Feat/updater

pyproject.toml

@@ -100,3 +100,17 @@ PYQT5 = false
 PYSIDE2 = false
 PYQT6 = true
 PYSIDE6 = false
+
+[tool.ruff]
+target-version = "py311"
+
+[tool.ruff.lint]
+# Subsets of B and PLR, the only ones that need no ignore list.
+select = ["B006", "B008", "E", "F", "I", "PLR1722", "RUF013", "RUF022", "SIM102", "UP"]
+ignore = [
+    "E501", # line-too-long
+    "E741", # ambiguous-variable-name
+]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]

src/mosaic/animation/_utils.py

@@ -11,7 +11,7 @@
 
 import numpy as np
 from PIL import Image
-from qtpy.QtGui import QImage, QGuiApplication
+from qtpy.QtGui import QGuiApplication, QImage
 from qtpy.QtWidgets import QFileDialog
 from vtkmodules.util import numpy_support
 from vtkmodules.vtkRenderingCore import vtkWindowToImageFilter

src/mosaic/animation/animations.py

@@ -1,9 +1,9 @@
 from abc import ABC, abstractmethod
 from enum import Enum
-from typing import List, Dict, Any
+from typing import Any
 
-from vtk import vtkTransform
 from qtpy.QtWidgets import QDialog
+from vtk import vtkTransform
 
 from ..stylesheets import Colors, Typography
 
@@ -44,7 +44,7 @@ def _init_parameters(self) -> None:
         pass
 
     @abstractmethod
-    def get_settings(self) -> List[Dict[str, Any]]:
+    def get_settings(self) -> list[dict[str, Any]]:
         """Return a list of setting definitions for the UI"""
         pass
 
@@ -180,7 +180,7 @@ def update_parameters(self, **kwargs):
 
         return super().update_parameters(**kwargs)
 
-    def get_settings(self) -> List[Dict[str, Any]]:
+    def get_settings(self) -> list[dict[str, Any]]:
         n_frames = getattr(self, "_trajectory", None)
         n_frames = n_frames.frames if n_frames is not None else 0
         available = self._available_trajectories()
@@ -271,7 +271,7 @@ def _get_axis_size(self, axis=None):
             return 0
         return shape[_mapping.get(axis.lower(), 0)]
 
-    def get_settings(self) -> List[Dict[str, Any]]:
+    def get_settings(self) -> list[dict[str, Any]]:
         projection = [
             self.volume_viewer.primary.project_selector.itemText(i)
             for i in range(self.volume_viewer.primary.project_selector.count())
@@ -396,7 +396,7 @@ def _init_parameters(self) -> None:
         self.stop_frame = 180
         self._transform = vtkTransform()
 
-    def get_settings(self) -> List[Dict[str, Any]]:
+    def get_settings(self) -> list[dict[str, Any]]:
         return [
             {
                 "label": "axis",
@@ -484,13 +484,13 @@ class ActorSelectionDialog(QDialog):
 
     def __init__(self, cdata, current_selection=None, parent=None):
         from qtpy.QtWidgets import (
-            QVBoxLayout,
+            QFrame,
+            QGroupBox,
             QHBoxLayout,
-            QTreeWidget,
             QLabel,
-            QFrame,
             QPushButton,
-            QGroupBox,
+            QTreeWidget,
+            QVBoxLayout,
         )
 
         from mosaic.widgets import DialogFooter
@@ -604,7 +604,7 @@ def _init_parameters(self) -> None:
         self._original_opacities = {}
         self._cached_actors = None
 
-    def get_settings(self) -> List[Dict[str, Any]]:
+    def get_settings(self) -> list[dict[str, Any]]:
         return [
             {
                 "label": "start_opacity",
@@ -775,6 +775,7 @@ def _clear_waypoints(self):
     def _init_spline(self):
         """Initialize the spline curve from waypoints."""
         import numpy as np
+
         from mosaic.parametrization import SplineCurve
 
         waypoints = self.parameters.get("waypoints", [])
@@ -911,7 +912,7 @@ def cleanup_preview(self):
         except Exception:
             self._path_actors.clear()
 
-    def get_settings(self) -> List[Dict[str, Any]]:
+    def get_settings(self) -> list[dict[str, Any]]:
         n = len(self.parameters.get("waypoints", []))
         count_text = f"{n} waypoint{'s' if n != 1 else ''} defined"
         return [
@@ -1015,7 +1016,7 @@ def _init_parameters(self) -> None:
         )
         self._initial_distance = None
 
-    def get_settings(self) -> List[Dict[str, Any]]:
+    def get_settings(self) -> list[dict[str, Any]]:
         return [
             {
                 "label": "zoom_factor",

src/mosaic/animation/compose.py

@@ -8,43 +8,43 @@
 
 import json
 from dataclasses import dataclass
-from typing import Dict, List, Any
+from typing import Any
 from uuid import uuid4
 
 import imageio
-from vtkmodules.vtkRenderingCore import vtkWindowToImageFilter
-from qtpy.QtCore import Qt, QTimer, QSize
+from qtpy.QtCore import QSize, Qt, QTimer
 from qtpy.QtGui import QKeySequence, QShortcut
 from qtpy.QtWidgets import (
+    QApplication,
+    QCheckBox,
     QDialog,
-    QWidget,
-    QVBoxLayout,
-    QHBoxLayout,
+    QFileDialog,
     QGridLayout,
-    QPushButton,
-    QToolButton,
-    QSpinBox,
     QGroupBox,
-    QFileDialog,
-    QApplication,
-    QSizePolicy,
-    QCheckBox,
+    QHBoxLayout,
     QMessageBox,
+    QPushButton,
+    QSizePolicy,
+    QSpinBox,
+    QToolButton,
+    QVBoxLayout,
+    QWidget,
 )
-from .timeline import TimelineWidget
-from .animations import AnimationType, BaseAnimation
-from .settings import AnimationSettings, ExportDialog
+from vtkmodules.vtkRenderingCore import vtkWindowToImageFilter
+
+from ..icons import icon
+from ..stylesheets import Colors
+from ..utils import Throttle
+from ..widgets import MosaicMessageBox
 from ._utils import (
     FrameWriter,
     capture_frame,
     read_frame,
     scaled_device_pixel_attributes,
 )
-
-from ..icons import icon
-from ..utils import Throttle
-from ..stylesheets import Colors
-from ..widgets import MosaicMessageBox
+from .animations import AnimationType, BaseAnimation
+from .settings import AnimationSettings, ExportDialog
+from .timeline import TimelineWidget
 
 
 @dataclass
@@ -66,7 +66,7 @@ class AnimationComposerDialog(QDialog):
 
     def __init__(self, vtk_widget, volume_viewer=None, cdata=None, parent=None):
         super().__init__(parent)
-        self.tracks: List[Track] = []
+        self.tracks: list[Track] = []
         self.selected_track = None
         self.current_frame = 0
 
@@ -393,7 +393,7 @@ def _on_track_moved(self, track_id: str, new_frame: int):
         self.properties_panel.global_start_spin.setValue(new_frame)
         self.timeline.update()
 
-    def _on_animation_changed(self, changes: Dict[str, Any]):
+    def _on_animation_changed(self, changes: dict[str, Any]):
         self.timeline.update()
 
     def _get_total_frames(self) -> int:
@@ -645,9 +645,7 @@ def export_animation(self):
             render_height = height * magnification
             render_window.SetSize(render_width, render_height)
 
-            pixel_scale = (
-                render_height / original_size[1] if original_size[1] else 1
-            )
+            pixel_scale = render_height / original_size[1] if original_size[1] else 1
             with scaled_device_pixel_attributes(render_window, pixel_scale):
                 render_window.Render()
 
@@ -749,7 +747,7 @@ def save_project(self):
         except Exception as e:
             MosaicMessageBox.warning(self, "Save Error", f"Failed to save project: {e}")
 
-    def _serialize_parameters(self, params: Dict) -> Dict:
+    def _serialize_parameters(self, params: dict) -> dict:
         """Convert parameters to JSON-serializable format."""
         serialized = {}
         for key, value in params.items():
@@ -787,7 +785,7 @@ def load_project(self):
             self.toggle_play()
 
         try:
-            with open(filename, "r") as f:
+            with open(filename) as f:
                 project_data = json.load(f)
         except Exception as e:
             MosaicMessageBox.warning(

src/mosaic/animation/settings.py

@@ -1,24 +1,25 @@
-from qtpy.QtCore import Signal, Qt
+from qtpy.QtCore import Qt, Signal
 from qtpy.QtWidgets import (
-    QWidget,
-    QDialog,
-    QVBoxLayout,
-    QHBoxLayout,
-    QLabel,
-    QLineEdit,
-    QSpinBox,
     QCheckBox,
     QComboBox,
-    QGroupBox,
-    QFormLayout,
+    QDialog,
     QDoubleSpinBox,
+    QFormLayout,
     QGridLayout,
+    QGroupBox,
+    QHBoxLayout,
+    QLabel,
+    QLineEdit,
     QPushButton,
     QSizePolicy,
+    QSpinBox,
+    QVBoxLayout,
+    QWidget,
 )
-from mosaic.widgets import create_setting_widget
+
 from mosaic.icons import icon
 from mosaic.stylesheets import Colors
+from mosaic.widgets import create_setting_widget
 
 
 class AnimationSettings(QGroupBox):

src/mosaic/animation/timeline.py

@@ -1,6 +1,6 @@
-from qtpy.QtCore import Qt, QRect, Signal
-from qtpy.QtWidgets import QWidget, QScrollArea, QApplication
-from qtpy.QtGui import QPainter, QColor, QPen, QFont, QMouseEvent
+from qtpy.QtCore import QRect, Qt, Signal
+from qtpy.QtGui import QColor, QFont, QMouseEvent, QPainter, QPen
+from qtpy.QtWidgets import QApplication, QScrollArea, QWidget
 
 from ..icons import icon
 from ..stylesheets import Colors, Typography

src/mosaic/commands/__init__.py

@@ -6,7 +6,7 @@
 Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 
-from .session import Session
 from .registry import CommandRegistry
+from .session import Session
 
-__all__ = ["Session", "CommandRegistry"]
+__all__ = ["CommandRegistry", "Session"]

src/mosaic/commands/parser.py

@@ -13,15 +13,15 @@
 import re
 import shlex
 from dataclasses import dataclass, field
-from typing import Any, Dict, List, Optional
+from typing import Any
 
-__all__ = ["ParsedCommand", "parse_command", "format_value", "format_kwargs"]
+__all__ = ["ParsedCommand", "format_kwargs", "format_value", "parse_command"]
 
 _TARGET_RE = re.compile(r"^#\d+(-\d+)?$")
 _SPECIAL_TARGETS = {"@last", "*"}
 
 
-def _split_tokens(text: str) -> List[str]:
+def _split_tokens(text: str) -> list[str]:
     """Split a command line into shell-like tokens.
 
     Quotes group tokens on every platform.  On Windows the backslash is kept
@@ -169,9 +169,9 @@ class ParsedCommand:
     """
 
     verb: str
-    targets: List[str] = field(default_factory=list)
-    args: List[str] = field(default_factory=list)
-    kwargs: Dict[str, Any] = field(default_factory=dict)
+    targets: list[str] = field(default_factory=list)
+    args: list[str] = field(default_factory=list)
+    kwargs: dict[str, Any] = field(default_factory=dict)
 
     def resolve_positional(self, params) -> None:
         """Map remaining positional *args* into *kwargs* by parameter order.
@@ -205,7 +205,7 @@ def resolve_positional(self, params) -> None:
         self.args = remaining
 
 
-def parse_command(text: str) -> Optional[ParsedCommand]:
+def parse_command(text: str) -> ParsedCommand | None:
     """Parse a text command into a :class:`ParsedCommand`.
 
     Parameters