Developer documentation# Contributing & Guidelines: How to Contribute to PANORAMA 🤝 Quick overview 🚀 Development Setup Our Development Workflow Coding Standards 📝 Writing Tests 🧪 Updating Documentation 📚 Pull Request Process 🔄 Tips and Tricks Getting Help 🆘 Recognition 🌟 Ready to Contribute? 🎉 Development Methods and Best Practices 💻 Setting Up Your Development Environment Code Style and Formatting Writing Clean, Maintainable Code Error Handling and Validation Performance and Optimization Code Organization Git Version Control Guidelines 🗃️ Understanding Our Branch Structure 🌿 Versioning and Releases 🏷️ Creating a Pull Request 🔄 Keeping Your Branch Updated Getting Help 🆘 For Contributors 🌍 Testing Guidelines for PANORAMA 🧪 What We’re Testing 🔭 General Testing Philosophy 📝 Setting Up Your Test Environment 🛠️ Running Tests ▶️ Test Quality and Coverage 📈 Working with CI Getting Help with Testing 🆘 For New Contributors 🌍 Building the Documentation 📚 Installing Documentation Dependencies 📦 Building and Previewing Documentation 🔨 Modifying Existing Documentation ✏️ Adding to Existing Documentation ➕ Creating Documentation from Scratch 🏗️ Getting Help 🆘 Tips and Tricks for PANORAMA Developers Table of Contents Code Quality Fundamentals Testing Strategy Debugging and Profiling Git Workflow Common Pitfalls 🚧 Codebase Internals: Class Architecture Inheritance overview Pangenome layer Gene family layer Region layer Systems layer How the layers connect Key PPanGGOLiN touchpoints Detection Workflow Prerequisites Step-by-step pipeline Data-flow summary Key parameters and their effect Compare Workflow Shared infrastructure (panorama.compare.utils) Spots comparison (panorama.compare.spots) Systems comparison (panorama.compare.systems) Parallel execution I/O Layer Module overview HDF5 structure Reading HDF5 files Writing HDF5 files Flat file outputs Adding a Subcommand 1. Implement the module 2. Register common arguments 3. Wire into main.py 4. Logging convention Checklist
