diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 0000000..2e84256 --- /dev/null +++ b/.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: [] diff --git a/.gitignore b/.gitignore index 047e5f0..f4c73aa 100644 --- a/.gitignore +++ b/.gitignore @@ -7,7 +7,6 @@ **/.vscode **/.pytest_cache **/*.egg* -*.gz # recovery_config files recovery_config_* diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 34cc148..7cdb73a 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -3,4 +3,5 @@ include: inputs: name: phoenix_bec target: phoenix_bec + branch: $CHILD_PIPELINE_BRANCH project: bec/awi_utils diff --git a/LICENSE b/LICENSE index 06070a5..f9b721a 100644 --- a/LICENSE +++ b/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: @@ -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. \ No newline at end of file diff --git a/bin/.gitignore b/bin/.gitignore new file mode 100644 index 0000000..20a11ba --- /dev/null +++ b/bin/.gitignore @@ -0,0 +1 @@ +# Add anything you don't want to check in to git, e.g. very large files \ No newline at end of file diff --git a/phoenix_bec/bec_widgets/auto_updates/__init__.py b/phoenix_bec/bec_widgets/auto_updates/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/scans/metadata_schema/__init__.py b/phoenix_bec/scans/metadata_schema/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/phoenix_bec/scans/metadata_schema/metadata_schema_registry.py b/phoenix_bec/scans/metadata_schema/metadata_schema_registry.py new file mode 100644 index 0000000..deb6ef4 --- /dev/null +++ b/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 diff --git a/phoenix_bec/scans/metadata_schema/metadata_schema_template.py b/phoenix_bec/scans/metadata_schema/metadata_schema_template.py new file mode 100644 index 0000000..c12e364 --- /dev/null +++ b/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. diff --git a/pyproject.toml b/pyproject.toml index f3dee8d..7da209c 100644 --- a/pyproject.toml +++ b/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" diff --git a/tests/tests_bec_ipython_client/README.md b/tests/tests_bec_ipython_client/README.md index 5762245..63d535f 100644 --- a/tests/tests_bec_ipython_client/README.md +++ b/tests/tests_bec_ipython_client/README.md @@ -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 ``. +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). - diff --git a/tests/tests_bec_widgets/README.md b/tests/tests_bec_widgets/README.md index 5762245..63d535f 100644 --- a/tests/tests_bec_widgets/README.md +++ b/tests/tests_bec_widgets/README.md @@ -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 ``. +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). - diff --git a/tests/tests_dap_services/README.md b/tests/tests_dap_services/README.md index 5762245..63d535f 100644 --- a/tests/tests_dap_services/README.md +++ b/tests/tests_dap_services/README.md @@ -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 ``. +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). - diff --git a/tests/tests_devices/README.md b/tests/tests_devices/README.md index 5762245..63d535f 100644 --- a/tests/tests_devices/README.md +++ b/tests/tests_devices/README.md @@ -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 ``. +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). - diff --git a/tests/tests_file_writer/README.md b/tests/tests_file_writer/README.md index 5762245..63d535f 100644 --- a/tests/tests_file_writer/README.md +++ b/tests/tests_file_writer/README.md @@ -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 ``. +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). - diff --git a/tests/tests_scans/README.md b/tests/tests_scans/README.md index 5762245..63d535f 100644 --- a/tests/tests_scans/README.md +++ b/tests/tests_scans/README.md @@ -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 ``. +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). -