
||||
|
||||
steps:
|
||||
- name: Setup Python
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: "${{ inputs.PYTHON_VERSION || '3.12' }}"
|
||||
|
||||
- name: Checkout BEC Plugin Repository
|
||||
uses: actions/checkout@v4
|
||||
with:
|
||||
repository: bec/mx_bec
|
||||
ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
|
||||
path: ./mx_bec
|
||||
|
||||
- name: Lint for merge conflicts from template updates
|
||||
shell: bash
|
||||
# Find all Copier conflicts except this line
|
||||
run: '! grep -r "<<<<<<< before updating" | grep -v "grep -r \"<<<<<<< before updating"'
|
||||
|
||||
- name: Checkout BEC Core
|
||||
uses: actions/checkout@v4
|
||||
with:
|
||||
repository: bec/bec
|
||||
ref: "${{ 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 ./mx_bec
|
||||
|
||||
- name: Run Pytest with Coverage
|
||||
id: coverage
|
||||
run: pytest --random-order --cov=./mx_bec --cov-config=./mx_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./mx_bec/tests/ || test $? -eq 5
|
||||
@@ -0,0 +1,70 @@
|
||||
name: Create template upgrade PR for mx_bec
|
||||
on:
|
||||
workflow_dispatch:
|
||||
|
||||
permissions:
|
||||
pull-requests: write
|
||||
|
||||
jobs:
|
||||
create_update_branch_and_pr:
|
||||
runs-on: ubuntu-latest
|
||||
permissions:
|
||||
contents: write
|
||||
pull-requests: write
|
||||
|
||||
steps:
|
||||
- name: Setup Python
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: "3.12"
|
||||
|
||||
- name: Checkout
|
||||
uses: actions/checkout@v4
|
||||
|
||||
- name: Create virtualenv
|
||||
run: |
|
||||
python -m virtualenv .venv
|
||||
|
||||
- name: Install tools
|
||||
run: |
|
||||
source .venv/bin/activate
|
||||
pip install copier PySide6 bec_lib
|
||||
|
||||
- name: Perform update
|
||||
run: |
|
||||
source .venv/bin/activate
|
||||
git config --global user.email "bec_ci_staging@psi.ch"
|
||||
git config --global user.name "BEC automated CI"
|
||||
|
||||
branch="chore/update-template-$(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 $branch)\",
|
||||
\"base\": \"main\"
|
||||
}"
|
||||
+180
@@ -0,0 +1,180 @@
|
||||
**/*_venv
|
||||
**/.idea
|
||||
*.log
|
||||
**/__pycache__
|
||||
**/.DS_Store
|
||||
**/out
|
||||
**/.vscode
|
||||
**/.pytest_cache
|
||||
**/*.egg*
|
||||
|
||||
# recovery_config files
|
||||
recovery_config_*
|
||||
|
||||
# file writer data
|
||||
**.h5
|
||||
|
||||
# Byte-compiled / optimized / DLL files
|
||||
__pycache__/
|
||||
*.py[cod]
|
||||
*$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/
|
||||
@@ -0,0 +1,29 @@
|
||||
|
||||
BSD 3-Clause License
|
||||
|
||||
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:
|
||||
|
||||
1. Redistributions of source code must retain the above copyright notice, this
|
||||
list of conditions and the following disclaimer.
|
||||
|
||||
2. Redistributions in binary form must reproduce the above copyright notice,
|
||||
this list of conditions and the following disclaimer in the documentation
|
||||
and/or other materials provided with the distribution.
|
||||
|
||||
3. Neither the name of the copyright holder nor the names of its
|
||||
contributors may be used to endorse or promote products derived from
|
||||
this software without specific prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
||||
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
|
||||
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||
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.
|
||||
@@ -0,0 +1 @@
|
||||
# Add anything you don't want to check in to git, e.g. very large files
|
||||
@@ -0,0 +1,6 @@
|
||||
# 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 mx_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
|
||||
@@ -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
|
||||
@@ -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.
|
||||
@@ -0,0 +1,12 @@
|
||||
"""
|
||||
Scan components for mx_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 MxBecScanComponents(ScanComponents):
|
||||
"""Scan components for mx_bec."""
|
||||
@@ -0,0 +1,33 @@
|
||||
"""
|
||||
Scan modifier plugin for mx_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 MxBecScanModifier(ScanModifier):
|
||||
"""
|
||||
Scan modifier for mx_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)
|
||||
|
||||
|
||||
@@ -0,0 +1,60 @@
|
||||
[build-system]
|
||||
requires = ["hatchling"]
|
||||
build-backend = "hatchling.build"
|
||||
|
||||
[project]
|
||||
name = "mx_bec"
|
||||
version = "0.0.1"
|
||||
description = "A shared repository for MX BEC components"
|
||||
requires-python = ">=3.11"
|
||||
classifiers = [
|
||||
"Development Status :: 3 - Alpha",
|
||||
"Programming Language :: Python :: 3",
|
||||
"Topic :: Scientific/Engineering",
|
||||
]
|
||||
dependencies = []
|
||||
|
||||
[project.optional-dependencies]
|
||||
dev = [
|
||||
"black",
|
||||
"copier",
|
||||
"isort",
|
||||
"coverage",
|
||||
"pylint",
|
||||
"pytest",
|
||||
"pytest-random-order",
|
||||
"ophyd_devices",
|
||||
"bec_server",
|
||||
]
|
||||
|
||||
[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.*",
|
||||
]
|
||||
|
||||
[tool.ruff]
|
||||
line-length = 100
|
||||
|
||||
[tool.ruff.format]
|
||||
skip-magic-trailing-comma = true
|
||||
|
||||
Reference in New Issue
Block a user