Introduction

Apply source control to your scientific code base

What you're reading is a guide to help non-IT background researchers and students manage code better.

From a personal perspective, the ad hoc way is becoming incapable to mange code and track changes efficiently once the code base becomes large. In a broader sence, we face reproducibility issues all the time for code in the public domain. Although Git is not the tool to deal with this directly, it significantly help producing higher quality code base, for others to read, study and execute.

The aim of this doc is

• to provide a gentle introduction to Git, so that you can continue on other deeper books

• to emphasize the practice of code management and version control. so that together we can contirbute to the reproducibility of public code.

We wish this doc can provide a guide, especailly for students who're relatively new to coding. The earlier you develop a good habbit, the longer the benefit. The doc starts with theories, moves on to practices, then ends up with recipes. For students, familiarity with basic concepts and basic operations will be sufficient for most tasks. The doc will be constantly revised, espacially with examples and illustrations. Some parts are still in progress.

Acknowledgement goes to the BiRT (Bio-focused Radiation Therapy) team in USyd, especially Erin Wang, in providing valuable feedback. Any further feedback and suggestions are warmly welcomed. Please contact [e-mail]