Bug fix in installing and lauching the program

INSTALL_TEST.md

@@ -0,0 +1,236 @@
+# Installation Testing Guide
+
+This guide helps you verify that the package installation works correctly.
+
+## Clean Installation Test
+
+### 1. Remove Any Previous Installations
+
+```bash
+# Deactivate any active virtual environment
+deactivate
+
+# Remove old virtual environment (if exists)
+rm -rf venv
+
+# Create fresh virtual environment
+python3 -m venv venv
+source venv/bin/activate  # On Linux/Mac
+# or
+venv\Scripts\activate  # On Windows
+```
+
+### 2. Install the Package
+
+#### Option A: Editable/Development Install
+
+```bash
+pip install -e .
+```
+
+This allows you to modify source code and see changes immediately.
+
+#### Option B: Regular Install
+
+```bash
+pip install .
+```
+
+This installs the package as if it were from PyPI.
+
+### 3. Verify Installation
+
+```bash
+# Check package is installed
+pip list | grep microscopy
+
+# Check version
+microscopy-detect --version
+# Expected output: microscopy-object-detection 1.0.0
+
+# Test Python import
+python -c "import src; print(src.__version__)"
+# Expected output: 1.0.0
+```
+
+### 4. Test Entry Points
+
+```bash
+# Test CLI
+microscopy-detect --help
+
+# Test GUI launcher (will open window)
+microscopy-detect-gui
+```
+
+### 5. Verify Package Contents
+
+```python
+# Run this in Python shell
+import src
+import src.database
+import src.model
+import src.gui
+
+# Check schema file is included
+from pathlib import Path
+import src.database
+db_path = Path(src.database.__file__).parent
+schema_file = db_path / 'schema.sql'
+print(f"Schema file exists: {schema_file.exists()}")
+# Expected: Schema file exists: True
+```
+
+## Troubleshooting
+
+### Issue: ModuleNotFoundError
+
+**Error:**
+```
+ModuleNotFoundError: No module named 'src'
+```
+
+**Solution:**
+```bash
+# Reinstall with verbose output
+pip install -e . -v
+
+# Or try regular install
+pip install . --force-reinstall
+```
+
+### Issue: Entry Points Not Working
+
+**Error:**
+```
+microscopy-detect: command not found
+```
+
+**Solution:**
+```bash
+# Check if scripts are in PATH
+which microscopy-detect
+
+# If not found, check pip install location
+pip show microscopy-object-detection
+
+# You might need to add to PATH or use full path
+~/.local/bin/microscopy-detect  # Linux
+```
+
+### Issue: Import Errors for PySide6
+
+**Error:**
+```
+ImportError: cannot import name 'QApplication' from 'PySide6.QtWidgets'
+```
+
+**Solution:**
+```bash
+# Install Qt dependencies (Linux only)
+sudo apt-get install libxcb-xinerama0
+
+# Reinstall PySide6
+pip uninstall PySide6
+pip install PySide6
+```
+
+### Issue: Config Files Not Found
+
+**Error:**
+```
+FileNotFoundError: config/app_config.yaml
+```
+
+**Solution:**
+The config file should be created automatically. If not:
+```bash
+# Create config directory in your home
+mkdir -p ~/.microscopy-detect
+cp config/app_config.yaml ~/.microscopy-detect/
+
+# Or run from source directory first time
+cd /home/martin/code/object_detection
+python main.py
+```
+
+## Manual Testing Checklist
+
+- [ ] Package installs without errors
+- [ ] Version command works (`microscopy-detect --version`)
+- [ ] Help command works (`microscopy-detect --help`)
+- [ ] GUI launches (`microscopy-detect-gui`)
+- [ ] Can import all modules in Python
+- [ ] Database schema file is accessible
+- [ ] Configuration loads correctly
+
+## Build and Install from Wheel
+
+```bash
+# Build the package
+python -m build
+
+# Install from wheel
+pip install dist/microscopy_object_detection-1.0.0-py3-none-any.whl
+
+# Test
+microscopy-detect --version
+```
+
+## Uninstall
+
+```bash
+pip uninstall microscopy-object-detection
+```
+
+## Development Workflow
+
+### After Code Changes
+
+If installed with `-e` (editable mode):
+- Python code changes are immediately available
+- No need to reinstall
+
+If installed with regular `pip install .`:
+- Reinstall after changes: `pip install . --force-reinstall`
+
+### After Adding New Files
+
+```bash
+# Reinstall to include new files
+pip install -e . --force-reinstall
+```
+
+## Expected Installation Output
+
+```
+Processing /home/martin/code/object_detection
+  Installing build dependencies ... done
+  Getting requirements to build wheel ... done
+  Preparing metadata (pyproject.toml) ... done
+Building wheels for collected packages: microscopy-object-detection
+  Building wheel for microscopy-object-detection (pyproject.toml) ... done
+Successfully built microscopy-object-detection
+Installing collected packages: microscopy-object-detection
+Successfully installed microscopy-object-detection-1.0.0
+```
+
+## Success Criteria
+
+Installation is successful when:
+1. ✅ No error messages during installation
+2. ✅ `pip list` shows the package
+3. ✅ `microscopy-detect --version` returns correct version
+4. ✅ GUI launches without errors
+5. ✅ All Python modules can be imported
+6. ✅ Database operations work
+7. ✅ Detection functionality works
+
+## Next Steps After Successful Install
+
+1. Configure image repository path
+2. Run first detection
+3. Train a custom model
+4. Export results
+
+For usage instructions, see [QUICKSTART.md](QUICKSTART.md)

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
+requires = ["setuptools>=45", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -63,10 +63,9 @@ Repository = "https://github.com/yourusername/object_detection"
 microscopy-detect = "src.cli:main"
 
 [project.gui-scripts]
-microscopy-detect-gui = "main:main"
+microscopy-detect-gui = "src.gui_launcher:main"
 
 [tool.setuptools]
-package-dir = { "" = "." }
 packages = [
     "src",
     "src.database",
@@ -77,10 +76,10 @@ packages = [
     "src.gui.widgets",
     "src.utils",
 ]
+include-package-data = true
 
 [tool.setuptools.package-data]
-src = ["database/*.sql"]
+"src.database" = ["*.sql"]
-"" = ["config/*.yaml"]
 
 [tool.black]
 line-length = 88

setup.py

@@ -44,7 +44,7 @@ setup(
             "microscopy-detect=src.cli:main",
         ],
         "gui_scripts": [
-            "microscopy-detect-gui=main:main",
+            "microscopy-detect-gui=src.gui_launcher:main",
         ],
     },
     keywords="microscopy yolov8 object-detection segmentation computer-vision deep-learning",

src/cli.py

@@ -44,7 +44,7 @@ Examples:
     if args.gui:
         # Launch GUI
         try:
-            from main import main as gui_main
+            from src.gui_launcher import main as gui_main
 
             gui_main()
         except Exception as e:

src/gui_launcher.py

@@ -0,0 +1,49 @@
+"""GUI launcher module for microscopy object detection application."""
+
+import sys
+from pathlib import Path
+
+from PySide6.QtWidgets import QApplication
+from PySide6.QtCore import Qt
+
+from src import __version__
+from src.gui.main_window import MainWindow
+from src.utils.logger import setup_logging
+from src.utils.config_manager import ConfigManager
+
+
+def main():
+    """Launch the GUI application."""
+    # Setup logging
+    config_manager = ConfigManager()
+    log_config = config_manager.get_section("logging")
+    setup_logging(
+        log_file=log_config.get("file", "logs/app.log"),
+        level=log_config.get("level", "INFO"),
+        log_format=log_config.get("format"),
+    )
+
+    # Enable High DPI scaling
+    QApplication.setHighDpiScaleFactorRoundingPolicy(
+        Qt.HighDpiScaleFactorRoundingPolicy.PassThrough
+    )
+
+    # Create Qt application
+    app = QApplication(sys.argv)
+    app.setApplicationName("Microscopy Object Detection")
+    app.setOrganizationName("MicroscopyLab")
+    app.setApplicationVersion(__version__)
+
+    # Set application style
+    app.setStyle("Fusion")
+
+    # Create and show main window
+    window = MainWindow()
+    window.show()
+
+    # Run application
+    sys.exit(app.exec())
+
+
+if __name__ == "__main__":
+    main()