This course is coordinated with the doctoral program Staromics of CUSO, whose members have the priority.

Overview

Git is an open source, distributed, version control system for tracking changes in source code and
other types of text documents. Created by Linus Torvald and first released in 2005, Git has become
the de-facto standard for project source code management, and is extensively used both in open
source and commercial software development. The usage of Git is not limited to code development,
but can also be used to keep track of data analysis scripts and pipelines.
This 2.5 day course gives a very comprehensive introduction to Git and its most useful commands, as well as an introduction to collaborative workflows and to using GitHub. The last half-day of the course is optional.

Audience

This course is aimed at people with no or little knowledge of Git, who are interested in using a version control system for collaborative work, or simply to keep track of modifications in their
scripts/code base/files.
This includes people working on code development, but also scientists interested in improving the
reproducibility of their data analyses by keeping track of their scripts using version control.

Learning objectives

At the end of the course, the participants are expected to have understood and practiced the following:

• Introduction to Version Control Systems.
• Basic Git concepts: commits, the HEAD pointer and the Git index.
• Git branches: introduction to branched workflows and collaborative workflow examples.
• Branch management: merge, rebase and cherry-pick.
• Retrieving data from the Git database: git checkout.
• Working with remotes: share your work and collaborate.
• Basics of GitHub and GitLab.

Prerequisites

Knowledge/competencies:

The course is focused on using Git in command line mode (no graphical user interface). It is therefore necessary to have some basic knowledge of UNIX command line, e.g. how to change directory or how to edit a file in a command line editor such as vim/nano.
If you are not familiar with these UNIX fundamentals, we strongly recommend you complete the following e-learning module before the start of the course.

Technical

• Your computer must be instllaed with a recent version of Git. Git is available on all major platforms (https://git-scm.com/download).
• For online classes, you should also have a working microphone as some exercises involve collaboration/communication with other participants.

Schedule

Day 1:

• Introduction to version control systems and Git.
• Git basics: your first commit.
• Git concepts: commits, the HEAD pointer and the Git index.
• Git branches: introduction to branched workflows and collaborative workflow examples.
• Branch management: merge, rebase and cherry-pick.
• Retrieving data from the Git database: git checkout.
• Working with remotes: collaborating with Git.
• GitHub: a brief overview.

Day 2:

• Rewriting history: interactive rebase, git reset and commit amending.
• The detached HEAD state explained.
• The Git stash: Git’s “cut and paste” functionality.
• Git tags: label important commits.
• GitHub: creating a new project, adding new users and collaborating wit them.

Day 3 (half-day):

The last half-day of the course is optional and covers two Git extensions that can be useful in
certain scenarios:

• Git LFS: versioning large files with Git.
• Git submodules: embed a Git repository as a subdirectory of another Git repo.

Application

Registration fees for academics are 200 CHF.

Deadline for free-of-charge cancellation is set is set to 02/10/2023. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and Time

The course will take place at the University of Lausanne.

Our courses usually start at 9:00 and end around 17:00. Precise information about location and time will be provided to the participants on due time.

Additional information

Coordination: Grégoire Rossier

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact training@sib.swiss.