# Pre-Publication Verification Report

## ✅ Completed Checks

### 1. Package Structure
- ✅ All modules properly structured (validation, cleaning, normalization, refinement, utils)
- ✅ All `__init__.py` files present
- ✅ All `__main__.py` files present for CLI support
- ✅ Package exports only Stage classes via `__all__`

### 2. Dependencies
- ✅ `requirements.txt` includes pandas and parallel-pandas
- ✅ RDKit properly documented (install via conda)
- ✅ All imports verified

### 3. Configuration Files
- ✅ `setup.py` - Complete with metadata
- ✅ `pyproject.toml` - Modern packaging configuration
- ✅ `MANIFEST.in` - Includes template and data files
- ✅ `LICENSE` - MIT License
- ✅ `.gitignore` - Comprehensive ignore rules

### 4. Documentation
- ✅ `README.md` - Complete with examples
- ✅ `INSTALL.md` - Detailed installation guide
- ✅ `PUBLISHING.md` - Publishing instructions
- ✅ `SETUP_CHECKLIST.md` - Pre-publication checklist

### 5. Repository URLs
- ✅ All GitHub URLs updated to: `https://github.com/biochem-data-sci/mehc-curation`
- ✅ setup.py URLs updated
- ✅ pyproject.toml URLs updated
- ✅ README.md URLs updated
- ✅ All documentation files updated

### 6. Code Quality
- ✅ No linter errors
- ✅ All unused imports removed
- ✅ All unused variables removed
- ✅ n_cpu validation implemented (-1, 0, negative, > max)
- ✅ Method renamed: `refine_smiles()` → `complete_refinement()`

### 7. Cache Cleanup
- ✅ All `__pycache__` directories removed
- ✅ All `.pyc` files removed
- ✅ All `.pyo` files removed
- ✅ Build/dist directories cleaned (if existed)

## ✅ Manual Updates Confirmed

### Author Information
- `setup.py` lists author `Thanh-Hoang Nguyen-Vo <nvthoang@gmail.com>`
- `pyproject.toml` authors table updated with the same name and email
- `README.md` citation block lists the full research author set

## 📝 Notes

1. **"FIXED" comments in code**: These are documentation comments explaining code fixes. They are acceptable and help explain the logic.

2. **RDKit dependency**: Not included in requirements.txt because it should be installed via conda. This is documented in INSTALL.md.

3. **Package structure**: Uses `find_packages()` to automatically discover all subpackages.

4. **Console scripts**: Will be available as:
   - `mehc-validation`
   - `mehc-cleaning`
   - `mehc-normalization`
   - `mehc-refinement`

## 🚀 Ready for Publication

After updating author information, the package is ready for:
1. Git commit and push
2. PyPI publication (follow PUBLISHING.md)

## Final Checklist Before Git Push

- [ ] Update author information in setup.py, pyproject.toml, and README.md
- [ ] Review all files one final time
- [ ] Test local installation: `pip install -e .`
- [ ] Test imports: `from mehc_curation.validation import ValidationStage` (etc.)
- [ ] Commit changes: `git add .` and `git commit -m "Prepare for publication"`
- [ ] Push to GitHub: `git push origin main`

