git

• Version Control System
• Developed by Linus Torvalds to work on the Linux Kernel with mutliple people
• Mainly for Code, but useful for many other things

Why Version Control?

• “forces” some good habits
  • structured thinking
  • structured working in small chunks
  • goal-oriented
• (supports Open-Source development)

Get git

• https://git-scm.com/download/
• preinstalled on most GNU/Linux distributions
• GUI Versions available

git Workflow

• Application with a learning curve
• Simple but easy to mess something up
• Core unit: A repository

git init    # to start

git status # to get infos

git add    # to add files to the tracking system

git commit # to define changed files as the new standard

Git Branches - The Tree Model

https://bluecast.tech/wp-content/uploads/2019/09/git-switch-branch

git branch # to create a new branch

git switch # to switch between branches

git merge  # to merge two branches together

.gitignore

• exclude files and filetypes
• typical example for an R project:

.Rhistory
/data/
*.tif

GitHub

• platform for code sharing
• smooth integration into the git workflow
• makes collaborations easy
• “Developers Social Media”
• scientific communication

GitHub

• “Cloud storage” for git repositories
• Contains files, code, documentation, installation guide, (data)…

Additional Features

• Wiki
• Issue - Tracker
• Automation
• …

Github Related Commands

git remote    # to get infos about remote

git push      # to send commits to remote

git pull      # to download commits from remote

git clone     # to download a repository

Further Actions

• Forking
• Pull requests

Overview

https://miro.medium.com/max/700/1*9qX9F9MGsWKfcmgTOR9BPw.png

Rstudio Integration

Rstudio is a powerful user interface for git!

Real World Example: R packages

https://github.com/HannaMeyer/CAST

Package Page created with pkgdown

install.packages("CAST")

devtools::install_github(repo = "https://github.com/HannaMeyer/CAST")

remotes::install_github(repo = "https://github.com/HannaMeyer/CAST")

Package Page created with pkgdown: https://hannameyer.github.io/CAST

Real World Example: Bugfix

There is a small Bug in the r-package getSpatialData

https://github.com/16EAGLE/getSpatialData

In the file R/internal_clients.R Line 40:

# wrong:
lapply(uuid, function(x) content(.get(paste0(cred[3], "/odata/v1/Products('", x, "')/", field), cred[1], cred[2])))

# correct:
lapply(uuid, function(x) content(.get(paste0(cred[3], "odata/v1/Products('", x, "')/", field), cred[1], cred[2])))

Which workflow do you propose?

Real World Example: Publications

All computations were done in R (Version 4.0.2; [38]). All presented methods are provided as the R-package uavRmp (https://gisma.github.io/uavRmp/) and the Metashape Python Scripts (https://github.com/envima/MetashapeTools). - Ludwig et al. 2020

The ELC10 dataset is available here: https://doi.org/10.5281/zenodo.4407051 JavaScript and R code to reproduce ELC10 is available here: https://github.com/NINAnor/ELC10 - Venter et al. 2021

GitHub Pages

Github can serve webpages!

• markdown based
• syntax highlighting

Contents of docs/index.Rmd

---
title: "Introduction to Version Control"
author: "Marvin Ludwig"
output: html_document
theme: slate
layout: page
---

# Github Pages Demo

This is a demonstration for a simple but effective webpage on Github.

Click [here](presentation.html) for a presentation about git and Github.

Include Large Files

• DVC: Data Version Control
• LFS: Large File Storage

Track large files by including them with text-based pointers

outs:
- md5: 13ff4c5c6672752b90da533b408d0024.dir
  size: 1416965813
  nfiles: 13
  path: data/sentinel2

Online Learning Ressources

Beginner’s Guide to Git and Github

Youtube Video: University lecture with comprehensive technical explanation

Official Github Ressources: Quickstart Guide