2348 Pyright

.github/workflows/conda.yml

@@ -101,6 +101,11 @@ jobs:
         run: |
           mypy --ignore-missing-imports mantidimaging
 
+      - name: pyright
+        shell: bash -l {0}
+        run: |
+          pyright mantidimaging
+
       - name: pytest
         timeout-minutes: 10
         shell: bash -l {0}

.github/workflows/windows.yml

@@ -90,6 +90,11 @@ jobs:
         run: |
           mypy --ignore-missing-imports mantidimaging
 
+      - name: pyright
+        shell: bash -l {0}
+        run: |
+          pyright mantidimaging
+
       - name: pytest
         timeout-minutes: 10
         shell: bash -l {0}

.pre-commit-config.yaml

@@ -23,7 +23,16 @@ repos:
         files: ^mantidimaging/
         args: [--ignore-missing-imports]
         additional_dependencies: [types-docutils, types-PyYAML, types-requests]
+-   repo: local
+    hooks:
+    -   id: pyright
+        name: pyright
+        description: Checks that all files pass pyright checks
+        entry: pyright
+        language: system
+        types: [python]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.3.3
     hooks:
     -   id: ruff
+

Makefile

@@ -64,6 +64,9 @@ test-screenshots-win:
 mypy:
 	python -m mypy --ignore-missing-imports ${SOURCE_DIRS}
 
+pyright:
+	python -m pyright ${SOURCE_DIRS}
+
 yapf:
 	python -m yapf --parallel --diff --recursive ${SOURCE_DIRS}
 

docs/release_notes/next/dev-2348-Pyright

@@ -0,0 +1 @@
+#2348: Pyright dependancy to project, configure pyright basic rulest and resolve issues raised by pyright in basic configuration

environment-dev.yml

@@ -27,6 +27,7 @@ dependencies:
   - pyfakefs==5.3.*
   - parameterized==0.9.*
   - pyinstaller==6.9.*
+  - pyright==1.1.*
   - make==4.3
   - ruff=0.3.3
   - pre-commit==3.5.*

mantidimaging/core/io/instrument_log.py

@@ -78,9 +78,9 @@ class InstrumentLogParser(BaseParser):
 
     """
 
-    def __init_subclass__(subcls) -> None:
+    def __init_subclass__(cls) -> None:
         """Automatically register subclasses"""
-        InstrumentLog.register_parser(subcls)
+        InstrumentLog.register_parser(cls)
 
     @abstractmethod
     def parse(self) -> LogDataType:
@@ -103,9 +103,9 @@ class InstrumentShutterCountParser(BaseParser):
 
     """
 
-    def __init_subclass__(subcls) -> None:
+    def __init_subclass__(cls) -> None:
         """Automatically register subclasses"""
-        ShutterCount.register_parser(subcls)
+        ShutterCount.register_parser(cls)
 
     @abstractmethod
     def parse(self) -> ShutterCountType:

mantidimaging/core/operations/monitor_normalisation/monitor_normalisation.py

@@ -16,10 +16,6 @@
     from PyQt5.QtWidgets import QFormLayout, QWidget
 
 
-def _divide_by_counts(data=None, counts=None):
-    data[:] = np.true_divide(data, counts)
-
-
 class MonitorNormalisation(BaseFilter):
     """Normalises the image data using the average count of a beam monitor from the
     experiment log file. This scaling operation is an alternative to ROI normalisation

mantidimaging/core/reconstruct/astra_recon.py

@@ -95,7 +95,7 @@ def find_cor(images: ImageStack, slice_idx: int, start_cor: float | np.ndarray,
         proj_angles = images.projection_angles(recon_params.max_projection_angle)
 
         def get_sumsq(image: np.ndarray) -> float:
-            return np.sum(image**2)
+            return float(np.sum(image**2))
 
         def minimizer_function(cor: float | np.ndarray) -> float:
             if isinstance(cor, np.ndarray):

mantidimaging/core/reconstruct/cil_recon.py

@@ -183,7 +183,7 @@ def set_approx_norm(A2d: BlockOperator, acquisition_data: AcquisitionGeometry,
 
     @staticmethod
     def get_data(sino: np.ndarray, ag: AcquisitionGeometry, recon_params: ReconstructionParameters,
-                 num_subsets: int) -> AcquisitionData:
+                 num_subsets: int) -> BlockDataContainer | AcquisitionData:
         data = AcquisitionData(sino, deep_copy=False, geometry=ag, suppress_warning=True)
 
         if recon_params.stochastic:

mantidimaging/core/utility/histogram.py

@@ -17,6 +17,7 @@ def set_histogram_log_scale(histogram: HistogramLUTItem) -> None:
     :param histogram: The HistogramLUTItem of an image.
     """
     x_data, y_data = histogram.plot.getData()
+    assert isinstance(x_data, np.ndarray) and isinstance(y_data, np.ndarray)
     histogram.plot.setData(x_data, np.log(y_data + 1))
 
 

mantidimaging/core/utility/memory_usage.py

@@ -28,26 +28,20 @@ def mb(self):
     return Value(meminfo.available - meminfo.total * MEMORY_CAP_PERCENTAGE)
 
 
-def get_memory_usage_linux(kb=False, mb=False):
+def get_memory_usage_linux() -> float:
     """
-    :param kb: Return the value in Kilobytes
-    :param mb: Return the value in Megabytes
+    Get the memory usage of the system in bytes
     """
     import psutil
 
     meminfo = psutil.virtual_memory()
-    tuple_to_return = ()  # start with empty tuple
     # meminfo.used gives the size in bytes
-    if kb:
-        tuple_to_return += (meminfo.used / 1024, )
-
-    if mb:
-        tuple_to_return += (meminfo.used / 1024 / 1024, )
-    return tuple_to_return
+    return meminfo.used
 
 
 def get_memory_usage_linux_str():
-    memory_in_kbs, memory_in_mbs = get_memory_usage_linux(kb=True, mb=True)
+    memory_in_kbs = get_memory_usage_linux() / 1024
+    memory_in_mbs = memory_in_kbs / 1024
     # handle caching
     memory_string = f"{memory_in_kbs} KB, {memory_in_mbs} MB"
 

mantidimaging/core/utility/test/memory_usage_test.py

@@ -28,9 +28,8 @@ def test_get_memory_usage_linux(self, mock_virtual_memory):
         mock_meminfo.used = 4 * 1024 * 1024 * 1024  # 4 GB
         mock_virtual_memory.return_value = mock_meminfo
 
-        memory_kb, memory_mb = get_memory_usage_linux(kb=True, mb=True)
-        self.assertEqual(memory_kb, 4 * 1024 * 1024)
-        self.assertEqual(memory_mb, 4 * 1024)
+        memory_in_bytes = get_memory_usage_linux()
+        self.assertEqual(memory_in_bytes, 4 * 1024 * 1024 * 1024)
 
 
 if __name__ == '__main__':

mantidimaging/eyes_tests/base_eyes.py

@@ -57,6 +57,7 @@
 @start_qapplication
 class BaseEyesTest(unittest.TestCase):
     eyes_manager: EyesManager
+    app: QApplication
 
     @classmethod
     def setUpClass(cls) -> None:
@@ -130,8 +131,8 @@ def _create_new_dataset(self) -> Dataset:
 
         return new_dataset
 
-    def _get_top_level_widget(cls, widget_type):
-        for widget in cls.app.topLevelWidgets():
+    def _get_top_level_widget(self, widget_type):
+        for widget in self.app.topLevelWidgets():
             if isinstance(widget, widget_type):
                 return widget
         raise ValueError(f"Could not find top level widget of type {widget_type.__name__}")

mantidimaging/eyes_tests/eyes_manager.py

@@ -36,7 +36,7 @@ class EyesManager:
 
     def __init__(self, application_name="Mantid Imaging", test_name=None):
         self.application_name = application_name
-        self.eyes = Eyes()
+        self.eyes = Eyes()  # type: ignore
         self.eyes.match_level = MatchLevel.IGNORE_COLORS
         self.eyes.configure.host_os = sys.platform
         self.eyes.branch_name = BRANCH_NAME
@@ -50,7 +50,7 @@ def set_match_level(self, level: MatchLevel):
         self.eyes.match_level = level
 
     def set_batch(self, batch_id):
-        batch_info = BatchInfo()
+        batch_info = BatchInfo()  # type: ignore
         batch_info.name = self.test_name
         batch_info.id = batch_id
         self.eyes.batch = batch_info

mantidimaging/gui/dialogs/async_task/presenter.py

@@ -59,7 +59,7 @@ def do_start_processing(self) -> None:
         self.view.show_delayed(1000)
 
     @property
-    def task_is_running(self) -> None:
+    def task_is_running(self) -> bool:
         return self.model.task_is_running
 
     def progress_update(self) -> None:

mantidimaging/gui/dialogs/cor_inspection/model.py

@@ -20,7 +20,6 @@
 
 
 class CORInspectionDialogModel:
-    step: int | float
 
     def __init__(self, images: ImageStack, slice_idx: int, initial_cor: ScalarCoR,
                  recon_params: ReconstructionParameters, iters_mode: bool):

mantidimaging/gui/dialogs/cor_inspection/view.py

@@ -77,7 +77,7 @@ def optimal_rotation_centre(self) -> ScalarCoR:
         return self.presenter.optimal_rotation_centre
 
     @property
-    def optimal_iterations(self) -> int:
+    def optimal_iterations(self) -> int | float:
         return self.presenter.optimal_iterations
 
     def mark_best_recon(self, diffs) -> None:

mantidimaging/gui/widgets/auto_colour_menu/auto_color_menu.py

@@ -26,7 +26,7 @@ def histogram(self) -> HistogramLUTItem:
         raise NotImplementedError('Required histogram property not implemented')
 
     @property
-    def image_data(self) -> np.ndarray:
+    def image_data(self) -> np.ndarray | None:
         raise NotImplementedError('Required image_data property not implemented')
 
     @property

mantidimaging/gui/widgets/line_profile_plot/view.py

@@ -91,7 +91,7 @@ def get_image_region(self) -> tuple[np.ndarray, np.ndarray] | None:
         return self.getArrayRegion(self._image_view.image_data,
                                    self._image_view.image_item,
                                    axes=(1, 0),
-                                   returnMappedCoords=True)
+                                   returnMappedCoords=True)  # type: ignore
 
     def reset(self) -> None:
         if self._image_data_exists() and self._roi_line_is_visible:
@@ -114,7 +114,7 @@ def _set_initial_state(self) -> None:
         # Prevent emitting a RegionChanged signal from setting the state programmatically
         with BlockQtSignals(self):
             initial_pos_x = 0
-            initial_pos_y = self._image_view.image_item.height() // 2
+            initial_pos_y = self._image_view.image_item.height() // 2  # type: ignore
             image_width = self._image_view.image_item.width()
             image_height = self._image_view.image_item.height()
 

mantidimaging/gui/widgets/mi_image_view/view.py

@@ -19,9 +19,10 @@
 from mantidimaging.gui.widgets.mi_image_view.presenter import MIImagePresenter
 from mantidimaging.gui.widgets.bad_data_overlay.bad_data_overlay import BadDataOverlay
 
+import numpy as np
+
 if TYPE_CHECKING:
     from pyqtgraph import HistogramLUTItem
-    import numpy as np
     from mantidimaging.core.utility.data_containers import ProjectionAngles
 
 
@@ -128,7 +129,7 @@ def histogram(self) -> HistogramLUTItem:
         return self.ui.histogram.item
 
     @property
-    def image_data(self) -> np.ndarray:
+    def image_data(self) -> np.ndarray | None:
         return self.image
 
     @property
@@ -202,6 +203,7 @@ def roiChanged(self) -> None:
         self._refresh_message()
 
     def _update_roi_region_avg(self) -> SensibleROI | None:
+        assert self.image is not None
         if self.image.ndim != 3:
             return None
         roi_pos, roi_size = self.get_roi()
@@ -264,15 +266,15 @@ def _update_message(self, pt) -> None:
         if self.image.ndim == 3:
             x = clip(pt.x, 0, self.image.shape[2] - 1)
             y = clip(pt.y, 0, self.image.shape[1] - 1)
-            value = self.image[self.currentIndex, y, x]
+            value = self.image[self.currentIndex, y, x] if self.image is not None else 0
             msg = f"x={y}, y={x}, z={self.currentIndex}, value={value :.6f}"
             if self.angles:
                 angle = degrees(self.angles.value[self.currentIndex])
                 msg += f" | angle = {angle:.2f}"
         else:
             x = clip(pt.x, 0, self.image.shape[1] - 1)
             y = clip(pt.y, 0, self.image.shape[0] - 1)
-            value = self.image[y, x]
+            value = self.image[y, x] if self.image is not None else 0
             msg = f"x={y}, y={x}, value={value}"
         if self.roiString is not None:
             msg += f" | roi = {self.roiString}"
@@ -307,6 +309,8 @@ def set_roi(self, coords: list[int] | None) -> None:
     def default_roi(self) -> None | list[int]:
         # Recommend an ROI that covers the top left quadrant
         # However set min dimensions to avoid an ROI that is so small it's difficult to work with
+        if self.image_data is None:
+            return None
         min_size = 20
         roi_width = max(round(self.image_data.shape[2] / 2), min_size)
         roi_height = max(round(self.image_data.shape[1] / 2), min_size)

mantidimaging/gui/widgets/mi_mini_image_view/view.py

@@ -72,14 +72,14 @@ def histogram(self) -> HistogramLUTItem:
 
     @property
     def histogram_region(self) -> tuple[int | list[int], int | list[int]]:
-        return self.hist.region.getRegion()
+        return self.hist.region.getRegion()  # type: ignore
 
     @histogram_region.setter
     def histogram_region(self, new_region: tuple[int | list[int], int | list[int]]) -> None:
         self.hist.region.setRegion(new_region)
 
     @property
-    def image_data(self) -> np.ndarray:
+    def image_data(self) -> np.ndarray | None:
         return self.im.image
 
     @property

mantidimaging/gui/widgets/palette_changer/presenter.py

@@ -114,7 +114,7 @@ def _update_ticks(self) -> None:
         self.main_hist.gradient.updateGradient()
         self.main_hist.gradient.sigGradientChangeFinished.emit(self.main_hist.gradient)
 
-    def _get_colours(self, num_ticks: int) -> list[float]:
+    def _get_colours(self, num_ticks: int) -> list:
         """
         Determine the colours that should be used for the new recon histogram ticks. Should ensure that there is a
         suitable amount of contrast between the different materials, even if the ticks are quite close together on

mantidimaging/gui/windows/main/view.py

@@ -495,7 +495,13 @@ def get_stack(self, stack_uuid: uuid.UUID) -> ImageStack:
         return self.presenter.get_stack(stack_uuid)
 
     def get_images_from_stack_uuid(self, stack_uuid) -> ImageStack:
-        return self.presenter.get_stack_visualiser(stack_uuid).presenter.images
+        stack_visualiser = self.presenter.get_stack_visualiser(stack_uuid)
+        if stack_visualiser is None:
+            raise ValueError(f"No stack visualiser found for UUID: {stack_uuid}")
+        images = stack_visualiser.presenter.images
+        if images is None:
+            raise ValueError(f"No images found for stack UUID: {stack_uuid}")
+        return images
 
     def get_dataset_id_from_stack_uuid(self, stack_id: uuid.UUID) -> uuid.UUID:
         return self.presenter.get_dataset_id_for_stack(stack_id)