Migrate to PySide6 with full feature set, theming, and CI/CD pipeline

.github/workflows/ci.yml

@@ -0,0 +1,29 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    name: Tests (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: pip install -e ".[dev]"
+
+      - name: Run tests
+        run: pytest tests/ -v
+        env:
+          QT_QPA_PLATFORM: offscreen  # headless Qt on Linux

.github/workflows/generate-icns.yml

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+name: Generate macOS Icon
+
+on:
+  workflow_dispatch:  # run manually from GitHub Actions UI
+
+jobs:
+  generate:
+    name: Generate Proteus.icns
+    runs-on: macos-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Generate .icns
+        run: |
+          mkdir -p packaging/Proteus.iconset
+          for size in 16 32 64 128 256 512; do
+            sips -z $size $size src/proteus/resources/Proteus.png \
+              --out packaging/Proteus.iconset/icon_${size}x${size}.png
+          done
+          iconutil -c icns packaging/Proteus.iconset -o packaging/Proteus.icns
+          echo "Generated: $(ls -lh packaging/Proteus.icns)"
+
+      - name: Upload .icns artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: Proteus-icns
+          path: packaging/Proteus.icns

.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+
+permissions:
+  contents: write  # needed to create GitHub Release
+
+jobs:
+  build:
+    name: Build (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            archive: Proteus-linux.tar.gz
+          - os: macos-latest
+            archive: Proteus-macos.tar.gz
+          - os: windows-latest
+            archive: Proteus-windows.zip
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Build (Linux / macOS)
+        if: runner.os != 'Windows'
+        run: bash packaging/build.sh --skip-tests
+
+      - name: Build (Windows)
+        if: runner.os == 'Windows'
+        run: packaging\build.bat --skip-tests
+
+      - name: Upload archive
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.archive }}
+          path: ${{ matrix.archive }}
+
+  release:
+    name: Create GitHub Release
+    needs: build
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download all archives
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+
+      - name: Create release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: ${{ github.ref_name }}
+          draft: false
+          prerelease: false
+          files: |
+            Proteus-linux.tar.gz
+            Proteus-macos.tar.gz
+            Proteus-windows.zip

.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+*.egg
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+
+# PyInstaller
+build/
+dist/
+*.spec.bak
+
+# IDE
+.vscode/
+.idea/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+
+# OS
+.DS_Store
+Thumbs.db

README.md

@@ -1 +1,150 @@
 # Proteus
+
+<p align="center">
+  <img src="src/proteus/resources/Proteus.png" alt="Proteus Logo" width="180">
+</p>
+
+<p align="center">
+  <strong>Scientific Image Processing Desktop Application</strong>
+</p>
+
+---
+
+Proteus is a desktop application for scientific image processing, built with PySide6 (Qt) and OpenCV. It provides an interactive canvas with real-time tools for enhancement, analysis, and visualization of grayscale and multi-band imagery.
+
+## Features
+
+- **Image Enhancement** — Histogram equalization, power-law (gamma) transform, partial inversion, pseudocolor mapping (JET colormap)
+- **Sharpen / Binarize** — Unsharp mask (Original), Otsu auto-threshold (B/W Auto), fixed threshold at 128 (B/W 128), custom threshold dialog (B/W Custom)
+- **Noise Reduction** — Gaussian denoising, blur-divide background correction
+- **Multi-Band Pseudocolor** — Merge two images with custom band labels (e.g. UV + IR), blend 50/50, apply JET colormap
+- **PCA Analysis** — Covariance and SVD-based principal component analysis for multi-band images (3–16 images), with Prev/Next result navigation
+- **Drawing Tools** — Freehand brush for mask creation and region annotation
+- **ROI Selection** — Region-of-interest cropping, auto-applied to PCA
+- **Undo/Redo** — Full operation history with Undo/Redo support
+- **Themes** — Light, Dark, and High-Contrast themes with a one-click toggle, persisted across sessions
+
+## Requirements
+
+- Python 3.10+
+- PySide6 >= 6.5.0
+- OpenCV >= 4.8.0
+- NumPy >= 1.24.0
+
+## Installation (development)
+
+```bash
+# Clone the repository
+git clone https://github.com/yiyang26/Proteus.git
+cd Proteus
+
+# Create a virtual environment
+python3 -m venv .venv
+source .venv/bin/activate   # Windows: .venv\Scripts\activate
+
+# Install in development mode
+pip install -e ".[dev]"
+```
+
+## Usage
+
+```bash
+# Run via entry point
+proteus
+
+# Or run as a module
+python -m proteus
+```
+
+## Running Tests
+
+```bash
+pytest
+```
+
+## Building a Standalone Executable
+
+The build scripts handle everything: creating a venv, installing dependencies, running tests, and producing an archive.
+
+> **Note:** Build on the target platform — Linux build for Linux, macOS for macOS, Windows for Windows.
+
+### Linux
+
+```bash
+bash packaging/build.sh
+
+# Skip tests
+bash packaging/build.sh --skip-tests
+```
+
+Output: `dist/Proteus/` + `Proteus-linux.tar.gz`
+
+### macOS
+
+**One-time icon prep** (requires macOS):
+```bash
+mkdir -p packaging/Proteus.iconset
+sips -z 1024 1024 src/proteus/resources/Proteus.png \
+    --out packaging/Proteus.iconset/icon_512x512@2x.png
+iconutil -c icns packaging/Proteus.iconset -o packaging/Proteus.icns
+```
+
+```bash
+bash packaging/build.sh
+
+# Skip tests
+bash packaging/build.sh --skip-tests
+```
+
+Output: `dist/Proteus.app` + `Proteus-macos.tar.gz`
+
+### Windows
+
+**One-time icon prep** (requires [ImageMagick](https://imagemagick.org)):
+```bat
+magick src\proteus\resources\Proteus.png ^
+    -define icon:auto-resize=256,128,64,32,16 packaging\Proteus.ico
+```
+
+```bat
+packaging\build.bat
+
+:: Skip tests
+packaging\build.bat --skip-tests
+```
+
+Output: `dist\Proteus\Proteus.exe` + `Proteus-windows.zip`
+
+## Project Structure
+
+```
+Proteus/
+├── src/proteus/
+│   ├── core/              # Processing logic (no UI dependencies)
+│   │   ├── processing.py  # Image enhancement & filtering functions
+│   │   ├── pca.py         # Principal component analysis
+│   │   ├── image_io.py    # Image load/save utilities
+│   │   ├── state.py       # ImageState & operation logging
+│   │   └── utils.py       # Shared helpers
+│   ├── ui/                # PySide6 interface
+│   │   ├── main_window.py # Main application window & signal wiring
+│   │   ├── canvas.py      # Interactive image canvas (QGraphicsView)
+│   │   ├── top_bar.py     # Logo, title, and theme toggle button
+│   │   ├── sidebar.py     # Collapsible tool panels
+│   │   ├── status_bar.py  # Status text and zoom controls
+│   │   ├── dialogs.py     # Parameter input dialogs
+│   │   └── theme.py       # Light / Dark / High-Contrast QSS theming
+│   ├── resources/          # App icon and assets
+│   └── app.py             # Application entry point
+├── tests/                  # Test suite
+├── packaging/              # Build scripts and PyInstaller spec
+│   ├── Proteus.spec        # PyInstaller configuration
+│   ├── version_info.txt    # Windows EXE version metadata
+│   ├── build.sh            # Linux / macOS build script
+│   └── build.bat           # Windows build script
+└── pyproject.toml          # Project metadata & dependencies
+```
+
+## License
+
+See [LICENSE](LICENSE) for details.