object-segmentation/INSTALL_TEST.md

Installation Testing Guide

This guide helps you verify that the package installation works correctly.

Clean Installation Test

1. Remove Any Previous Installations

# 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

pip install -e .

This allows you to modify source code and see changes immediately.

Option B: Regular Install

pip install .

This installs the package as if it were from PyPI.

3. Verify Installation

# 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

# Test CLI
microscopy-detect --help

# Test GUI launcher (will open window)
microscopy-detect-gui

5. Verify Package Contents

# 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:

# 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:

# 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:

# 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:

# 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

# 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

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

# 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