chore: Drop napari<0.6 and pydantic<2

.github/project_dict.pws

@@ -1,4 +1,4 @@
-personal_ws-1.1 en 31
+personal_ws-1.1 en 32
 napari
 autoupdate
 aspell
@@ -30,3 +30,4 @@ ImageJ
 QtViewer
 ubuntu
 numpy
+pydantic

.github/workflows/base_test_workflow.yml

@@ -38,10 +38,6 @@ on:
         required: false
         type: number
         default: 60
-      pydantic:
-        required: false
-        type: string
-        default: ""
       artifact_suffix:
         required: false
         type: string
@@ -50,7 +46,7 @@ on:
 
 jobs:
   test:
-    name: ${{ inputs.os }} py ${{ inputs.python_version }} ${{ inputs.napari }} ${{ inputs.qt_backend }} ${{ inputs.pydantic }}
+    name: ${{ inputs.os }} py ${{ inputs.python_version }} ${{ inputs.napari }} ${{ inputs.qt_backend }}
     runs-on: ${{ inputs.os }}
     env:
       NAPARI: ${{ inputs.napari }}
@@ -92,8 +88,8 @@ jobs:
           # shellcheck disable=SC2086
           python -m tox $TOX_ARGS -- package/tests/test_PartSegImage $PYTEST_ARGS
         env:
-          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
-          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
+          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version) || 'requirements/version_denylist.txt' }}
+          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version) || 'requirements/version_denylist.txt' }}
 
       - name: Test with tox PartSegCore
         if: ${{ inputs.napari == 'latest' }}
@@ -102,8 +98,8 @@ jobs:
           # shellcheck disable=SC2086
           python -m tox $TOX_ARGS --  package/tests/test_PartSegCore $PYTEST_ARGS
         env:
-          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
-          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
+          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version) || 'requirements/version_denylist.txt' }}
+          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version ) || 'requirements/version_denylist.txt' }}
 
       - name: Test with tox PartSeg
         if: ${{ inputs.napari == 'latest' }}
@@ -113,8 +109,8 @@ jobs:
           # shellcheck disable=SC2086
           python -m tox $TOX_ARGS -- package/tests/test_PartSeg $PYTEST_ARGS
         env:
-          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
-          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
+          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version ) || 'requirements/version_denylist.txt' }}
+          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version ) || 'requirements/version_denylist.txt' }}
 
       - name: Test with tox all
         if: ${{ inputs.napari != 'latest' }}
@@ -124,8 +120,8 @@ jobs:
           # shellcheck disable=SC2086
           python -m tox $TOX_ARGS ${PYTEST_ARGS:+-- $PYTEST_ARGS}
         env:
-          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
-          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || 'requirements/version_denylist.txt' }}
+          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version ) || 'requirements/version_denylist.txt' }}
+          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}.txt', inputs.python_version ) || 'requirements/version_denylist.txt' }}
 
 
       - uses: actions/upload-artifact@v7

.github/workflows/test_napari_widgets.yml

@@ -31,17 +31,13 @@ jobs:
       qt_backend: ${{ matrix.qt_backend }}
       timeout: 10
 
-  test-pyqt5:
+  test-qt5:
     name: PyQt5 ${{ matrix.napari }}
     strategy:
       fail-fast: false
       matrix:
-        napari: ["napari419", "napari54"]
-        qt_backend: ["PyQt5"]
-        include:
-          - napari: "napari54"
-            qt_backend: "PySide2"
-    if: github.event_name == 'push'
+        napari: ["napari62"]
+        qt_backend: ["PyQt5", "PySide2"]
     uses: ./.github/workflows/base_test_workflow.yml
     with:
       python_version: "3.10"

.github/workflows/tests.yml

@@ -77,17 +77,12 @@ jobs:
           - python_version: "3.12"
             os: "ubuntu-22.04"
             qt_backend: "PyQt6"
-          - python_version: "3.10"
-            os: "ubuntu-22.04"
-            qt_backend: "PyQt5"
-            pydantic: "_pydantic_1"
     with:
       test_data: True
       python_version: ${{ matrix.python_version }}
       os: ${{ matrix.os }}
       qt_backend: ${{ matrix.qt_backend }}
       tox_args: ${{ matrix.tox_args }}
-      pydantic: ${{ matrix.pydantic }}
 
   base-test-main:
     name: Base py${{ matrix.python_version }}
@@ -110,10 +105,6 @@ jobs:
           - python_version: "3.11"
             os: "ubuntu-22.04"
             qt_backend: "PyQt6"
-          - python_version: "3.11"
-            os: "ubuntu-22.04"
-            qt_backend: "PyQt5"
-            pydantic: "_pydantic_1"
         exclude:
           - python_version: "3.11"
             qt_backend: "PySide2"
@@ -126,7 +117,6 @@ jobs:
       python_version: ${{ matrix.python_version }}
       os: ${{ matrix.os }}
       qt_backend: ${{ matrix.qt_backend }}
-      pydantic: ${{ matrix.pydantic }}
       artifact_suffix: "-main"
       pytest_args: "-v"
 

.github/workflows/upgrade-dependencies.yml

@@ -37,7 +37,6 @@ jobs:
 
           for pyv in 3.10 3.11 3.12 3.13 3.14; 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
           uv pip compile --python-version 3.12 --upgrade --output-file requirements/constraints_py3.12_docs.txt pyproject.toml --extra docs --extra pyqt6
       # END PYTHON DEPENDENCIES

package/PartSeg/common_backend/load_backup.py

@@ -27,7 +27,7 @@ def import_config():
     if os.path.exists(state_store.save_folder):
         return
     version = packaging.version.parse(parsed_version.base_version)
-    base_folder = os.path.dirname(state_store.save_folder)
+    base_folder: str = os.path.dirname(state_store.save_folder)
     possible_folders = glob(os.path.join(base_folder, "*"))
     versions = sorted(
         (
@@ -46,15 +46,11 @@ def import_config():
             "Import from old version",
             "There is no configuration folder for this version of PartSeg\n"
             "Would you like to import it from " + before_name + " version of PartSeg",
-            QMessageBox.Yes | QMessageBox.No,
-            QMessageBox.Yes,
+            QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
+            QMessageBox.StandardButton.Yes,
         )
-        if resp == QMessageBox.Yes:
+        if resp == QMessageBox.StandardButton.Yes:
             shutil.copytree(os.path.join(base_folder, before_name), state_store.save_folder)
             if os.path.exists(os.path.join(state_store.save_folder, IGNORE_FILE)):
                 os.remove(os.path.join(state_store.save_folder, IGNORE_FILE))
-            napari_settings = napari_get_settings(state_store.save_folder)
-            if hasattr(napari_settings, "load") and napari_settings.load is not None:
-                napari_settings.load()
-            elif getattr(napari_settings, "_load", None) is not None:
-                napari_settings._load()  # pylint: disable=protected-access
+            napari_get_settings(state_store.save_folder)

package/PartSeg/common_gui/algorithms_description.py

@@ -383,6 +383,7 @@ def _any():
 
 class FormWidget(QWidget):
     value_changed = Signal()
+    _model_class: type[BaseModel] | None = None
 
     def __init__(
         self,

package/PartSeg/common_gui/error_report.py

@@ -18,7 +18,6 @@
 import sentry_sdk
 from napari.settings import get_settings
 from napari.utils.theme import get_theme
-from packaging.version import parse as parse_version
 from qtpy.QtGui import QIcon
 from qtpy.QtWidgets import (
     QApplication,
@@ -54,7 +53,6 @@
 _FEEDBACK_URL = "https://sentry.io/api/0/projects/{organization_slug}/{project_slug}/user-feedback/".format(
     organization_slug="cent", project_slug="partseg"
 )
-_napari_ge_5 = parse_version(version("napari")) >= parse_version("0.5.0a1")
 
 
 def _print_traceback(exception, file_):
@@ -84,10 +82,7 @@ def __init__(self, exception: Exception, description: str, additional_notes: str
         self.create_issue_btn = QPushButton("Create issue")
         self.cancel_btn = QPushButton("Cancel")
         self.error_description = QTextEdit()
-        if _napari_ge_5:
-            theme = get_theme(get_settings().appearance.theme)
-        else:
-            theme = get_theme(get_settings().appearance.theme, as_dict=False)
+        theme = get_theme(get_settings().appearance.theme)
         self._highlight = Pylighter(self.error_description.document(), "python", theme.syntax_style)
         self.traceback_summary = additional_info
         if additional_info is None:

package/PartSeg/common_gui/napari_image_view.py

@@ -212,11 +212,7 @@ def setup_ui(self):
         layout.addWidget(self.viewer_widget)
 
         self.setLayout(layout)
-
-        if hasattr(self.viewer_widget.canvas, "background_color_override"):
-            self.viewer_widget.canvas.background_color_override = "black"
-            self.viewer.scale_bar.color = "white"
-            self.viewer.scale_bar.colored = True
+        self.viewer_widget.canvas.background_color_override = "black"
 
     def _connect_to_settings(self):
         self.settings.mask_changed.connect(self.set_mask)
@@ -327,21 +323,13 @@ def update_spacing_info(self, image: Image | None = None) -> None:
             image_info.mask.scale = image.normalized_scaling()
 
     def _active_layer(self):
-        if hasattr(self.viewer.layers, "selection"):
-            return self.viewer.layers.selection.active
-        return self.viewer.active_layer
+        return self.viewer.layers.selection.active
 
-    def _coordinates(self):
+    def _coordinates(self) -> list[int] | None:
         active_layer = self._active_layer()
         if active_layer is None:
             return None
-        if (
-            hasattr(self.viewer, "cursor")
-            and hasattr(self.viewer.cursor, "position")
-            and hasattr(active_layer, "world_to_data")
-        ):
-            return [int(x) for x in active_layer.world_to_data(self.viewer.cursor.position)]
-        return [int(x) for x in active_layer.coordinates]
+        return [int(x) for x in active_layer.world_to_data(self.viewer.cursor.position)]
 
     def print_info(self, event=None):
         cords = self._coordinates()

package/PartSeg/plugins/napari_io/loader.py

@@ -1,9 +1,7 @@
 import os
 import typing
-from importlib.metadata import version
 
 import numpy as np
-from packaging.version import parse as parse_version
 
 from PartSeg.plugins.napari_widgets._settings import get_settings
 from PartSegCore import UNIT_SCALE
@@ -40,19 +38,10 @@ def adjust_color(color: str | list[int]) -> str | tuple[float]:
     return color
 
 
-if parse_version(version("napari")) >= parse_version("0.4.19a1"):
-
-    def add_color(image: Image, idx: int) -> dict:
-        return {
-            "colormap": adjust_color(image.get_colors()[idx]),
-        }
-
-else:
-
-    def add_color(image: Image, idx: int) -> dict:  # noqa: ARG001
-        # Do nothing, as napari is not able to pass hex color to image
-        # the image and idx are present to keep the same signature
-        return {}
+def add_color(image: Image, idx: int) -> dict:
+    return {
+        "colormap": adjust_color(image.get_colors()[idx]),
+    }
 
 
 def _image_to_layers(project_info, scale, translate):

package/PartSeg/plugins/napari_widgets/_settings.py

@@ -2,6 +2,7 @@
 
 from magicgui.widgets import Container, create_widget
 from napari.layers import Layer
+from platformdirs import user_config_dir
 
 from PartSeg._roi_analysis.partseg_settings import PartSettings
 from PartSeg.common_backend import napari_get_settings
@@ -43,10 +44,10 @@ def get_settings() -> PartSegNapariSettings:
     global _SETTINGS  # noqa: PLW0603  # pylint: disable=global-statement
     if _SETTINGS is None:
         napari_settings = napari_get_settings()
-        if hasattr(napari_settings, "path"):
-            save_path = napari_settings.path
-        else:
+        if napari_settings.config_path is not None:
             save_path = os.path.dirname(napari_settings.config_path)
+        else:
+            save_path = user_config_dir("napari", False)  # pragma: no cover
         _SETTINGS = PartSegNapariSettings(os.path.join(save_path, "PartSeg_napari_plugins"))
         _SETTINGS.load()
     return _SETTINGS

package/PartSeg/plugins/napari_widgets/lables_control.py

@@ -1,18 +1,14 @@
 from collections.abc import Sequence
-from importlib.metadata import version
 
 from napari import Viewer
 from napari.layers import Labels
 from napari.utils.colormaps import DirectLabelColormap
-from packaging.version import parse as parse_version
 from qtpy.QtWidgets import QHBoxLayout, QPushButton, QTabWidget
 
 from PartSeg.common_backend.base_settings import BaseSettings
 from PartSeg.common_gui.label_create import LabelChoose, LabelEditor, LabelShow
 from PartSeg.plugins.napari_widgets._settings import get_settings
 
-NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
-
 
 class NapariLabelShow(LabelShow):
     def __init__(self, viewer: Viewer, name: str, label: list[Sequence[float]], removable, parent=None):

package/PartSegCore/analysis/measurement_base.py

@@ -247,7 +247,7 @@ def replace(self, **kwargs) -> Leaf:
         if getattr(self, key) is not None and (key != "parameters" or dict(self.parameters)):
             del kwargs[key]
 
-    return self.copy(update=kwargs)
+    return self.model_copy(update=kwargs)
 
 
 Leaf.replace_ = replace

package/PartSegCore/mask_create.py

@@ -200,7 +200,7 @@ def _fill_holes(mask_description: MaskProperty, mask: np.ndarray) -> np.ndarray:
     if mask_description.save_components:
         border = 1
         res_slice = tuple(slice(border, -border) for _ in range(mask.ndim))
-        mask_description_copy = mask_description.copy(update={"save_components": False})
+        mask_description_copy = mask_description.model_copy(update={"save_components": False})
         mask_prohibited = mask > 0
         for component, slice_arr, cmp_num in _cut_components(mask, mask, border):
             mask_prohibited_component = mask_prohibited[slice_arr]

package/PartSegCore/utils.py

@@ -444,12 +444,18 @@ class Config:
         extra = "forbid"
 
     def __getitem__(self, item):
-        if item in self.__fields__:
+        if item in self.__class__.model_fields:
             warnings.warn("Access to attribute by [] is deprecated. Use . instead", FutureWarning, stacklevel=2)
             return getattr(self, item)
         raise KeyError(f"{item} not found in {self.__class__.__name__}")
 
-    def copy(self: PydanticBaseModel, *, validate: bool = True, **kwargs: typing.Any) -> PydanticBaseModel:
+    def model_copy(self: typing.Self, *, validate: bool = True, **kwargs: typing.Any) -> typing.Self:
+        copy_res = super().model_copy(**kwargs)
+        if validate:
+            return self.__class__(**{name: getattr(copy_res, name) for name in copy_res.model_fields_set})
+        return copy_res
+
+    def copy(self: typing.Self, *, validate: bool = True, **kwargs: typing.Any) -> typing.Self:
         copy_res = super().copy(**kwargs)
         if validate:
             return self.validate(