chore: Drop python 3.8

.github/workflows/test_napari_widgets.yml

@@ -27,7 +27,7 @@ jobs:
     with:
       python_version: "3.10"
       os: ${{ matrix.os }}
-      napari: "napari5"
+      napari: "napari54"
       qt_backend: ${{ matrix.qt_backend }}
       timeout: 10
 
@@ -36,10 +36,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        napari: ["napari417", "napari418"]
+        napari: ["napari419", "napari54"]
         qt_backend: ["PyQt5"]
         include:
-          - napari: "napari417"
+          - napari: "napari54"
             qt_backend: "PySide2"
     if: github.event_name == 'push'
     uses: ./.github/workflows/base_test_workflow.yml

.github/workflows/tests.yml

@@ -50,24 +50,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
         os: ["ubuntu-20.04"]
         qt_backend: ["PyQt5"]
         tox_args: [ "" ]
         include:
-          - python_version: "3.9"
+          - python_version: "3.11"
             os: "macos-13"
             qt_backend: "PyQt5"
-          - python_version: "3.9"
+          - python_version: "3.11"
             os: "windows-2019"
             qt_backend: "PyQt5"
-          - python_version: "3.9"
+          - python_version: "3.10"
             os: "ubuntu-20.04"
             qt_backend: "PySide2"
-          - python_version: "3.9"
+          - python_version: "3.10"
             os: "ubuntu-22.04"
             qt_backend: "PySide6"
-          - python_version: "3.10"
+          - python_version: "3.12"
             os: "ubuntu-22.04"
             qt_backend: "PyQt6"
           - python_version: "3.10"
@@ -90,20 +90,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
         os: ["ubuntu-20.04", "macos-13", "windows-2019"]
         qt_backend: ["PySide2", "PyQt5"]
         include:
-          - python_version: "3.11"
+          - python_version: "3.12"
             qt_backend: "PyQt5"
             os: "ubuntu-22.04"
-          - python_version: "3.9"
+          - python_version: "3.10"
             os: "ubuntu-22.04"
             qt_backend: "PySide6"
-          - python_version: "3.9"
+          - python_version: "3.11"
             os: "ubuntu-22.04"
             qt_backend: "PyQt6"
-          - python_version: "3.10"
+          - python_version: "3.11"
             os: "ubuntu-22.04"
             qt_backend: "PyQt5"
             pydantic: "_pydantic_1"
@@ -124,8 +124,8 @@ jobs:
     uses: ./.github/workflows/base_test_workflow.yml
     with:
       test_data: True
-      python_version: "3.10"
-      tox_args: "-e py310-PyQt5-coverage"
+      python_version: "3.12"
+      tox_args: "-e py312-PyQt5-coverage"
       coverage: true
 
   test_minimal:
@@ -134,8 +134,8 @@ jobs:
     uses: ./.github/workflows/base_test_workflow.yml
     with:
       test_data: True
-      python_version: "3.8"
-      tox_args: "-e py38-PyQt5-minimal"
+      python_version: "3.9"
+      tox_args: "-e py39-PyQt5-minimal"
       coverage: true
 
   coverage_prepare:

.github/workflows/upgrade-dependencies.yml

@@ -35,7 +35,7 @@ jobs:
           pip install -U uv
           flags=(--extra pyqt6 --extra pyside2 --extra pyside6 --extra test --extra pyinstaller_base)
 
-          for pyv in 3.8 3.9 3.10 3.11 3.12; do
+          for pyv in 3.9 3.10 3.11 3.12; do
             uv pip compile --python-version ${pyv} --upgrade --output-file requirements/constraints_py${pyv}.txt pyproject.toml requirements/version_denylist.txt "${flags[@]}"
             uv pip compile --python-version ${pyv} --upgrade --output-file requirements/constraints_py${pyv}_pydantic_1.txt pyproject.toml requirements/version_denylist.txt "${flags[@]}" --constraint requirements/pydantic_1.txt
           done

azure-pipelines.yml

@@ -23,7 +23,7 @@ stages:
           displayName: "download data"
         - task: UsePythonVersion@0
           inputs:
-            versionSpec: '3.9'
+            versionSpec: '3.11'
           displayName: 'Use Python $(python.version)'
         - script: python build_utils/cut_changelog.py changelog_cut.md
           displayName: "Cut changelog"

package/PartSeg/_launcher/check_version.py

@@ -40,8 +40,9 @@ def run(self):
             return
         try:
             if os.path.exists(os.path.join(state_store.save_folder, IGNORE_FILE)):
-                with open(os.path.join(state_store.save_folder, IGNORE_FILE), encoding="utf-8") as f_p, suppress(
-                    ValueError
+                with (
+                    open(os.path.join(state_store.save_folder, IGNORE_FILE), encoding="utf-8") as f_p,
+                    suppress(ValueError),
                 ):
                     old_date = date.fromisoformat(f_p.read())
                     if (date.today() - old_date).days < IGNORE_DAYS:

package/PartSeg/_launcher/main_window.py

@@ -2,7 +2,7 @@
 import os
 import warnings
 from functools import partial
-from typing import TYPE_CHECKING, Type
+from typing import TYPE_CHECKING
 
 from qtpy.QtCore import QSize, Qt, QThread, Signal
 from qtpy.QtGui import QIcon
@@ -34,7 +34,7 @@ def run(self):
 
         plugins.register()
         main_window_module = importlib.import_module(self.module)
-        main_window: Type[BaseMainWindow] = main_window_module.MainWindow
+        main_window: type[BaseMainWindow] = main_window_module.MainWindow
         settings: BaseSettings = main_window.get_setting_class()(main_window_module.CONFIG_FOLDER)
         self.errors = settings.load()
         reader = TiffImageReader()

package/PartSeg/_roi_analysis/advanced_window.py

@@ -2,7 +2,7 @@
 import os
 from contextlib import suppress
 from copy import deepcopy
-from typing import List, Optional, Tuple, Type, Union, cast
+from typing import Optional, Union, cast
 
 from qtpy.QtCore import QEvent, Qt, Slot
 from qtpy.QtGui import QIcon
@@ -49,7 +49,7 @@
 from PartSegCore.universal_const import UNIT_SCALE, Units
 from PartSegData import icons_dir
 
-_DialogType = Union[Type[str], Type[int], Type[float]]
+_DialogType = Union[type[str], type[int], type[float]]
 
 
 def h_line():
@@ -366,7 +366,7 @@ class MeasurementSettings(QWidget):
     def __init__(self, settings: PartSettings, parent=None):  # noqa: PLR0915
         super().__init__(parent)
         self.chosen_element: Optional[MeasurementListWidgetItem] = None
-        self.chosen_element_area: Optional[Tuple[AreaType, float]] = None
+        self.chosen_element_area: Optional[tuple[AreaType, float]] = None
         self.settings = settings
         self.profile_list = QListWidget(self)
         self.profile_description = QTextEdit(self)
@@ -841,7 +841,7 @@ def __init__(
         self,
         text: str,
         help_text: str = "",
-        objects_list: Optional[List[Union[Tuple[str, _DialogType], Tuple[str, _DialogType, str]]]] = None,
+        objects_list: Optional[list[Union[tuple[str, _DialogType], tuple[str, _DialogType, str]]]] = None,
         parent: Optional[QWidget] = None,
     ):
         if objects_list is None:  # pragma: no cover

package/PartSeg/_roi_analysis/batch_window.py

@@ -74,7 +74,7 @@ def get_name(cls) -> str:
         return "Excel (*.xlsx)"
 
     @classmethod
-    def get_fields(cls) -> typing.List[typing.Union[AlgorithmProperty, str]]:
+    def get_fields(cls) -> list[typing.Union[AlgorithmProperty, str]]:
         return []
 
 
@@ -376,7 +376,7 @@ class CalculationPrepare(QDialog):
 
     def __init__(
         self,
-        file_list: typing.List[os.PathLike],
+        file_list: list[os.PathLike],
         calculation_plan: CalculationPlan,
         measurement_file_path: os.PathLike,
         settings: PartSettings,

package/PartSeg/_roi_analysis/export_batch.py

@@ -308,7 +308,7 @@ def _excel_path_changed(self):
 
 def _extract_information_from_excel_to_export(
     excel_path: typing.Union[str, Path], base_folder: typing.Union[str, Path]
-) -> typing.List[typing.Tuple[str, bool]]:
+) -> list[tuple[str, bool]]:
     """Extract information from Excel file to export"""
     file_list = []
     file_set = set()

package/PartSeg/_roi_analysis/main_window.py

@@ -1,6 +1,5 @@
 import os
 from contextlib import suppress
-from typing import Type
 
 from qtpy.QtCore import QByteArray, Qt
 from qtpy.QtGui import QIcon, QKeyEvent, QKeySequence, QResizeEvent
@@ -534,7 +533,7 @@ class MainWindow(BaseMainWindow):
     settings: PartSettings
 
     @classmethod
-    def get_setting_class(cls) -> Type[PartSettings]:
+    def get_setting_class(cls) -> type[PartSettings]:
         return PartSettings
 
     initial_image_path = PartSegData.segmentation_analysis_default_image

package/PartSeg/_roi_analysis/measurement_widget.py

@@ -1,7 +1,6 @@
 import locale
 import os
 from enum import Enum
-from typing import List, Tuple
 
 from qtpy.QtCore import Qt
 from qtpy.QtGui import QKeyEvent, QResizeEvent
@@ -56,7 +55,7 @@ def clear(self):
         self.header = []
         self.max_rows = 0
         self.content = []
-        self.measurements: List[MeasurementResult] = []
+        self.measurements: list[MeasurementResult] = []
 
     def get_size(self, save_orientation: bool):
         if save_orientation:
@@ -116,13 +115,13 @@ def get_val_as_str(self, x: int, y: int, save_orientation: bool) -> str:
         val = sublist[y]
         return locale.str(val) if isinstance(val, float) else str(val)
 
-    def get_header(self, save_orientation: bool) -> List[str]:
+    def get_header(self, save_orientation: bool) -> list[str]:
         if save_orientation:
             return [str(i) for i in range(self.max_rows)]
 
         return self.header
 
-    def get_rows(self, save_orientation: bool) -> List[str]:
+    def get_rows(self, save_orientation: bool) -> list[str]:
         return self.get_header(not save_orientation)
 
 
@@ -315,7 +314,7 @@ def update_measurement_list(self):
         self.measurement_type.blockSignals(False)
 
     @staticmethod
-    def _move_widgets(widgets_list: List[Tuple[QWidget, int]], layout1: QBoxLayout, layout2: QBoxLayout):
+    def _move_widgets(widgets_list: list[tuple[QWidget, int]], layout1: QBoxLayout, layout2: QBoxLayout):
         for el in widgets_list:
             layout1.removeWidget(el[0])
             layout2.addWidget(el[0], el[1])

package/PartSeg/_roi_analysis/partseg_settings.py

@@ -31,7 +31,7 @@ class PartSettings(BaseSettings):
     json_encoder_class = PartSegEncoder
     load_metadata = staticmethod(load_metadata)
     last_executed_algorithm: str
-    save_locations_keys: typing.ClassVar[typing.List[str]] = [
+    save_locations_keys: typing.ClassVar[list[str]] = [
         "open_directory",
         "save_directory",
         "export_directory",
@@ -132,7 +132,7 @@ def set_project_info(self, data: typing.Union[ProjectTuple, MaskInfo, PointsInfo
             )
             self.algorithm_changed.emit()
 
-    def get_save_list(self) -> typing.List[SaveSettingsDescription]:
+    def get_save_list(self) -> list[SaveSettingsDescription]:
         return [
             *super().get_save_list(),
             SaveSettingsDescription("segmentation_pipeline_save.json", self._segmentation_pipelines_dict),
@@ -142,27 +142,27 @@ def get_save_list(self) -> typing.List[SaveSettingsDescription]:
         ]
 
     @property
-    def segmentation_pipelines(self) -> typing.Dict[str, SegmentationPipeline]:
+    def segmentation_pipelines(self) -> dict[str, SegmentationPipeline]:
         warnings.warn("segmentation_pipelines is deprecated, use roi_pipelines", DeprecationWarning, stacklevel=2)
         return self.roi_pipelines
 
     @property
-    def roi_pipelines(self) -> typing.Dict[str, SegmentationPipeline]:
+    def roi_pipelines(self) -> dict[str, SegmentationPipeline]:
         return self._segmentation_pipelines_dict.get(self._current_roi_dict, EventedDict())
 
     @property
-    def segmentation_profiles(self) -> typing.Dict[str, ROIExtractionProfile]:
+    def segmentation_profiles(self) -> dict[str, ROIExtractionProfile]:
         warnings.warn("segmentation_profiles is deprecated, use roi_profiles", DeprecationWarning, stacklevel=2)
         return self.roi_profiles
 
     @property
-    def roi_profiles(self) -> typing.Dict[str, ROIExtractionProfile]:
+    def roi_profiles(self) -> dict[str, ROIExtractionProfile]:
         return self._segmentation_profiles_dict.get(self._current_roi_dict, EventedDict())
 
     @property
-    def batch_plans(self) -> typing.Dict[str, CalculationPlan]:
+    def batch_plans(self) -> dict[str, CalculationPlan]:
         return self._batch_plans_dict.get(self._current_roi_dict, EventedDict())
 
     @property
-    def measurement_profiles(self) -> typing.Dict[str, MeasurementProfile]:
+    def measurement_profiles(self) -> dict[str, MeasurementProfile]:
         return self._measurement_profiles_dict.get(self._current_roi_dict, EventedDict())

package/PartSeg/_roi_analysis/prepare_plan_widget.py

@@ -294,17 +294,15 @@ def enable_protect(self):
             self.protect = previous
 
     @classmethod
-    def refresh_profiles(
-        cls, list_widget: typing.Union[QListWidget, SearchableListWidget], new_values: typing.List[str]
-    ):
+    def refresh_profiles(cls, list_widget: typing.Union[QListWidget, SearchableListWidget], new_values: list[str]):
         index = cls.get_index(list_widget.currentItem(), new_values)
         list_widget.clear()
         list_widget.addItems(new_values)
         if index != -1:
             list_widget.setCurrentRow(index)
 
     @staticmethod
-    def get_index(item: QListWidgetItem, new_values: typing.List[str]) -> int:
+    def get_index(item: QListWidgetItem, new_values: list[str]) -> int:
         if item is None:
             return -1
         text = item.text()
@@ -319,7 +317,7 @@ class OtherOperations(ProtectedGroupBox):
 
     def __init__(self, parent=None):
         super().__init__("Other operations:", parent)
-        self.save_translate_dict: typing.Dict[str, SaveBase] = {x.get_short_name(): x for x in save_dict.values()}
+        self.save_translate_dict: dict[str, SaveBase] = {x.get_short_name(): x for x in save_dict.values()}
         self.save_constructor = None
 
         self.change_root = QEnumComboBox(self, enum_class=RootType)
@@ -642,7 +640,7 @@ def __init__(self, settings: PartSettings, parent: typing.Optional[QWidget] = No
 
         self.add_mask_btn.setDisabled(True)
 
-    def update_mask_set(self, mask_set: typing.Set[str]):
+    def update_mask_set(self, mask_set: set[str]):
         self.mask_set = mask_set
 
     def set_replace(self, replace: bool):
@@ -692,7 +690,7 @@ class CreatePlan(QWidget):
     def __init__(self, settings: PartSettings):
         super().__init__()
         self.settings = settings
-        self.save_translate_dict: typing.Dict[str, SaveBase] = {x.get_short_name(): x for x in save_dict.values()}
+        self.save_translate_dict: dict[str, SaveBase] = {x.get_short_name(): x for x in save_dict.values()}
         self._mask_set = set()
         self.plan = PlanPreview(self)
         self.save_plan_btn = QPushButton("Save")

package/PartSeg/_roi_analysis/profile_export.py

@@ -153,10 +153,10 @@ def get_checked(self):
 class ImportDialog(QDialog):
     def __init__(
         self,
-        import_dict: typing.Dict[str, typing.Any],
-        local_dict: typing.Dict[str, typing.Any],
-        viewer: typing.Type[ObjectPreviewProtocol],
-        expected_type: typing.Optional[typing.Type] = None,
+        import_dict: dict[str, typing.Any],
+        local_dict: dict[str, typing.Any],
+        viewer: type[ObjectPreviewProtocol],
+        expected_type: typing.Optional[type] = None,
         parent: typing.Optional[QWidget] = None,
     ):
         """