flowchart TD
classDef layer fill:#f7f9fc,stroke:#c7d2e0,color:#1f2933;
P["<b>Preface and Introduction</b><br/>what this is, who it is for"]:::layer
A["<b>Part 1: Pedagogy</b><br/>why the workshop is shaped this way"]:::layer
B["<b>Part 2: Prerequisites</b><br/>accounts and software, for learner and instructor"]:::layer
C["<b>Part 3: Three-org setup</b><br/>create the iteration org and the website"]:::layer
D["<b>Part 4: Delivering the session</b><br/>pre-flight checks and the run of show"]:::layer
E["<b>Part 5: Reusing and re-running</b><br/>next iteration, license, citation"]:::layer
F["<b>Appendices</b><br/>printable checklists, the concept drawings, learner personas, references"]:::layer
P --> A --> B --> C --> D --> E --> F
1 Introduction
1.1 The workshop in one page
Git for Scientists is a four-hour, hands-on workshop, taught in person; the delivery mechanics (a done-signal, handouts, the regroup rhythm) have a video-call variant so remote participants can follow along (Chapter 11). It teaches researchers the foundations of Git and GitHub, with collaboration as the central theme. Learners leave able to create and clone repositories, work through a Git cycle (pull, stage, commit, push), use branches, and open and merge a pull request.
The focus is doing all of this through the point-and-click interface: the buttons and menus in RStudio and on the GitHub website, not commands typed at a prompt. Researchers do not need to memorize Git commands to collaborate well, and starting with the graphical interface lowers the barrier and keeps attention on the workflow rather than on syntax.
The workshop assumes learners can already use R and RStudio at a basic level: install a package, run a script, edit a document, find their way around the RStudio IDE interface. Git is the new thing; R is the familiar ground it stands on.
Along the way, learners pick up side benefits almost for free: a little more comfort with R and RStudio, a first taste of Quarto for authoring, and reversibility as a habit. There is no terminal work in the base workshop. Working with Git at the command line matters less than it used to, now that agentic coding tools can drive Git on your behalf, so this workshop builds confidence with the concepts and vocabulary first. That foundation is exactly what a follow-up workshop on agentic tools builds on. Chapter 3 says more about this.
1.2 How this handbook is organized
Read the parts in order the first time through. Parts 2 and 3 are the setup core: the checklists there get you from nothing to a working course infrastructure. Part 4 is the day itself. Part 5 is what you do afterwards and the next time round.
1.3 A map of the moving pieces
The workshop is not a single repository. It is a small family of repositories spread across three GitHub organizations, plus the accounts and software each person needs. Before any of that makes sense, it helps to see the whole board.
flowchart TD
classDef layer fill:#f7f9fc,stroke:#c7d2e0,color:#1f2933;
P["People<br/><b>Instructor</b> and <b>Learner</b>"]:::layer
A["Accounts and software<br/>GitHub account · R and RStudio · Git · personal access token"]:::layer
O["Three GitHub organizations<br/><b>gitforsci</b> (handbook, citation, DOI)<br/><b>gitforsci-dev</b> (templates, material)<br/><b>gitforsci-00x</b> (one per cohort)"]:::layer
P --> A
A --> O
Read it top to bottom. People (you and your learners) each need the accounts and software in the middle row. Those, in turn, are what let everyone work across the three GitHub organizations at the bottom: the instructor sets up the iteration org from the templates in the development org, the canonical citation flows down from the central org, and learners live in the iteration org. The detail of those three organizations is the whole of Part 3 (Chapter 7).
The detail comes later. Part 2 covers the accounts and software box, and Part 3 covers the three organizations. The point of the map is that everything in this handbook is somewhere on it.