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Chore/migrate to copier #22

Merged
perl_d merged 2 commits from chore/migrate_to_copier into main 2025-05-20 10:45:14 +02:00
Conversation 4 Commits 2 Files Changed 26 +191 -115
26 changed files with 191 additions and 115 deletions
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9
.copier-answers.yml Normal file
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@@ -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: pxiii_bec
widget_plugins_input: null

3
.git_hooks/post-commit Normal file
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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__

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.git_hooks/pre-commit Normal file
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@@ -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')

3
.gitignore vendored
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@@ -8,6 +8,9 @@
**/.pytest_cache
**/*.egg*
# recovery_config files
recovery_config_*
# file writer data
**.h5

12
.gitlab-ci.yml
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@@ -1,7 +1,7 @@
include:
- project: bec/awi_utils
file: /templates/plugin-repo-template.yml
inputs:
name: "pxiii"
target: "pxiii_bec"
branch: $CHILD_PIPELINE_BRANCH
- file: /templates/plugin-repo-template.yml
inputs:
name: pxiii_bec
target: pxiii_bec
branch: $CHILD_PIPELINE_BRANCH
project: bec/awi_utils

5
LICENSE
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@@ -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:
@@ -25,4 +26,4 @@ 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.

1
bin/.gitignore vendored Normal file
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# Add anything you don't want to check in to git, e.g. very large files

11
deployment/autodeploy_versions
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@@ -1,11 +0,0 @@
# This file is used to select the BEC and Ophyd Devices version for the auto deployment process.
# Do not edit this file unless you know what you are doing!
# The version can be a git tag, branch or commit hash.
# BEC version to use
BEC_AUTODEPLOY_VERSION="master"
# ophyd_devices version to use
OPHYD_DEVICES_AUTODEPLOY_VERSION="master"

18
deployment/bec-server-config.yaml
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@@ -1,18 +0,0 @@
redis:
host: localhost
port: 6379
mongodb:
host: localhost
port: 27017
scibec:
host: http://[::1]
port: 3030
beamline: "PXIII"
service_config:
general:
reset_queue_on_cancel: True
enforce_ACLs: False
file_writer:
plugin: default_NeXus_format
base_path: ./

29
deployment/deploy.sh
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@@ -1,29 +0,0 @@
# deployment script to be translated to Ansible
# can be removed once we have the autodeployment in place
BEAMLINE_REPO=gitlab.psi.ch:bec/pxiii-bec.git
git clone git@$BEAMLINE_REPO
module add psi-python311/2024.02
# start redis
docker run --network=host --name redis-bec -d redis
# alternative:
# conda install -y redis; redis-server &
# get the target versions for ophyd_devices and BEC
source ./pxiii-bec/deployment/autodeploy_versions
git clone -b $OPHYD_DEVICES_AUTODEPLOY_VERSION https://gitlab.psi.ch/bec/ophyd_devices.git
git clone -b $BEC_AUTODEPLOY_VERSION https://gitlab.psi.ch/bec/bec.git
# install BEC
cd bec
source ./bin/install_bec_dev.sh
cd ../
pip install -e ./pxiii-bec
# start the BEC server
bec-server start --config ./pxiii-bec/deployment/bec-server-config.yaml

0
pxiii_bec/bec_widgets/auto_updates/__init__.py Normal file
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0
pxiii_bec/bec_widgets/widgets/__init__.py Normal file
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0
pxiii_bec/deployments/__init__.py Normal file
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0
pxiii_bec/deployments/device_server/__init__.py Normal file
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11
pxiii_bec/deployments/device_server/startup.py Normal file
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@@ -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()

0
pxiii_bec/scans/metadata_schema/__init__.py Normal file
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12
pxiii_bec/scans/metadata_schema/metadata_schema_registry.py Normal file
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@@ -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

34
pxiii_bec/scans/metadata_schema/metadata_schema_template.py Normal file
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@@ -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
pxiii_bec/services/__init__.py Normal file
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16
pyproject.toml
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@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
[project]
name = "pxiii_bec"
version = "0.0.0"
description = "Custom device implementations based on the ophyd hardware abstraction layer"
description = "A plugin repository for BEC"
requires-python = ">=3.10"
classifiers = [
"Development Status :: 3 - Alpha",
@@ -28,19 +28,21 @@ dependencies = [
[project.optional-dependencies]
dev = [
"black",
"copier",
"isort",
"coverage",
"pylint",
"pytest",
"pytest-random-order",
"pytest-redis",
"ophyd_devices",
"bec_server",
]
[project.entry-points."bec"]
plugin_bec = "pxiii_bec"
[project.entry-points."bec.deployment.device_server"]
plugin_ds_startup = "pxiii_bec.deployment.device_server.startup:run"
plugin_ds_startup = "pxiii_bec.deployments.device_server.startup:run"
[project.entry-points."bec.file_writer"]
plugin_file_writer = "pxiii_bec.file_writer"
@@ -48,12 +50,18 @@ plugin_file_writer = "pxiii_bec.file_writer"
[project.entry-points."bec.scans"]
plugin_scans = "pxiii_bec.scans"
[project.entry-points."bec.scans.metadata_schema"]
plugin_metadata_schema = "pxiii_bec.scans.metadata_schema"
[project.entry-points."bec.ipython_client_startup"]
plugin_ipython_client_pre = "pxiii_bec.bec_ipython_client.startup.pre_startup"
plugin_ipython_client_post = "pxiii_bec.bec_ipython_client.startup"
[project.entry-points."bec.widgets.auto_updates"]
plugin_widgets_update = "pxiii_bec.bec_widgets.auto_updates:PlotUpdate"
plugin_widgets_update = "pxiii_bec.bec_widgets.auto_updates"
[project.entry-points."bec.widgets.user_widgets"]
plugin_widgets = "pxiii_bec.bec_widgets.widgets"
[tool.hatch.build.targets.wheel]
include = ["*"]

21
tests/tests_bec_ipython_client/README.md
View File

@@ -1,31 +1,34 @@
# 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
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```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).

21
tests/tests_bec_widgets/README.md
View File

@@ -1,31 +1,34 @@
# 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
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```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).

21
tests/tests_dap_services/README.md
View File

@@ -1,31 +1,34 @@
# 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
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```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).

21
tests/tests_devices/README.md
View File

@@ -1,31 +1,34 @@
# 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
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```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).

34
tests/tests_file_writer/README.md Normal file
View File

@@ -0,0 +1,34 @@
# Getting Started with Testing using pytest
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed 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>`.
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
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).

21
tests/tests_scans/README.md
View File

@@ -1,31 +1,34 @@
# 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
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```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).