chore: Drop python 3.8 (#1206)

Python 3.8 reached EOL so it is time to drop it.

## Summary by Sourcery

Drop support for Python 3.8 across the codebase and CI configuration.
Update type annotations to use modern Python syntax and refactor code
for improved readability and consistency.

Enhancements:
- Update type annotations to use Python 3.9+ syntax, replacing
typing.List and typing.Dict with list and dict.
- Refactor test cases to use updated type annotations and improve
readability.
- Refactor code to use context managers with parentheses for better
readability and consistency.

CI:
- Remove Python 3.8 from the CI configuration as it has reached
end-of-life.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Updated Python version support for testing workflows to include
versions 3.9 to 3.12.
- Updated napari versions in testing configurations to the latest
releases.

- **Bug Fixes**
- Corrected inconsistencies in method signatures and type annotations
throughout the codebase.

- **Chores**
- Removed deprecated Python 3.8 references from testing workflows and
configuration files.
- Eliminated constraints files for Python 3.8 to streamline dependency
management.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

.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,
     ):
         """