Introduction to GitHub

MMED 2024

Carl

Slide Set Citation: DOI:10.6084/m9.figshare.5043139

The ICI3D Figshare Collection

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Goals

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• Understand why we use version control

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• Understand GitHub basic commands

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• Be able to use GitHub for your projects

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What is version control?

• "...the management of changes to documents, computer programs, large web sites, and other collections of information." ~ Wikipedia, Version control

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What is Git?

• "...a distributed version-control system for tracking changes in source code during software development." ~ Wikipedia, Git

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Benefits of using Git

modified from SEAMS

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• Roll-back: access to previous versions (while keeping your directories neat)
• Tracking: easily compare versions
• Accountability: see who did what and when
• Branching: have both working and development versions without duplication
• Comprehensibility: document changes with helpful comments

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Distributed version control system

Getting started on GitHub

• Command line (Git Bash, terminal)
• GitHub Desktop
• GitKraken
• …

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Getting started with your terminal

• pwd

Prints current working directory

• cd

Change directory

• mkdir

Make directory

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Exercise 1

• Open a terminal / Git bash
• Figure out where you are (eg: pwd)
• Navigate to the directory where you will store your MMED files (eg: cd path)
• Create directory for the git session (eg: mkdir MMEDGit)
• Change into the directory (eg: cd MMEDGit)

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Getting started on GitHub

• git clone

Clone a remote repository to your local computer

• cd

Change directory

• cd ..

Change directory one up

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Exercise 2

• on Github: Fork the repository - this gives you a copy you control

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• Clone your fork repository to an appropriate location on your local machine (eg: git clone https://github.com/ICI3D/Sandbox.git)

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• Change into the directory of the cloned repository (eg: cd Sandbox)

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Getting started on GitHub

• git pull

Pulls recently modified files from the remote repository to the local repository

• git status

Info about modified files

• git add file1 file2

stages the changes you made

• git commit –m “descriptive message”

Commits staged files

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Exercise 3

• Check the status of your repo (eg: git status)
• Open Participants2023_XXX.md with notepad

Edit file

Rename it as <your name>.md

Save file

• Check status (git status)
• Add name.md (eg: git add name.md)
• Commit files (eg: git commit –m “message”)

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Getting started on GitHub

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• git pull
• Pulls recently modified files from the remote repository to the local repository

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• git push
• Pushes files to remote repository

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Exercise 4

• Pull files from your remote repo to the local repo (eg: git pull)
• Push the modified files to the remote repo (eg: git push)

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Git commands chart

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clone

CONFLICT RESOLUTION

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CONFLICT RESOLUTION

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CONFLICT RESOLUTION

• pull = fetch + merge
• fetch always works (gets the information)
• merge usually works
• if it doesn't work, you have a conflict and you should try to resolve it:

identify conflicted files

edit them (however you usually edit files, or with nano)

fix them

add them (with add or at the same time as commit with -a)

• commit
• You should generally pull and make sure the merge is OK before you push.

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Each time you're ready to start working�

• Pull changes from origin/master (git pull)

If you're following the workflow there should not be conflicts, but if there are, see below

• Work on your files

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Each time you're ready to add content to the master branch

• Add and commit the changes that are ready for inclusion in origin/master (eg: git add <newfilesifany>; git commit -m '<your commit message>')
• Pull changes from origin/master (git pull)
• While there are conflicts

Resolve conflicts

Add and commit the new changes

• Push the changes to origin/master (git push)

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Troubleshoot

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This presentation is made available through a Creative Commons Attribution-Noncommercial license. Details of the license and permitted uses are available at� http://creativecommons.org/licenses/by-nc/3.0/

Title: {Introduction to GitHub}

Attribution: {Zinhle Mthombothi, Jonathan Dushoff & Juliet Pulliam}, Clinic on the Meaningful Modeling of Epidemiological Data

Source URL: {FIGSHARE URL}

For further information please contact admin@ici3d.org.

© {2019} International Clinics on Infectious Disease Dynamics and Data

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