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# Collaborative Document Unix & Git Workshop WUR June 22-23, 2026

Date: June 22-23, 2026.
Location: Wageningen University and Research

Welcome to The Workshop Collaborative Document.

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## 🫱🏽‍🫲🏻 Code of Conduct

Participants are expected to follow these guidelines:
* Use welcoming and inclusive language.
* Be respectful of different viewpoints and experiences.
* Gracefully accept constructive criticism.
* Focus on what is best for the community.
* Show courtesy and respect towards other community members.

## ⚖️ License

All content is publicly available under the Creative Commons Attribution License: [creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/).

## 🖥 Workshop website with program

* [Workshop website](https://4turesearchdata-carpentries.github.io/2026-04-22-tudelft/)

## Pre-workshop survey

Did you already fill in the [pre-workshop survey](https://carpentries.typeform.com/to/wi32rS?slug=2026-06-22-tudelft&typeform-source=4turesearchdata-carpentries.github.io)?

## 🙋Getting help

To ask a question, just raise your hand.

## Instructor

Leila Iñigo de la Cruz, Trainer of Digital Competencies at 4TU.ResearchData
John Bons, Research IT Consultant Department of Built Environment

## Helpers

Dylan Feldner-Busztin, Data Manager in the Research Center for Materials-Driven Regeneration, TU/e

Özgün Balaban, Postdoc, Built Environment, Information Systems in the Built Environment, TU/e

## Ice breaker Day 1

#### On the goat-scale, how are you feeling today?


1. A calm goat.
2. A happy goat.
3. A confused goat.
4. A stressed goat.
5. A focused goat.
6. A tired , need coffe ASAP goat.

**Name / role / github username / icebreaker answer**

## 🗓️ Agenda

April 22, 2026
Day 1 – Unix Shell & Git (Local)
• 09:30 – Welcome, installation check & housekeeping
• 09:45 – Introducing the Unix Shell
• 10:30 – Working with Files and Directories
• 11:15 – Break
• 11:30 – Pipes, Loops and Shell scripts
• 12:00 – Lunch
• 13:00 – Version Control with Git (Local Repositories)
• 14:45 – Break
• 15:00 – Tracking Changes & Commit History
• 16:30 – Wrap-up and End

April 23rd ,2026
Day 2 – Git remotes and Get to know 4TU.ResearchData
• 09:30 – Recap of local Git
• 09:45 – Remotes in Git
• 10:15 – Push/Pull to GitHub
• 10:45 – Break
• 11:00 – Collaboration practices
• 12:00 – Lunch
• 13:00 – Getting to know 4TU.ResearchData: The repository for the Natural Sciences and Engineering in NL.
• 16:00- Post workshop survey
• 16:30 – Wrap up and End

### Why teach Git on the command-line (Unix shell) rather than with a GUI (Graphical User Interface)?:

- **Deep conceptual understanding** (the CLI forces you to perform each Git operation explicitly, so you see exactly how things work, whereas GUIs often bundle actions behind buttons, obscuring the underlying mechanics.)

- **Environment-agnostic skills** (the Unix-shell CLI is consistent across Linux, macOS, Windows (via WSL) and remote/headless systems(HPC servers), while each GUI client has its own interface and may not be available in all environments.)

- **Scriptability for reproducibility and automation**: (CLI commands can be composed into scripts or integrated into automated pipelines—key for reproducible research)

## 🏢 Location logistics

* Coffee and toilets?
* In case of an emergency
* **Wifi**: Eduroam should work. Or tue-guest (4 hour tokens)

## 🧠 Collaborative Notes

- [SSH permission denied publickey](https://docs.github.com/en/authentication/troubleshooting-ssh/error-permission-denied-publickey)

- [Version Control Intro presentation](https://zenodo.org/records/19603828)

- [Unix shell Intro presentation](https://zenodo.org/records/19604954)

## Exercises

### Unix Exercise I

**Relative Path Resolution**
(https://swcarpentry.github.io/shell-novice/instructor/02-filedir.html)

Using the filesystem diagram below :
<img src="https://swcarpentry.github.io/shell-novice/fig/filesystem-challenge.svg" width="350" />

if `pwd` displays `/Users/thing`,what will `ls -F ../backup` display?

1. `../backup: No such file or directory`
2. `2012-12-01 2013-01-08 2013-01-27`
3. `2012-12-01/ 2013-01-08/ 2013-01-27/`
4. `original/ pnas_final/ pnas_sub/`

### Unix Exercise II

**List filenames matching a pattern**

https://swcarpentry.github.io/shell-novice/instructor/03-create.html#operations-with-multiple-files-and-directories

When run in the alkanes directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

1. ls *t*ane.pdb
2. ls *t?ne.*
3. ls *t??ne.pdb
4. ls ethane.*

### Git exercise I

- Create new repository and use the modify-add-commit cycle.

- Create and initialize a repository called ‘my-repo’
- Create a file ‘research.txt’ with the sentence “Science is awesome”.
- Add and commit the changes. Remember to use a meaningful message.
- Change sentence in ‘research.txt’ to “Science is messy” Add and commit.
- Create a folder called “raw-data”
- Ignore the raw-data folder and commit it
- ( bonus) Check your history log – you should have 3 commits.

## Lesson notes day I

Day 1

## Feedback
Day 1

+ (+) what went well

- (-) what could be improved

## Day 2

### Ice breaker Day 2

#### On the goat-scale, how are you feeling today?


1. A calm goat.
2. A happy goat.
3. A confused goat.
4. A stressed goat.
5. A focused goat.
6. A tired , need coffe ASAP goat.

**Name / icebreaker answer**

### Git exercise II

Final Exercise: Working with Issues and PRs

- Assignment:
- flow
Find issue as person "in the wild" → Fork → Clone → Create branch → Edit → add → commit (repeat) → Push to your fork → Open Pull Request
1. Write an Issue in your patients-analysis repo. Options:

- Add a multiplication function
- Improve calculate_mean with full documentation
- Create a README.md file

2. Pair up:

- Clone or fork each other’s repositories.
- Create a branch, solve the issue.
- Open a Pull Request with your changes.

3. Review and integrate PRs if possible.

4. Reflect:

- What worked well?
- What was confusing?
- Did you encounter merge conflicts?
- How would you improve the process next time?

## Lesson notes day II

## Post-workshop survey
Please fill in the [post-workshop survey](https://carpentries.typeform.com/to/UgVdRQ?slug=2026-06-22-tudelft)

## 📚 Resources

### Workshop materials

[Git Introductory slides](https://zenodo.org/records/19603828)
[Unix Introductory slides](https://zenodo.org/records/19604954)
[4TU.ResearchData slides](https://zenodo.org/records/15010667)

[Carpentry lesson on Unix](https://swcarpentry.github.io/shell-novice/index.html)
[Carpentry lesson on Git](https://swcarpentry.github.io/git-novice/index.html)

### Git and Unix
[Git cheat sheet](https://education.github.com/git-cheat-sheet-education.pdf)
[Unix cheat sheet](https://www.stationx.net/unix-commands-cheat-sheet/)
[Unix for data science](https://datasciencepractice.study/unix-systems.html)
[Git for Matlab](https://nl.mathworks.com/help/matlab/matlab_prog/use-git-in-matlab.html)
[Text editors for software development](https://coderefinery.github.io/installation/editors/#)
[Link to git visializing environment ](https://git-school.github.io/visualizing-git/) Usefull to doublecheck how git flow is working

### Project management with GitHub

[Planning and tracking work for your team or project using GitHub](https://docs.github.com/en/issues/tracking-your-work-with-issues/planning-and-tracking-work-for-your-team-or-project)
[Project planning for developers](https://github.com/features/issues)

### FAIR principles and reproducibility

[Scientific computing](https://scicomp.aalto.fi/scicomp/zen-of-scicomp/)
[Reproducible research video](https://youtu.be/MxZF1gEJoWw)
[Data + Code + Software = PDF - Slides to an overview on integrating data and software into a PDF.](https://zenodo.org/record/5508797)
[5 Recommendations for FAIR software](https://fair-software.nl/)
[Guide for Reproducible Research](https://the-turing-way.netlify.app/reproducible-research/reproducible-research.html)
[4TU.ResearchData community environment](https://community.data.4tu.nl/)
[4TU.ResearchData test environment](https://next.data.4tu.nl/)
[4TU.ResearchData ](https://data.4tu.nl/)

### Web Application Programming Interface (Web API) of 4TU.ResearchData

[Documentation](https://djehuty.4tu.nl/#x1-600005)

### More training we offer at 4TU.ResearchData

[Introduction to programming in research with Python](https://community.data.4tu.nl/introduction-to-programming-in-research-with-python/)

### Documentation about 4TU.ResearchData

[Documentation about 4TU.ResearchData](https://oit.tudelft.nl/FAIR4TU_Submission_Help/main/intro.html)