lecture_lab07.qmd

---
title: "Lecture Lab 7"

author: "Nils Hofmann"
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    footer: "R for Bio Data Science"
---

## Which questions you can answer after today's lecture?

-   What does version control mean?

    -   How does Git and GitHub relate to this and what is their difference?

-   Why do Git and teamwork go hand in hand in data science?

-   How to use Git in a team

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## Git/GitHub - Why you should care

-   Teamwork and Git belong together in Data Science/Computer Science

-   GitHub and reproducible data science go hand in hand

-   There will be the moment when git will safe a lot of time in a big project

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## Things that happen without version control

![](images/memes_lab07.png){fig-align="center"}

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## Version Control - What and why

Think about your own a experiences with coding and how a system could remove these issues. Also what should this system have if you work with others on one project

Collect your ideas at the course [Padlet](https://padlet.com/s2206721/what-could-version-control-mean-yj6uerzlld8eu3rg)

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## Version Control - Definition

-   Version control is like a special "undo" button for your work.

-   remembers all the changes you make, so you can always go back to an older version

-   Lets you and your friends work on the same project without mixing up each other's changes.

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## Git - An open source version control system

-   installed locally on your device

-   keeps track of your file changes

    -   each change is indexed, so you can revert your current state

-   You interact with it via the terminal and control your **local repository**

![](images/Git_logo.jpg){fig-align="center"}

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## GitHub

-   Hub = Server where you can find, store and manage repositories

    -   everything is remote

-   a platform which provides a GUI for your repository and enables users to share code easily

-   you interact with it via an application or a web browser and control your **remote repository**

![](images/github_logo.jpg){fig-align="center"}

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## Git and GitHub together

-   GitHub allows you to have the project repository remotely

-   Multiple people who have git installed can then access this repository and create a copy

-   GitHub introduces visual features and eases the project management

![](images/git_github_basic_workflow.png){fig-align="center"}

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## Git - The basics

staging area = like a container with the changes for the next commit

![](images/git_workflow.jpeg){fig-align="center"}

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## Git - simple workflow when working together

![](images/workflow_git_simple.png){fig-align="center"}

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## If you forget to pull...

-   if you and your teammate work on the same codeline and both push the results to the remote repository, git will detect a merge conflict

-   conflict = two changes in the same line of the same file

    ! git will not know the version you prefer

![](images/no_pulling_conflict.png){fig-align="center"}

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## Git in RStudio

![](images/git_gui_rstudio.png){fig-align="center"}

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## Git in RStudio - Commit in GUI

-   commit message = very short summary of new changes to your project

![](images/git_gui_commiting.png){fig-align="center"}

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## GitHub - Overview

-   you can browse through all open source software

![](images/github_basic_overview.png){fig-align="center"}

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## GitHub - Use the README!

-   README.md is like a quarto document
    -   you can combine code and text to design a short "manual" for your users

![](images/readme_github.png){fig-align="center"}

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## Git - working together with clone or fork

-   you can create a copy of the current state of the project by cloning or forking

    -   cloning: work in same remote repository

    -   forking: create and work in your own remote repository

![](images/fork%20and%20clone(2).png){fig-align="center"}

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## Git - When should I use clone and fork now?

-   it is a question of:

    -   How much control do I want?

    -   How do I want to continue with the project as a collaborator?

-   fork = you will have complete control over the repository

    -   **BUT** your collaborators will not be able to apply and use your changes

-   If you **plan to contribute** to a target repository you typically **clone it**

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## Git - Branches

-   branch: new **separate** and **isolated** version of the mother branch

    -   useful for: experimenting, bug fixing, adding features

    -   see it as a structural component for **organizing a project**

![](images/git_branch_example.png){fig-align="center"}

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## Git - Merge

-   helps to combine changes from two branches into a single branch

-   **current branch**: The branch to be merged

-   **target branch**: The branch in which we want to merge the current branch

-   Why F in merged target branch?

    = new index for a new commit

![](images/git_merge.png){fig-align="center"}

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## Questions? ...