# TRAligner Package Migration - Completion Summary

## ✅ Migration Successfully Completed - November 6, 2025

### What Was Accomplished

**1. Package Restructuring**
   - ✅ Migrated to professional `src/` layout
   - ✅ Moved source code to `src/traligner/`
   - ✅ Reorganized tests to `tests/` directory
   - ✅ Preserved full Git history from published version

**2. Files Created/Updated**
   - ✅ `src/traligner/__init__.py` - Proper package initialization with exports
   - ✅ `setup.py` - Complete package metadata and dependencies
   - ✅ `pyproject.toml` - Modern Python packaging configuration
   - ✅ `CHANGELOG.md` - Comprehensive version history
   - ✅ `tests/__init__.py` - Test suite initialization
   - ✅ Copied `LICENSE` from published version
   - ✅ Preserved `README.md` and `API_REFERENCE.md`

**3. Git Operations**
   - ✅ Copied `.git` repository from `published/TRAlignerP`
   - ✅ Committed all changes with detailed release notes
   - ✅ Tagged release as `v0.2.0`
   - ✅ Preserved complete version history

**4. Cleanup**
   - ✅ Created backups in `backups/` directory
   - ✅ Archived `published/TRAlignerP` to `archive/TRAlignerP_v0.1.0_20251106`

---

## Current Structure

```
TRAligner/                          # ← SINGLE SOURCE OF TRUTH
├── .git/                          # Git repository (from published)
├── .gitignore                     # Ignore patterns
├── src/
│   └── traligner/                # Main package
│       ├── __init__.py           # v0.2.0, proper exports
│       ├── text_alignment_clean.py
│       └── alignment_tools.py
├── tests/
│   ├── __init__.py
│   └── test_alignment.py
├── setup.py                       # Package configuration
├── pyproject.toml                 # Modern packaging
├── LICENSE                        # MIT License
├── README.md                      # Comprehensive docs
├── API_REFERENCE.md              # API documentation
└── CHANGELOG.md                   # Version history
```

---

## Next Steps

### 1. Test the Package Locally

```bash
cd TRAligner/

# Option A: Install in virtual environment (recommended)
python3 -m venv venv
source venv/bin/activate
pip install -e .

# Option B: If you use pipenv
pipenv install -e .

# Test import
python -c "import traligner; print(f'Version: {traligner.__version__}')"
```

### 2. Run Tests

```bash
# Install test dependencies
pip install pytest pytest-cov

# Run tests
pytest tests/

# Run with coverage
pytest tests/ --cov=traligner
```

### 3. Push to GitHub

```bash
cd TRAligner/

# Verify remote is set correctly
git remote -v

# If remote doesn't exist or is wrong:
git remote set-url origin https://github.com/millerhadar/traligner.git
# Or add if missing:
# git remote add origin https://github.com/millerhadar/traligner.git

# Push everything
git push -u origin main --tags
```

### 4. Publish to PyPI (When Ready)

```bash
# Install build tools
pip install build twine

# Clean any old builds
rm -rf dist/ build/ src/*.egg-info

# Build distribution packages
python -m build

# Check the distribution
twine check dist/*

# Upload to TestPyPI first (recommended)
twine upload --repository testpypi dist/*

# Test installation from TestPyPI
pip install --index-url https://test.pypi.org/simple/ traligner==0.2.0

# If all looks good, upload to production PyPI
twine upload dist/*
```

### 5. Future Development Workflow

```bash
# All development happens in TRAligner/
cd TRAligner/

# Create feature branch
git checkout -b feature/new-alignment-method

# Make changes
# ... edit files in src/traligner/ ...

# Test locally
pip install -e .
pytest tests/

# Commit changes
git add .
git commit -m "Add new alignment method"

# Push branch
git push origin feature/new-alignment-method

# Merge to main when ready
git checkout main
git merge feature/new-alignment-method

# For new release:
# 1. Update version in setup.py and pyproject.toml
# 2. Update CHANGELOG.md
# 3. Commit and tag
git commit -m "Bump version to 0.3.0"
git tag -a v0.3.0 -m "Version 0.3.0"
# 4. Build and publish
python -m build
twine upload dist/*
# 5. Push to GitHub
git push origin main --tags
```

---

## Backup Locations

In case you need to rollback:

- **Current backup**: `backups/TRAligner_backup_20251106/`
- **Published backup**: `backups/TRAlignerP_backup_20251106/`
- **Archived published**: `archive/TRAlignerP_v0.1.0_20251106/`

---

## Key Benefits Achieved

✅ **Single source of truth** - All development in `TRAligner/`
✅ **Professional structure** - Follows Python packaging best practices  
✅ **Version control** - Full Git history preserved
✅ **Easy testing** - `pip install -e .` for local development
✅ **Clear versioning** - setup.py + pyproject.toml  
✅ **Ready for PyPI** - Complete package metadata
✅ **Documented changes** - CHANGELOG.md tracks all versions
✅ **API documentation** - Comprehensive API_REFERENCE.md

---

## Git Status

```bash
Current branch: main
Latest commit: ddeaa04 "Release v0.2.0: Restructure package..."
Tags: v0.2.0
Remote: origin -> https://github.com/millerhadar/traligner.git
Status: Ready to push
```

---

## What Changed in v0.2.0

**Added:**
- Proper src/ package layout
- Comprehensive documentation (API_REFERENCE.md, CHANGELOG.md)
- Modern packaging (pyproject.toml)
- LLM-based token comparison support
- Enhanced morphology embedding matching

**Fixed:**
- IndexError in calc_token_value
- Parameter mapping in increment2one dictionary
- Test suite parameter ordering

**Improved:**
- Package structure (src/ layout)
- Documentation (README with examples)
- Alignment scoring mechanisms

---

## Contact & Support

If you encounter any issues:
1. Check Git status: `git status`
2. Check Git log: `git log --oneline`
3. Verify structure: `tree -L 3 TRAligner/`
4. Test imports: `python -c "import sys; sys.path.insert(0, 'src'); import traligner"`

---

**Migration completed successfully! 🎉**

TRAligner is now properly structured and ready for:
- ✅ Continued development in the TRAligner directory
- ✅ Git version control and GitHub hosting
- ✅ PyPI publishing when ready
- ✅ Professional Python package distribution
