BUG: and ENH:Fix and improve github actions for formatting (#26)

Also updated files based on ruff results.

.github/workflows/auto-format.yml

@@ -0,0 +1,26 @@
+name: "Auto-Format"
+
+on: [push]
+
+jobs:
+  ruff-check:
+    name: "Auto-Format"
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - uses: psf/black@stable
+        with:
+          use_pyproject: true
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "check --fix --config pyproject.toml"
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          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

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "minder3d"
 description = "Using AI to foster innovation in the exploration of radiological images."
 license = {text = "Apache 2.0"}
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Python :: 3"
 ]
@@ -25,11 +25,11 @@ dependencies = [
 minder3d = "minder3d.main:main"
 
 [project.optional-dependencies]
-
 develop = [
-  'black',
+  'black==24.4.2',
   'pylint',
-  'flake8'
+  'flake8',
+  'pre-commit',
 ]
 
 [tool.setuptools.packages.find]
@@ -41,22 +41,12 @@ readme = {file = ["README.md"]}
 
 [tool.black]
 line-length = 80
-skip-string-normalization = 1
+skip-string-normalization = true
 target_version = ['py311']
-exclude = '''
+include = ["src"]
+force-exclude = '''
 (
-  /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | build
-    | dist
-  )/
-  | .gitignore
+  ui_.*|.*\.ui|\.gitignore|.*\.yml|.*\.yaml|.*\.toml
 )
 '''
 
@@ -66,8 +56,13 @@ extend-ignore = ["E501"]
 
 [tool.isort]
 profile = "black"
-skip_glob = "src/ui_*"
+skip_glob = ["ui_*", "*.ui"]
 line_length = 80
 
 [tool.pylint]
 max-line-length = 80
+
+[tool.ruff]
+include = ["*.py"]
+exclude = ["*.ui", "ui_*", ".gitignore"]
+line-length = 80

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/sovChatPanelWidget.py

@@ -1,4 +1,3 @@
-from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QWidget
 
 from .ui_sovChatPanelWidget import Ui_ChatPanelWidget

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 (
@@ -135,13 +136,13 @@ def fill_table(self):
                 self.imageTableWidget.setItem(
                     img_num, 2, QTableWidgetItem(file.filename)
                 )
-                if type(file.file_size) is type([]) and len(file.file_size) > 0:
+                if isinstance(file.file_size, []) and len(file.file_size) > 0:
                     size_str = [str(i) for i in file.file_size]
                     self.imageTableWidget.setItem(
                         img_num, 3, QTableWidgetItem('x'.join(size_str))
                     )
                 if (
-                    type(file.file_spacing) is type([])
+                    isinstance(file.file_spacing, [])
                     and len(file.file_spacing) > 0
                 ):
                     spacing_str = [f'{i:.4f}' for i in file.file_spacing]

src/minder3d/lib/sovInfoTablePanelWidget.py

@@ -1,9 +1,4 @@
-from PySide6.QtWidgets import (
-    QHeaderView,
-    QTableWidget,
-    QTableWidgetItem,
-    QWidget,
-)
+from PySide6.QtWidgets import QTableWidget, QTableWidgetItem, QWidget
 
 from .sovUtils import time_and_log
 from .ui_sovInfoTablePanelWidget import Ui_InfoTablePanelWidget

src/minder3d/lib/sovLungCTALogic.py

@@ -1,4 +1,5 @@
 import importlib.util as imp
+import subprocess
 import sys
 
 import itk

src/minder3d/lib/sovLungCTAPanelWidget.py

@@ -1,5 +1,3 @@
-import numpy as np
-from PySide6.QtGui import QCloseEvent
 from PySide6.QtWidgets import QMessageBox, QWidget
 
 from .sovLungCTALogic import LungCTALogic

src/minder3d/lib/sovOtsuPanelWidget.py

@@ -1,7 +1,3 @@
-import importlib.util as imp
-
-import numpy as np
-from PySide6.QtGui import QCloseEvent
 from PySide6.QtWidgets import QWidget
 
 from .sovOtsuLogic import OtsuLogic

src/minder3d/lib/sovScreenCapturePanelWidget.py

@@ -1,4 +1,3 @@
-from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QWidget
 
 from .ui_sovScreenCapturePanelWidget import Ui_ScreenCapturePanelWidget

src/minder3d/lib/sovTubesPanelWidget.py

@@ -1,4 +1,3 @@
-from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QWidget
 
 from .ui_sovPreProcessPanelWidget import Ui_PreProcessPanelWidget

src/minder3d/lib/sovUtils.py

@@ -15,7 +15,6 @@
 import os
 import time
 import uuid
-from typing import Union
 
 import itk
 import numpy as np

src/minder3d/lib/sovView2DPanelWidget.py

@@ -222,17 +222,13 @@ def create_new_image(self):
 
     @time_and_log
     def update_image(self):
-        imin = self.state.image_min[self.state.current_image_num]
-        imax = self.state.image_max[self.state.current_image_num]
-        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 +268,11 @@ 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 +362,11 @@ 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/lib/sovView3DRenderWindowInteractor.py

@@ -1,4 +1,3 @@
-import itk
 from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
 from vtkmodules.vtkInteractionStyle import vtkInteractorStyleTrackballCamera
 from vtkmodules.vtkRenderingCore import (

src/minder3d/lib/sovView3DUtils.py

@@ -1,5 +1,4 @@
 import itk
-import numpy as np
 from vtkmodules.vtkCommonCore import vtkDoubleArray, vtkPoints
 from vtkmodules.vtkCommonDataModel import vtkCellArray, vtkPolyData, vtkPolyLine
 from vtkmodules.vtkFiltersCore import vtkSurfaceNets3D, vtkTubeFilter

src/minder3d/main.py

@@ -4,7 +4,6 @@
 Launch the minder3D application
 """
 
-import sys
 
 from PySide6.QtCore import Qt
 from PySide6.QtGui import QColor, QPalette
@@ -13,6 +12,7 @@
 from .config import parse_config
 from .minder3DWindow import Minder3DWindow
 
+
 def main():
     """
     Application entrypoint.
@@ -56,5 +56,6 @@ 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