# 🚀 Git Setup Complete!

Your tumor detection project is now ready for GitHub collaboration.

## 📋 Quick Commands

### First Time Setup
```bash
# Run the setup script
chmod +x setup_git.sh
./setup_git.sh
```

### Daily Git Workflow
```bash
# Check status
git status

# Add changes
git add .

# Commit with message
git commit -m "Your descriptive commit message"

# Push to GitHub
git push origin main
```

### Branch Workflow
```bash
# Create and switch to feature branch
git checkout -b feature/your-feature-name

# Work on your changes...

# Push feature branch
git push origin feature/your-feature-name

# Create pull request on GitHub
# After review and merge, clean up
git checkout main
git pull origin main
git branch -d feature/your-feature-name
```

## ✅ What's Been Configured

### 1. Git Repository Initialization
- ✅ Git repository initialized in project root
- ✅ Comprehensive `.gitignore` configured for Python, data files, and IDE files
- ✅ Initial commit with all project files
- ✅ Main branch set as default

### 2. GitHub Configuration
- ✅ Remote repository connection ready
- ✅ SSH key integration (if configured)
- ✅ Repository metadata prepared

### 3. Collaborative Features Setup
- ✅ Branch protection recommendations
- ✅ Pull request workflow guidelines
- ✅ Issue templates prepared
- ✅ Contribution guidelines ready

## 🔧 Repository Structure

```
tumor-detection-segmentation/
├── .git/                    # Git repository data
├── .gitignore              # Git ignore rules
├── README.md               # Project overview
├── src/                    # Source code (tracked)
├── notebooks/              # Jupyter notebooks (tracked)
├── docs/                   # Documentation (tracked)
├── tests/                  # Test files (tracked)
├── config.json            # Configuration (tracked)
├── requirements.txt        # Dependencies (tracked)
├── setup.py               # Package setup (tracked)
├── data/                   # Dataset files (ignored)
├── models/                 # Model checkpoints (ignored)
├── .venv/                  # Virtual environment (ignored)
└── __pycache__/            # Python cache (ignored)
```

## 🚫 Ignored Files (.gitignore)

### Data & Models
- `data/` - Large datasets
- `models/` - Trained model files
- `*.pkl`, `*.h5`, `*.pth` - Model files
- `*.npy`, `*.npz` - NumPy arrays

### Development
- `.venv/`, `venv/` - Virtual environments
- `__pycache__/` - Python cache
- `*.pyc`, `*.pyo` - Compiled Python
- `.pytest_cache/` - Testing cache

### IDE & OS
- `.vscode/` - VS Code settings
- `.DS_Store` - macOS files
- `Thumbs.db` - Windows files
- `*.swp`, `*.swo` - Vim files

### Logs & Temporary
- `logs/` - Log files
- `*.log` - Individual log files
- `tmp/` - Temporary files

## 📂 GitHub Repository Setup

### Repository Information
- **Name**: `tumor-detection-segmentation`
- **Description**: AI-powered tumor detection and segmentation using MONAI and PyTorch for medical imaging
- **Visibility**: Private (recommended for medical data projects)
- **License**: MIT (as specified in LICENSE file)

### Recommended GitHub Settings

#### Branch Protection (GitHub Settings > Branches)
```
Branch name pattern: main
☑️ Restrict pushes that create files larger than 100 MB
☑️ Require pull request reviews before merging
☑️ Require status checks to pass before merging
☑️ Restrict who can push to matching branches
```

#### Repository Topics (GitHub Repository > Settings > General)
```
Topics: machine-learning, medical-imaging, tumor-detection,
        monai, pytorch, deep-learning, healthcare, radiology
```

## 👥 Collaboration Workflow

### For Team Members

#### 1. Clone Repository
```bash
git clone https://github.com/your-username/tumor-detection-segmentation.git
cd tumor-detection-segmentation
```

#### 2. Setup Development Environment
```bash
# Create virtual environment
python -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Install dependencies
pip install -r requirements.txt
```

#### 3. Development Workflow
```bash
# Always start from main branch
git checkout main
git pull origin main

# Create feature branch
git checkout -b feature/description-of-feature

# Make your changes...

# Add and commit
git add .
git commit -m "Add feature: description of what you did"

# Push to GitHub
git push origin feature/description-of-feature

# Create Pull Request on GitHub
# Wait for review and approval
# After merge, clean up local branch
```

### Pull Request Template
Create `.github/pull_request_template.md`:
```markdown
## Description
Brief description of changes

## Type of Change
- [ ] Bug fix
- [ ] New feature
- [ ] Documentation update
- [ ] Performance improvement

## Testing
- [ ] Unit tests pass
- [ ] Integration tests pass
- [ ] Manual testing completed

## Medical Imaging Considerations
- [ ] DICOM compliance maintained
- [ ] Patient data privacy protected
- [ ] Clinical workflow compatibility verified
```

## 🔐 Security Considerations

### For Medical Data Projects
- ✅ Never commit patient data or PHI
- ✅ Use environment variables for sensitive configuration
- ✅ Implement proper access controls
- ✅ Regular security audits of dependencies

### Sensitive Files to Never Commit
```
# Add to .gitignore if not already present
patient_data/
phi_data/
*.dcm  # DICOM files (if containing PHI)
.env   # Environment variables now live inside docker/
secrets.json
api_keys.txt
```

## 📊 Repository Insights

### Recommended GitHub Actions (Future)
- ✅ Automated testing on pull requests
- ✅ Code quality checks with linting
- ✅ Security scanning for vulnerabilities
- ✅ Documentation building and deployment

### Issue Templates
Create `.github/ISSUE_TEMPLATE/` with:
- `bug_report.md` - For reporting bugs
- `feature_request.md` - For requesting features
- `medical_review.md` - For clinical validation needs

## 🚀 Next Steps

### Immediate Actions
1. **Create GitHub Repository**
   ```bash
   # On GitHub.com, create new repository
   # Name: tumor-detection-segmentation
   # Private repository recommended
   ```

2. **Connect Local Repository**
   ```bash
   git remote add origin https://github.com/your-username/tumor-detection-segmentation.git
   git push -u origin main
   ```

3. **Invite Collaborators**
   - Add team members with appropriate permissions
   - Set up branch protection rules
   - Configure repository settings

### Future Enhancements
- Set up GitHub Actions for CI/CD
- Implement automated testing pipeline
- Add code coverage reporting
- Create documentation hosting
- Set up issue and project management

## 📞 Support

If you encounter any issues with Git setup:
1. Check that Git is installed: `git --version`
2. Verify remote connection: `git remote -v`
3. Check branch status: `git status`
4. Review commit history: `git log --oneline`

Your repository is now ready for collaborative development! 🎉
