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Ten Simple Rules for Taking Advantage of Git and GitHub

DOI:https://doi.org/10.1371/journal.pcbi.1004947

Summarized by Patricia Kruisz, Herbert Michlmayr, Thomas Svoboda, Krisztian Twaruschek

Rule 1: Use GitHub to Track Your Projects

• Tony Rossini: “commit early, commit often, and commit in a repository from which we can easily roll-back your mistakes,”
• Recommended Reading: A quick Introduction to Version Control with Git and GitHub

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Version Control with IPython notebooks

Challenges

• IPython notebooks are based on the .json format and contain many different types of data (code, markdown, binary data i.e. images, metadata, ...)
• Basic version control (staging, committing) works, but more complex functionalities can be difficult or even make the file unusable { "cells": [ { "cell_type": "code",

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**Group 5 - Communicating with the remote repository**

Remote repository
  -	This command is used to create, view and delete connections to other repositories
  -	git remote command is an easier way to pass URLs to the commands (push, pull,…)
  -	Remote connections are more like bookmarks rather than direct links into other repositories
  -	However, the information is not automatically passed back and forth between repositories – it is necessary to
    manually pull upstream commits into their local repository or manually push their local commits back up to the central repository

Create and modify remote configurations:

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- git reset

It modifies the index (the so-called "staging area"). Or it changes which commit a branch head is currently pointing at. A reset is an operation that takes a specified commit and resets the "three trees" to match the state of the repository at that specified commit. Git reset should generally be considered a 'local' undo method because it adds complications when working with a shared remote repository. If we have a shared remote repository that has a commit pushed to it, and we try to git push a branch where we have reset the history, Git will catch this and throw an error. Git will assume that the branch being pushed is not up to date because of its missing commits. In these scenarios, git revert should be the preferred undo method.

A reset can be invoked in three different modes which correspond to the three trees:

• --soft – The staged snapshot and working directory are not altered in any way.

• --mixed – The staged snapshot is updated to match the specified commit, but the workin

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Git configuration, alias and using the .gitignore file

Git configuration

configuration files to determine non-default behavior:

level	file		command
system-wide	[path]/etc/gitconfig file	settings to every user and all repositories	$ git config --system
global	~/.gitconfig	specific to each user	$ git config --global
local	.git/config	in the Git directory/specific to a repository	$ git config --local

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Working with Branches

What are Branches?

• Branches in GitHub are a very easy way to work on a code file parallel, while the origin file stays untouched. In most other VCS you will need two files to do this.
• In Git, it is a lot less space consuming - you create Branches. Each Branch is a tip of a commit series. Because of this, Git only creates new Bubbles for the different parts between the files and reconstruct the files like it also does it normally.
• To summarize, Git Branches are only a history of commits divided from the main Branch at some point.