Basics and motivation

Questions

• What is version control and why?

• What are commits and branches?

• What are forks and clones?

Objectives

• Get a mental representation for commits and branches.

• Understand the difference between forks and clones.

• Understand the difference between Git and GitHub.

What we will not cover

• Command line interface

• Cloning using SSH protocol and SSH keys

• Rebasing and squashing

• Many Git tricks which can be explored later

Version control

Why version control?

Version control is the answer to these questions:

• “It broke … hopefully I have a working version somewhere?”

• “Can you please send me the latest version?”

• “Where is the latest version?”

• “Which version are you using?”

• “Which version have the authors used in the paper I am trying to reproduce?”

• “Found a bug! Since when was it there?”

• “I am sure it used to work. When did it change?”

What are version control tools?

• Version control is a tool that can record snapshots of a project.

• You can think of version control like regularly taking a photo of your work (movie sets take regular polaroids to be able to recreate a scene the next day).

Snapshots (commits) in the EHT-imaging repository.

What we typically like to version control (or “snapshot”)?

• Software (this is how it started but Git/GitHub can track a lot more)

• Scripts

• Documents (plain text file much better suitable than Word documents)

• Manuscripts (Git is great for collaborating/sharing LaTeX manuscripts)

• Configuration files

• Website sources

• Data

Why are snapshots valuable? Reproducibility!

• We can always go back if we make a mistake.

• We can test new ideas without editing the working version

• If we discover a problem, we can find out when it was introduced.

• We have the means to refer to a well-defined version of a project when sharing, collaborating, and publishing.

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Difference between Git and GitHub

Git

• Tool that can record and synchronize snapshots.

• Not the only tool that can record snapshots (other popular tools are Subversion and Mercurial).

• Not only a tool but also a format that can be read by many different tools.

GitHub

• Service that provides hosting for Git repositories with a nice web interface.

• Not the only service that provides this (other popular services are GitLab and Bitbucket).

GitHub Desktop

• Graphical user interface to Git and GitHub which runs locally on your computer.

• There are other tools that can do this, too (e.g. Sourcetree).

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Commits, branches, repositories, forks, clones

• repository: The project, contains all data and history (commits, branches, tags).

• branch: Independent development line, often we call the main development line master.

• commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

• tag: A pointer to one commit, to be able to refer to it later. Like a sticky note that you attach to a particular commit (e.g. phd-printed or paper-submitted).

• cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

• forking: Taking a copy of a repository (which is typically not yours) - your copy (fork) stays on GitHub and you can make changes to your copy.

GitHub file view of the EHT-imaging repository. This is the version of all files at a single point in time.

Github history view of the EHT-imaging repository. This is the progression of the repository (with the commit message over time).

Network graph of all commits in the EHT-imaging repository. This shows the relationship between different forks of people who are contributing and sharing code.

Interesting repositories to explore these concepts

• Event Horizon Telescope imaging software

  • Repository: https://github.com/achael/eht-imaging

  • Commits, branches, forks: https://github.com/achael/eht-imaging/network

• Activity inequality study

  • Contains data and code necessary to create figures from their article.

  • Data: https://github.com/timalthoff/activityinequality/tree/master/data

• FiveThirtyEight story Why We’re Sharing 3 Million Russian Troll Tweets

  • Contains data and readme file, no code.

  • Data: https://github.com/fivethirtyeight/russian-troll-tweets

• The NY Times Coronavirus (Covid-19) Data in the United States

  • Contains data, readme, license, but no code. As of 2020.april, being updated every day.

  • Data: https://github.com/nytimes/covid-19-data

  • Website: https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html

• CSV exports of the Getty Provenance Index

  • Data: https://github.com/thegetty/provenance-index-csv

• Entire books are written using Git/GitHub:

  • https://github.com/rust-lang/book

  • https://github.com/ropensci/dev_guide

  • https://github.com/alan-turing-institute/the-turing-way

• Papers under open review:

  • https://github.com/openjournals/joss-reviews/issues

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Why use repositories? Think of your usecases for the following:

• All changes are recorded.

• We do not have to send changes via email.

• We can experiment with several ideas which might not work out (using branches).

• Several people can work on the same project at the same time (using branches).

• We do not have to wait for others to send us “the latest version” over email.

• We do not have to merge parallel developments by hand.

• Group-based access model where shared access is the default, instead of everything fundamentally owned by individuals who manage sharing as-needed: with Git you can easily have collaboration be the default.

• It is possible to serve websites directly from a repository.

Discussion: workflows without version control

• How have you solved these in the past without version control?