| No | Date | Title | Notes | Contents | Reading | Survey |
|---|---|---|---|---|---|---|
| 1 | 2023-10-20 | Introduction to version control | Organisational matters Overview of seminar sessions Computational reproducibility Introduction to version control Introduction to Git and its advantages |
Intro to version control | Course introduction survey | |
| 2 | 2023-10-27 | Command line | File Systems Benefits of the Command Line Basic Command Line commands |
Command Line | Command Line survey | |
| 3 | 2023-11-03 | Git Basics | Installation and configuration of Git Initializing a Git repository Basic Git commands Ignoring files with .gitignore Good commit messages |
Installation, setup, first steps with Git | Installation survey, Git Basics survey | |
| 4 | 2023-11-10 | Cancelled | Cancelled | |||
| 5 | 2023-11-17 | Basic Git workflow | Practicing basic Git commands Ignoring files with .gitignore Good commit messages |
First steps with Git | Git Basics survey | |
| 6 | 2023-11-24 | Cancelled | Cancelled | |||
| 7 | 2023-12-01 | Quarto workshop | Introduction to Quarto Usecases as a scientist Markdown Syntax Using code chunks |
Workshop Slides | ||
| 8 | 2023-12-08 | Git Branching and Merging | Understanding branches in Git Creating and switching between branches Merging branches: fast-forward and recursive Resolving merge conflicts Stashing and retrieving changes Undoing changes Removing files |
Branches | Git branches survey | |
| 9 | 2023-12-15 | Introduction to GitHub | Introduction to remote repositories Creating a GitHub account Creating and managing repositories on GitHub Cloning/Forking a remote repository Pushing and pulling changes Branching and merging in a collaborative environment Graphical User Interfaces (GUIs), e.g., GitKraken |
GitHub Intro | GitHub Survey | |
| 10 | 2023-12-22 | Repetition and practice | Initializing repository Staging and committing Creating and merging branches |
|||
| 11 | 2024-01-12 | GitHub: Collaboration | Organizing Git repositories and projects Collaborating with team members using issues and pull requests Using pull requests Understanding different Git workflows Introduction to Gitflow workflow Working with feature branches in Gitflow |
|||
| 12 | 2024-01-19 | GitHub: Advanced, Tags/Releases | README.md Licenses Contributions Forking Practicing GitHub workflow Introduction to tags and their importance Best practices for tagging in Git Integration with Zenodo |
|||
| 13 | 2024-01-26 | Introduction to DataLad - Version control of (large) datasets | Guest Lecture by Adina Wagner (DataLad Developer & Project Lead of the DataLad Handbook) | |||
| 14 | 2024-02-02 | Summary & Wrap-Up | Summary & Wrap-Up |
Effective Progress Tracking and Collaboration: An Introduction to Version Control of Code and Data
Session 1
October 20, 2023
Team
Who are you?
- Your name?
- Your preferred pronouns?
- Which study program are you currently enrolled in?
- What did you study before and where?
- What do you expect from this course?
- A fun fact about you?
- Your mood on rubber duck scale?
Collaborative notes
HedgeDoc (UHH Pad)
- HedgeDoc (UHH Pad)
- Notepad for Session 1
- Edit notes using Markdown (see HedgeDoc Features and Session 4)
- No account or log-in required
- Notes are public! Don’t use it for personal or sensitive data!
- One notepad per session
- Notepad will be locked at the next session
Two RA positions in our group!
Version Control of Code & Data
- 📓 Tasks: Support our teaching project!
- 📆 Duration: as soon as possible until March 31 2024
- 🕐 Time: flexible, up to 37 hours / month (WHK)
- 💰 Salary: 12.00 € / hour (SHK) / 13.95 € / hour (WHK)
- ✉️ Contact: lennart.wittkuhn@uni-hamburg.de
Memory reactivation in older adults
- 📓 Tasks: Support of fMRI data collection
- 📆 Duration: as soon as possible
- 🕐 Time: flexible, 60 - 80 hours / month
- 💰 Salary: 12.00 € / hour (SHK) / 13.95 € / hour (WHK)
- ✉️ Contact: erc-studies-luv.psych@uni-hamburg.de
Why we need version control …
… for code (text files) 
… for data (binary files) 
When everything is relevant …
… track everything.
What is version control
“Version control is a systematic approach to record changes made in a […] set of files, over time. This allows you and your collaborators to track the history, see what changed, and recall specific versions later […]” (Turing Way)
keep track of changes in a directory (a “repository”)
take snapshots (“commits”) of your repo at any time
know the history: what was changed when by whom
compare commits and go back to any previous state
work on parallel “branches” & flexibly “merge” them
“push” your repo to a “remote” location & share it
share repos on platforms like GitHub or GitLab
work together on the same files at the same time
others can read, copy, edit and suggest changes
make your repo public and openly share your work
What are git and DataLad?
- most popular version control system
- free, open-source command-line tool
- graphical user interfaces exist, e.g., GitKraken
- standard tool for most (all?) software developers
- 100 million GitHub users 1
- “git for (large) data”
- free, open-source command-line tool
- builds on top of git and git-annex
- allows to version control arbitrarily large datasets 2
- graphical user interface exists: DataLad Gooey
Note: We will mainly focus on Git and only refer to DataLad as an outlook.