2024 12 08 test dependencies

.github/workflows/python-package.yml

@@ -1,77 +1,34 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Python package
-
 on:
   push:
     branches: [ master ]
     tags: '*'
   pull_request:
     branches: [ master ]
-
 jobs:
-  build:
-
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.11", "3.12", "3.13"]
-
+  build-python-package:
+    uses: nion-software/github-workflows/.github/workflows/build-python-package.yml@main
+    secrets:
+      anaconda-token: ${{ secrets.ANACONDA_TOKEN }}
+  pypi-publish:
+    name: Upload release to PyPI
+    needs: [build-python-package]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+    environment: release
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Display Python version
-      run: python -c "import sys; print(sys.version)"
-    - name: Build Distribution
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install build
-        python -m build
-    - name: Install Test Dependencies
-      run: |
-        pip install -r test-requirements.txt
-        python -m pip install mypy
-        mypy --version
-    - name: Type Checking
-      run: |
-        # use mypy -p to work around mypy issue 8944
-        mypy --namespace-packages --ignore-missing-imports --follow-imports=silent --strict --no-warn-redundant-casts --no-warn-unused-ignores -p nionswift_plugin.usim
-    - name: Test
+    - name: Download All Artifacts
+      uses: actions/download-artifact@v4
+    - name: Copy files to upload to PyPI to dist.
+      shell: bash
       run: |
-        python -m unittest discover -s nionswift_plugin/usim/test/ -p "*_test.py"
-    - name: Upload Artifacts
-      uses: actions/upload-artifact@v4
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
-      with:
-        name: distribution
-        path: dist
-    - name: Publish package to PyPI
+        mkdir dist
+        find . -name "*.whl" -exec cp {} dist \;
+        ls -lR .
+    - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
-      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
       with:
         skip-existing: true
-        user: __token__
-        password: ${{ secrets.pypi_password }}
-    - name: Set up Miniconda for conda-build
-      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        auto-update-conda: true
-        python-version: '3.11'
-    - name: Build/publish anaconda package
-      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
-      shell: bash -l {0}
-      run: |
-        # make a directory to avoid name conflicts with the channel. argh.
-        mkdir conda_build
-        pushd conda_build
-        conda update -n base --all -y
-        conda update --all -y
-        conda install conda-build anaconda-client -y
-        conda build -q --python ${{ matrix.python-version }} -c nion -c conda-forge --override-channels --skip-existing --user nion --token ${{ secrets.anaconda_token }} ..
-        popd
+        print-hash: true

meta.yaml

@@ -24,6 +24,7 @@ requirements:
 
 test:
   imports:
+    - nion.usim_device
     - nionswift_plugin.usim
     - nionswift_plugin.usim.test
 

mypy.ini

@@ -0,0 +1,9 @@
+# Global options:
+
+[mypy]
+ignore_missing_imports = True
+follow_imports = silent
+strict = True
+warn_redundant_casts = False
+warn_unused_ignores = False
+packages = nionswift_plugin.usim, nion.usim_device

nionswift_plugin/usim/CameraDevice.py → nion/usim_device/CameraDevice.py

@@ -23,36 +23,33 @@
 
 # other plug-ins
 from nion.instrumentation import camera_base
-from . import RonchigramCameraSimulator
-from . import EELSCameraSimulator
+from nion.instrumentation import stem_controller
+from nion.device_kit import InstrumentDevice
+from nion.device_kit import ScanDevice
 
-if typing.TYPE_CHECKING:
-    from . import InstrumentDevice
-    from . import CameraSimulator
-    from . import ScanDevice
 
 _NDArray = numpy.typing.NDArray[typing.Any]
 
 _ = gettext.gettext
 
 
+class CameraSimulatorLike(typing.Protocol):
+    def close(self) -> None: ...
+    def get_dimensional_calibrations(self, readout_area: typing.Optional[Geometry.IntRect], binning_shape: typing.Optional[Geometry.IntSize]) -> typing.Sequence[Calibration.Calibration]: ...
+    def get_frame_data(self, readout_area: Geometry.IntRect, binning_shape: Geometry.IntSize, exposure_s: float, scan_context: stem_controller.ScanContext, probe_position: typing.Optional[Geometry.FloatPoint]) -> DataAndMetadata.DataAndMetadata: ...
+
+
 class Camera(camera_base.CameraDevice3):
     """Implement a camera device."""
 
-    def __init__(self, camera_id: str, camera_type: str, camera_name: str, instrument: InstrumentDevice.Instrument):
+    def __init__(self, camera_id: str, camera_type: str, camera_name: str, simulator: CameraSimulatorLike, instrument: InstrumentDevice.Instrument):
         self.camera_id = camera_id
         self.camera_type = camera_type
         self.camera_name = camera_name
         self.__camera_task: typing.Optional[CameraTask] = None
         self.__instrument = instrument
         self.__scan_device: typing.Optional[ScanDevice.Device] = None
-        self.__simulator: CameraSimulator.CameraSimulator
-        if camera_type == "ronchigram":
-            self.__simulator = RonchigramCameraSimulator.RonchigramCameraSimulator(instrument, Geometry.IntSize.make(instrument.camera_sensor_dimensions("ronchigram")), instrument.counts_per_electron, instrument.stage_size_nm)
-        elif camera_type == "eels":
-            self.__simulator = EELSCameraSimulator.EELSCameraSimulator(instrument, Geometry.IntSize.make(instrument.camera_sensor_dimensions("eels")), instrument.counts_per_electron)
-        else:
-            raise ValueError(f"Unsupported camera type '{camera_type}'.")
+        self.__simulator = simulator
         self.__sensor_dimensions = instrument.camera_sensor_dimensions(camera_type)
         self.__readout_area = instrument.camera_readout_area(camera_type)
         self.__symmetric_binning = True
@@ -74,9 +71,10 @@ def __init__(self, camera_id: str, camera_type: str, camera_name: str, instrumen
         self.__thread.start()
 
         # Also register the camera device and use a unique name for it so that we can directly access it
-        if Registry.get_component(f"usim_{camera_type}_camera_device"):
-            raise RuntimeError(f"Component 'usim_{camera_type}_camera_device' is already registered.")
-        Registry.register_component(self, {f"usim_{camera_type}_camera_device"})
+        camera_device_id = f"{camera_id}_device"
+        if Registry.get_component(camera_device_id):
+            raise RuntimeError(f"Component '{camera_device_id}' is already registered.")
+        Registry.register_component(self, {camera_device_id})
 
         # TODO Define external trigger interface and the mechanism for aqcuiring multiple sequences
         self._external_trigger = False # Just here for testing, we need to decide on how to specify external trigger mode in the base class
@@ -124,7 +122,7 @@ def mask_array(self) -> typing.Optional[_NDArray]:
         return self.__mask_array
 
     @property
-    def simulator(self) -> CameraSimulator.CameraSimulator:
+    def simulator(self) -> CameraSimulatorLike:
         return self.__simulator
 
     def get_expected_dimensions(self, binning: int) -> typing.Tuple[int, int]:
@@ -344,7 +342,7 @@ def acquire_synchronized_begin(self, camera_frame_parameters: camera_base.Camera
         scan_controller = self.__instrument.scan_controller
         assert scan_controller
         scan_device = scan_controller.scan_device
-        self.__scan_device = typing.cast("ScanDevice.Device", scan_device)
+        self.__scan_device = typing.cast(ScanDevice.Device, scan_device)
         self.__camera_task = CameraTask(self, camera_frame_parameters, collection_shape)
         self.__camera_task.start()
         return camera_base.PartialData(self.__camera_task._xdata_ex, False, False, None, 0)
@@ -432,7 +430,7 @@ def grab_partial(self, *, update_period: float = 1.0) -> typing.Tuple[bool, bool
         return True, True, 0
 
 
-class CameraSettings:
+class CameraSettings(camera_base.CameraSettings):
 
     def __init__(self, camera_id: str):
         # these events must be defined
@@ -581,16 +579,3 @@ def __init__(self, stem_controller_id: str, camera_device: Camera, camera_settin
         self.camera_device = camera_device
         self.camera_settings = camera_settings
         self.priority = 20
-
-
-def run(instrument: InstrumentDevice.Instrument) -> None:
-    component_types = {"camera_module"}  # the set of component types that this component represents
-    camera_device = Camera("usim_ronchigram_camera", "ronchigram", _("uSim Ronchigram Camera"), instrument)
-    setattr(camera_device, "camera_panel_type", "ronchigram")
-    camera_settings = CameraSettings("usim_ronchigram_camera")
-    Registry.register_component(CameraModule("usim_stem_controller", camera_device, camera_settings), component_types)
-
-    camera_device = Camera("usim_eels_camera", "eels", _("uSim EELS Camera"), instrument)
-    setattr(camera_device, "camera_panel_type", "eels")
-    camera_settings = CameraSettings("usim_eels_camera")
-    Registry.register_component(CameraModule("usim_stem_controller", camera_device, camera_settings), component_types)

nionswift_plugin/usim/CameraSimulator.py → nion/usim_device/CameraSimulator.py

@@ -7,13 +7,11 @@
 
 from nion.data import Calibration
 from nion.data import DataAndMetadata
+from nion.device_kit import InstrumentDevice
+from nion.instrumentation import stem_controller
 from nion.utils import Geometry
-from nion.utils import Registry
+from nion.usim_device import InstrumentDevice as InstrumentDevice_
 
-if typing.TYPE_CHECKING:
-    from . import InstrumentDevice
-    from . import ScanDevice
-    from nion.instrumentation import stem_controller
 
 _NDArray = numpy.typing.NDArray[typing.Any]
 
@@ -28,11 +26,15 @@ class FrameSettings:
     sample_name: str
 
 
+def get_value_manager(instrument: InstrumentDevice.Instrument) -> InstrumentDevice_.ValueManager:
+    return typing.cast(InstrumentDevice_.ValueManager, instrument.value_manager)
+
+
 class CameraSimulator:
 
     depends_on: typing.List[str] = list() # subclasses should define the controls and attributes they depend on here
 
-    def __init__(self, instrument: InstrumentDevice.Instrument, camera_type: str, sensor_dimensions: Geometry.IntSize, counts_per_electron: int) -> None:
+    def __init__(self, instrument: InstrumentDevice_.Instrument, camera_type: str, sensor_dimensions: Geometry.IntSize, counts_per_electron: int) -> None:
         self.__instrument = instrument
         self._camera_type = camera_type
         self._sensor_dimensions = sensor_dimensions
@@ -44,7 +46,7 @@ def property_changed(name: str) -> None:
             if name in self.depends_on:
                 self._needs_recalculation = True
 
-        self.__property_changed_event_listener = instrument.property_changed_event.listen(property_changed)
+        self.__property_changed_event_listener = get_value_manager(instrument).property_changed_event.listen(property_changed)
 
         # we also need to inform the cameras about changes to the (parked) probe position
         def probe_state_changed(probe_state: str, probe_position: typing.Optional[Geometry.FloatPoint]) -> None:
@@ -64,7 +66,7 @@ def _camera_shape(self) -> Geometry.IntSize:
         return self._sensor_dimensions
 
     @property
-    def instrument(self) -> InstrumentDevice.Instrument:
+    def instrument(self) -> InstrumentDevice_.Instrument:
         return self.__instrument
 
     def get_dimensional_calibrations(self, readout_area: typing.Optional[Geometry.IntRect], binning_shape: typing.Optional[Geometry.IntSize]) -> typing.Sequence[Calibration.Calibration]:
@@ -102,4 +104,5 @@ def _get_frame_settings(self, readout_area: Geometry.IntRect, binning_shape: Geo
                 probe_position = scan_device.current_probe_position
             elif self.instrument.probe_state == "parked" and parked_probe_position is not None:
                 probe_position = parked_probe_position
-        return FrameSettings(readout_area, binning_shape, exposure_s, copy.deepcopy(scan_context), probe_position, self.instrument.sample.title)
+        scan_data_generator = typing.cast(InstrumentDevice_.ScanDataGenerator, self.instrument.scan_data_generator)
+        return FrameSettings(readout_area, binning_shape, exposure_s, copy.deepcopy(scan_context), probe_position, scan_data_generator.sample.title)

nion/usim_device/DeviceConfiguration.py

@@ -0,0 +1,45 @@
+import gettext
+
+from nion.device_kit import CameraDevice
+from nion.instrumentation import camera_base
+from nion.instrumentation import scan_base
+from nion.instrumentation import stem_controller
+from nion.usim_device import EELSCameraSimulator
+from nion.usim_device import InstrumentDevice
+from nion.usim_device import RonchigramCameraSimulator
+from nion.usim_device import ScanDevice
+from nion.utils import Geometry
+
+
+_ = gettext.gettext
+
+
+class AcquisitionContextConfiguration:
+    def __init__(self, *, sample_index: int = 0) -> None:
+        self.instrument_id = "usim_stem_controller"
+        value_manager = InstrumentDevice.ValueManager()
+        axis_manager = InstrumentDevice.AxisManager()
+        scan_data_generator = InstrumentDevice.ScanDataGenerator(sample_index=sample_index)
+        instrument = InstrumentDevice.Instrument(self.instrument_id, value_manager, axis_manager, scan_data_generator)
+        self._instrument = instrument
+        self.instrument: stem_controller.STEMController = instrument
+        self.ronchigram_camera_device_id = "usim_ronchigram_camera"
+        self.eels_camera_device_id = "usim_eels_camera"
+        self._scan_module = ScanDevice.ScanModule(instrument)
+        self.scan_module: scan_base.ScanModule = self._scan_module
+
+        ronchigram_simulator = RonchigramCameraSimulator.RonchigramCameraSimulator(instrument, Geometry.IntSize.make(instrument.camera_sensor_dimensions("ronchigram")), instrument.counts_per_electron, instrument.stage_size_nm)
+        self._ronchigram_camera_device = CameraDevice.Camera("usim_ronchigram_camera", "ronchigram", _("uSim Ronchigram Camera"), ronchigram_simulator, instrument)
+        self._ronchigram_camera_settings = CameraDevice.CameraSettings(self.ronchigram_camera_device_id)
+
+        eels_camera_simulator = EELSCameraSimulator.EELSCameraSimulator(instrument, Geometry.IntSize.make(instrument.camera_sensor_dimensions("eels")), instrument.counts_per_electron)
+        self._eels_camera_device = CameraDevice.Camera("usim_eels_camera", "eels", _("uSim EELS Camera"), eels_camera_simulator, instrument)
+        self._eels_camera_settings = CameraDevice.CameraSettings(self.eels_camera_device_id)
+
+        self.ronchigram_camera_device: camera_base.CameraDevice3 = self._ronchigram_camera_device
+        self.ronchigram_camera_settings: camera_base.CameraSettings = self._ronchigram_camera_settings
+        self.eels_camera_device: camera_base.CameraDevice3 = self._eels_camera_device
+        self.eels_camera_settings: camera_base.CameraSettings = self._eels_camera_settings
+
+        value_manager.ronchigram_camera = self._ronchigram_camera_device
+        value_manager.eels_camera = self._eels_camera_device