Research Software Engineering

• Computational Project
  • Definition
  • Good Scientific Practice
• 4 Pillars of SoC
  • The Four Pillars of SoC
  • Project Scaffolding
  • Template Repository
• Introduction to Version Control
  • Why Use Version Control?
  • Git Basics
  • Basic Git Workflow
  • Versioning
  • Further Resources and Topics
• Project Documentation
  • Why Document?
  • The README.md File
  • Project Title & Description
  • Installation & Usage & Methodology
  • Data & Licensing & Citation
  • Acknowledgments & Contributing & Contact
• Extended Documentation
  • Extended Documentation Requirements
  • Documentation Tools and Hosting
  • Building Documentation with Sphinx
• Managing Data
  • Linking Data to a Project
  • Versioning Data 1.0
  • Versioning Data 2.0
  • Accessing Object Storage
  • Managing Hugging Face Models
• Code Structure
  • Codebase Architecture
  • The src/ Layout
  • Testing and Documentation
  • Dependency Separation via pyproject.toml
  • Container Blueprints
• Environments 1.0
  • Python Environments
• Primer on Software Development
  • Why Software Development Principles?
  • Good Coding Practices
  • Orthogonal Code
  • The DRY Principle
  • Single Source of Truth (SSOT)
• Software Development Strategies
  • Rubber Ducking
  • Functions & Classes
  • Unit Testing
• Refactoring
  • Definition
• Notes on Python
• Efficiency in Python
  • Slow & Popular
  • Python’s Elephant in the Room
  • Gotcha 1: Parallelization
  • Gotcha 2: Context Switches
  • Profiling and Debugging
• Primer on Parallelism
• Primer On Parallelism
• Primer on Parallelism
  • Implementing Parallelism: Multi-Threading vs. Multi-Processing
  • Parallelism in Python: Capabilities and Constraints
• Environments 2.0
  • Virtualized Environments