Version control, clean code and documentation

Comprehensive training materials for teaching researchers how to write maintainable, well-documented code and collaborate effectively using version control. Includes crash courses and a full 4-day course with practical examples in Python and R, plus AI-assisted coding workflows.

What’s Included

• Full 4-day course (15+ hours) covering Git, GitHub, clean code principles, documentation, AI-assisted coding, and research data publishing
• Quick crash courses (3-6 hours) for focused topics
• Hands-on exercises and real-world examples in Python and R
• Ready-to-use slides and materials for instructors
• New for 2026: AI-assisted coding session with Claude Code and PyCharm

Creator

These materials were created by the University of Basel’s Research and Infrastructure Support RISE (rise@unibas.ch) between 2023 and 2026.

Documentation

Read this file on GitHub pages.

Course Variants

Note that there are different versions of this course, see the changelog for details.

Full 4-Day Course

Course on version control, clean code and documentation in clean-code/course

Comprehensive 4-day hands-on course (15+ hours) covering:

• Git and GitHub fundamentals
• Clean code principles and file organization
• Documentation with Sphinx and docstrings
• AI-assisted coding with Claude Code and PyCharm (new for 2026)
• PyCharm integration and automated workflows
• Research data publishing with GitHub-Zenodo

Target audience: Researchers and graduate students wanting comprehensive software development skills

Crash Courses (Condensed Formats)

Crash-course on version control, clean code and documentation in clean-code/crash-course

Condensed version covering core topics in 3-6 hours.

Crash-course on version control and documentation with GitHub in clean-code/crash-course-github

Focused crash course on GitHub workflows and documentation.

License

This work is licensed under a Creative Commons Attribution 4.0 International License.