clean-code
Training materials and slides for courses on version control, clean code and documentation with practical examples and exercises in Python and R
Course on version control, clean code and documentation
A 4-day hands-on course teaching researchers how to write maintainable code, document effectively, and collaborate using Git and GitHub. Includes practical examples in Python and R, plus AI-assisted coding workflows with Claude Code and PyCharm.
Course Structure
Day 1 (3 hours): Git, Documentation & GitHub - Version control basics and collaborative workflows
Day 2 (6 hours): Clean Code & AI-Assisted Coding - Code quality principles, file structures, and hands-on AI tools session
Day 3 (3 hours): Advanced Tools & Publishing - PyCharm integration, Sphinx documentation, GitHub-Zenodo pipeline
Day 4 (3 hours): Bring Your Own Data - Apply learned concepts to your own research projects
See detailed program for full schedule.
Target Audience
Researchers and graduate students working with code (Python, R, or similar) who want to improve their software development practices. Basic programming experience required.
Creator
These materials were created by the University of Basel’s Research and Infrastructure Support RISE (rise@unibas.ch) between 2024 and 2026.
File Structure
The file structure mirrors the outline of the course:
- Introduction - Full course overview and detailed 4-day program
course/intro - Git - Version control basics with Git
course/git - Documentation - Documentation principles with Python examples (Sphinx, docstrings)
course/docs - GitHub - Collaborative workflows and GitHub-Zenodo integration
course/github - Clean Code in Context - File structures, data formats, and coding best practices
course/clean_code_in_context - AI-Assisted Coding - Using Claude Code with PyCharm for refactoring and documentation
course/ai_tools
Upcoming and past course dates
- 2026-01-12, 2026-01-19, 2026-01-26 and 2026-01-28: course “Clean Code, Documentation & Version Control”, WWZ / S16 / Peter Merian-Weg 6, Basel, course details
- 2025-03-03, 2025-02-10 and 2025-02-12: course “Clean Code, Documentation & Version Control”, WWZ / S16 / Peter Merian-Weg 6, Basel, course details
- 2024-04-10, 2024-04-11 and 2024-04-13: course “Clean Code, Documentation & Version Control”, WWZ / S16 / Peter Merian-Weg 6, Basel, course details
For Instructors
These materials are designed to be modular and adaptable:
- Each module contains slides/notes that can be presented directly
- Hands-on exercises included in relevant sections
- Timing suggestions provided in the detailed program
- Prerequisites: Participants should have WSL installed (Windows), PyCharm IDE, and basic programming knowledge
License
This work is licensed under a Creative Commons Attribution 4.0 International License.