ENH:Updating formatting

.github/workflows/auto-format.yml

@@ -14,13 +14,13 @@ jobs:
           ref: ${{ github.head_ref }}
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: "3.11"
       - uses: psf/black@stable
         with:
           use_pyproject: true
       - uses: chartboost/ruff-action@v1
         with:
-          args: 'check --fix --config pyproject.toml ./src'
+          args: "check --fix --config pyproject.toml ./src"
       - uses: stefanzweifel/git-auto-commit-action@v5
         with:
-          commit-message: 'STYLE:Fixes by auto-format'
+          commit-message: "STYLE:Fixes by auto-format"

.pre-commit-config.yaml

@@ -4,11 +4,10 @@ repos:
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
-      - id: requirements-txt-fixer
       - id: trailing-whitespace
       - id: double-quote-string-fixer
   - repo: https://github.com/python/black.git
-    rev: 22.10.0
+    rev: 24.4.2
     hooks:
       - id: black
         language_version: python3
@@ -30,4 +29,4 @@ repos:
     hooks:
       - id: prettier
         stages: [commit]
-exclude: ["src/ui_*", "*.md"]
+exclude: "ui_.*|.*md|.*ui"

pyproject.toml

@@ -28,7 +28,8 @@ minder3d = "minder3d.main:main"
 develop = [
   'black==24.4.2',
   'pylint',
-  'flake8'
+  'flake8',
+  'pre-commit',
 ]
 
 [tool.setuptools.packages.find]
@@ -40,13 +41,12 @@ readme = {file = ["README.md"]}
 
 [tool.black]
 line-length = 80
-skip-string-normalization = 1
+skip-string-normalization = true
 target_version = ['py311']
-required_version = "24.4.2"
 include = ["src"]
 force-exclude = '''
 (
-  ui_.*|.*\.ui|\.gitignore
+  ui_.*|.*\.ui|\.gitignore|.*\.yml|.*\.yaml|.*\.toml
 )
 '''
 

src/minder3d/__init__.py

@@ -1 +1 @@
-__version__ = "0.9.0"
+__version__ = '0.9.0'

src/minder3d/config.py

@@ -13,13 +13,14 @@ def parse_config() -> argparse.Namespace:
     """
 
     parser = argparse.ArgumentParser(
-        description="Enabling innovative AI for medical imaging.")
+        description='Enabling innovative AI for medical imaging.'
+    )
 
     parser.add_argument(
-        "--load-image", type=str, required=False, help="Path to image"
+        '--load-image', type=str, required=False, help='Path to image'
     )
     parser.add_argument(
-        "--load-scene", type=str, required=False, help="Path to scene"
+        '--load-scene', type=str, required=False, help='Path to scene'
     )
 
     args = parser.parse_args()

src/minder3d/lib/sovImageTablePanelWidget.py

@@ -1,4 +1,5 @@
 """This module provides the ImageTablePanelWidget class."""
+
 from PySide6.QtCore import QSize
 from PySide6.QtGui import QIcon, QPixmap
 from PySide6.QtWidgets import (

src/minder3d/lib/sovView2DPanelWidget.py

@@ -227,12 +227,12 @@ def update_image(self):
         irange = imax - imin
 
         auto_range = np.quantile(self.state.image_array[-1], [0.1, 0.9])
-        self.state.view2D_intensity_window_min[
-            self.state.current_image_num
-        ] = auto_range[0]
-        self.state.view2D_intensity_window_max[
-            self.state.current_image_num
-        ] = auto_range[1]
+        self.state.view2D_intensity_window_min[self.state.current_image_num] = (
+            auto_range[0]
+        )
+        self.state.view2D_intensity_window_max[self.state.current_image_num] = (
+            auto_range[1]
+        )
 
         self.update_gui = False
 
@@ -272,11 +272,11 @@ def update_overlay(self):
             self.state.image[self.state.current_image_num],
             self.state.overlay_array[self.state.current_image_num],
         )
-        self.state.overlay[
-            self.state.current_image_num
-        ] = itk.GetImageFromArray(
-            self.state.overlay_array[self.state.current_image_num],
-            ttype=self.state.overlay_type,
+        self.state.overlay[self.state.current_image_num] = (
+            itk.GetImageFromArray(
+                self.state.overlay_array[self.state.current_image_num],
+                ttype=self.state.overlay_type,
+            )
         )
         self.state.overlay[self.state.current_image_num].CopyInformation(
             self.state.image[self.state.current_image_num]
@@ -366,11 +366,11 @@ def redraw_object(self, so):
                 self.state.image[self.state.current_image_num],
                 self.state.overlay_array[self.state.current_image_num],
             )
-        self.state.overlay[
-            self.state.current_image_num
-        ] = itk.GetImageFromArray(
-            self.state.overlay_array[self.state.current_image_num],
-            ttype=self.state.overlay_type,
+        self.state.overlay[self.state.current_image_num] = (
+            itk.GetImageFromArray(
+                self.state.overlay_array[self.state.current_image_num],
+                ttype=self.state.overlay_type,
+            )
         )
         self.state.overlay[self.state.current_image_num].CopyInformation(
             self.state.image[self.state.current_image_num]

src/minder3d/lib/sovView2DRenderWindowInteractor.py

@@ -120,12 +120,12 @@ def reset_camera(self):
 
     @time_and_log
     def update_image(self):
-        self.state.view2D_intensity_window_min[
-            self.state.current_image_num
-        ] = self.state.image_min[self.state.current_image_num]
-        self.state.view2D_intensity_window_max[
-            self.state.current_image_num
-        ] = self.state.image_max[self.state.current_image_num]
+        self.state.view2D_intensity_window_min[self.state.current_image_num] = (
+            self.state.image_min[self.state.current_image_num]
+        )
+        self.state.view2D_intensity_window_max[self.state.current_image_num] = (
+            self.state.image_max[self.state.current_image_num]
+        )
         if self.view2D is None:
             self.view2D = vtk.vtkImageViewer2()
             self.view2D.SetupInteractor(self)

src/minder3d/main.py

@@ -13,6 +13,7 @@
 from .config import parse_config
 from .minder3DWindow import Minder3DWindow
 
+
 def main():
     """
     Application entrypoint.
@@ -56,5 +57,6 @@ def main():
 
     app.exec()
 
-if __name__ == "__main__":
+
+if __name__ == '__main__':
     main()

src/minder3d/minder3DState.py

@@ -1,4 +1,5 @@
 """The global state of the Minder3D application."""
+
 import logging
 
 import itk

src/minder3d/minder3DWindow.py

@@ -5,7 +5,6 @@
 import vtk
 from PySide6.QtWidgets import QFileDialog, QInputDialog, QMainWindow, QTabBar
 
-from .minder3DState import Minder3DState
 from .lib.sovColorMapUtils import get_nearest_color_index_and_name
 from .lib.sovImageTablePanelUtils import get_qthumbnail_from_array
 from .lib.sovImageTablePanelWidget import ImageTablePanelWidget
@@ -25,6 +24,7 @@
 from .lib.sovView3DPanelWidget import View3DPanelWidget
 from .lib.sovVisualizationPanelWidget import VisualizationPanelWidget
 from .lib.sovWelcomePanelWidget import WelcomePanelWidget
+from .minder3DState import Minder3DState
 from .ui_minder3DWindow import Ui_MainWindow