8 Git (Version Control)

Author: Charles J. Geyer

8.1 License

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (http://creativecommons.org/licenses/by-sa/4.0/).

8.2 R

• The version of R used to make this document is 3.5.1.

• The version of the rmarkdown package used to make this document is 1.10.

• The version of the knitr package used to make this document is 1.20.

8.3 Version Control

8.3.1 What is It?

• revision control

• version control

• version control system (VCS)

• source code control

• source code management (SCM)

• content tracking

all mean the same thing.

It isn’t just for source code. It’s for any “content.”

I use it for

• classes (slides, handouts, homework assignments, tests, solutions),

• papers (versions of the paper, tech reports, data, R scripts for data analysis),

• R packages (the traditional use of source code control, although there is a lot besides source code in an R package),

• notes (long before they turn into papers, I put them under version control).

8.3.2 Very Old Fashioned Version Control

asterLA.7-3-09.tex    asterLA.10-3.tex
asterLA.7-16.tex      asterLA.10-3c.tex
asterLA.7-16c.tex     asterLA10-4.tex
asterLA.7-19.tex      asterLA10-4c.tex
asterLA.7-19c.tex     asterLA10-4d.tex
asterLA.7-19z.tex     asterLA01-12.tex
asterLA8-19.tex       asterLA01-12c.tex
asterLA8-19c.tex      asterLA01-20.tex
asterLA.9-1.tex       asterLA01-20c.tex
asterLA.9-1c.tex      asterLA02-22.tex
asterLA.9-11.tex

A real example, file names of versions of a paper I wrote with a co-author without version control. This works but is highly sub-optimal. Only one author can work at a time because there is no good way to merge simultaneous changes. Nor is there any obvious ownership of the versions. It is hard to tell who did what when.

Using Dropbox for version control isn’t any better.

8.3.3 A Plethora of Version Control Systems

Ripped off from Wikipedia (under “Version control”).

Local Only	Client-Server	Distributed
SCCS (1972)	CVS (1986)	BitKeeper (1998)
RCS (1982)	ClearCase (1992)	GNU arch (2001)
	Perforce (1995)	Darcs (2002)
	Subversion (2000)	Monotone (2003)
		Bazaar (2005)
		Git (2005)
		Mercurial (2005)

There were more, but I’ve only kept the ones I’d heard of.

Don’t worry. We’re only going to talk about one (git).

8.3.4 Why?

Section 28.1.1.1 of the GNU Emacs manual.

Version control systems provide you with three important capabilities:

• Reversibility: the ability to back up to a previous state if you discover that some modification you did was a mistake or a bad idea.

• Concurrency: the ability to have many people modifying the same collection of files knowing that conflicting modifications can be detected and resolved.

• History: the ability to attach historical data to your data, such as explanatory comments about the intention behind each change to it. Even for a programmer working solo, change histories are an important aid to memory; for a multi-person project, they are a vitally important form of communication among developers.

8.3.5 Mindshare

Starting from nowhere in 2005, git and GitHub (https://github.com/) have gotten dominant mindshare, at least among free and open source systems.

In Google Trends, the only searches that are trending up are for git and github. Searches for competing version control systems are trending down.

Many well known open-source projects are on git. The Linux kernel (of course since Linus Torvalds wrote git to be the VCS for the kernel), android (as in phones), Python, Go, Ruby on Rails, Gnome, Qt, KDE, X, Perl, Vim, and GNU Emacs.

Some aren’t. R is still on Subversion. Firefox is still on Mercurial.

8.4 Git

8.4.1 Git versus GitHub

Git is a version control system. It is a command line program that can be used by itself (and, in fact, is best used that way).

GUI applications are available on all platforms to dumb down Git with menus and buttons.

GitHub is a company (recently purchased by Microsoft) that is just as famous as Facebook or Google in the geek world. It offers “social coding.” Thus it is something like Facebook for software developers. You can use git without GitHub (or one of its competitors) but GitHub helps you show the world what you do and collaborate with the world.

One of the GitHub developers wrote the best book introducing Git; Pro Git.

Still, I want to emphasize that you do not need GitHub to use Git any more than you need RStudio to use R.

8.4.2 Git and GitHub and RStudio

RStudio facilitates using Git for R projects. It seems to require also using GitHub (but this can be worked around).

But if you only know how to use Git via RStudio, you will not know how to use Git for non-R projects.

8.4.3 Getting Git

Type ``git’’ into Google and follow the first link it gives you http://git-scm.com/.

Under “downloads” it tells you how to get Git for Windows and for Mac OS X.

If you have Linux, it just comes with (use the installer for your distribution).

E. g., on Ubuntu

sudo apt-get update
sudo apt-get install git

8.4.4 What?

From Wikipedia under Git:

• Torvalds has quipped about the name git, which is British English slang meaning “unpleasant person.” Torvalds said: “I’m an egotistical bastard, and I name all my projects after myself. First ‘Linux’, now ‘git’.”

• The man page describes Git as “the stupid content tracker”.

From memory:

• Linus has also said that it was a short name that hadn’t already been used for a UNIX command.

8.4.5 Using Git

8.4.5.1 From the Command Line

There is only one command to use Git and it is called git. The first command line argument specifies one of many subcommands.

git help

shows the frequently used subcommands (many more than we will discuss here).

As this also says at the bottom git help -a shows all subcommands and git help -g shows “concept guides.”

For example

git help everyday

shows about 20 git subcommands that are enough for straightforward use of git. (We won’t even discuss that many.)

8.4.5.2 With a GUI Application

We won’t discuss this. They are all different.

If you are using a GUI application there is usually a way to get a UNIX command line. So anything that cannot be done graphically (menus and buttons, drag and drop) can still be done. The GUI is not as helpful as you might think.

8.4.5.3 With RStudio

It is hopeless to try to describe how to do anything with a WIMP application like RStudio. If it isn’t obvious, you’re in trouble.

Nevertheless, I made detailed instructions for how to avoid almost everything below and just use RStudio to do the simplest baby project. They are https://github.com/IRSAAtUMn/RWorkshop18/blob/master/notes/08-git.md.

8.5 Tell Git Who You Are

Before doing anything else. You have to tell Git who you are.

The UNIX commands

git config --global user.name "Charles J. Geyer"
git config --global user.email charlie@stat.umn.edu

do this. Of course, replace my name and e-mail address with yours.

If you are using a GUI application or RStudio, you probably need to escape to the command line to do this.

8.6 Starting a New Project Locally

Create a directory (a. k. a. folder) that will contain your project. Change directory into it and do git init. In UNIX (e. g. Linux or OS X), if the directory is Foo, then

cd Foo
git init

does the job.

The UNIX command

ls -A

shows that there is a new directory .git that is the hallmark of a git repository (“repo” for short). Now all Git subcommands work in this directory. The .git subdirectory is where Git stores all information it keeps track of. The rest of the directory is where you work.

If you have created the project using RStudio (as discussed above), then RStudio has run git init for you so you do not have to do it yourself.

8.7 Starting an R Project that will be a CRAN Package

If you are starting an R Project that will provide an R package, especially one intended to eventually be on CRAN, put the directory that contains the package in the Git repo. Do not try to make the Git repo the same directory as the R package. A Git repo contains a lot of stuff that an R package is not allowed to have.

8.8 Cloning an Existing Project

git clone git://github.com/cjgeyer/foo.git

clones an already existing project on which a lot of work has been done (and you get it all, including all of the version control history).

This requires that you have set up SSH for use with Git, which will be discussed below (Section GitHub and SSH keys).

Alternatively,

git clone https://github.com/cjgeyer/foo.git

(This is easier to use in the beginning but rapidly becomes a nuisance.)

This (clone an existing project) is what RStudio wants us to do and what we discussed above.

8.9 GitHub and SSH keys

To use GitHub productively, you need to make an SSH key pair and tell GitHub about the public key. This allows you to only type the SSH passphrase for the key once per reboot of your computer. This is secure. Your computer remembers what it needs to remember to access github (or use SSH in other ways without typing a password or passphrase, but we won’t cover that).

If you don’t do this, you will have to type your GitHub password frequently to use Git. This is a nuisance.

Recent updates of Microsoft Windows 10 have an OpenSSH client. AFAICS it works like it does on UNIX (Linux or OS X). It is a command line tool.

To make keys, you do from the command line

ssh-keygen

(this is one UNIX command, the hyphen is part of the name). Do what it says (successfully type the same passphrase twice and after having accepted the default location for the keys or having specified another location).

If you manage to do this successfully, there will be two new files

id_rsa
id_rsa.pub

created somewhere (the default is the .ssh subdirectory of your home directory). The first is the private key; the second is the public key.

Upload the public key to GitHub. Log in to your account; on the menu triangle next to your picture (upper right corner) choose “Settings”; on the settings page, choose “SSH and GPG keys” in the navigation area on the left; then on the page that takes you to click the green button labeled “New SSH key” and fill in the resulting text area. The title can be anything. Into the “Key” textarea you cut-and-paste the contents of the id_rsa.pub file. To get the contents in UNIX, do

cat id_rsa.pub

at the command line. What you see is what you cut-and-paste into the GitHub textarea. Then click the green button labeled “Add SSH key”. If you did this successfully, it will show the “fingerprint” of the key.

8.10 Halftime Summary

We are perhaps not halfway done, but the worst is over. Everything we have talked about so far only needs to be done once. It is painfully complicated, but once it is done you only need to do it again very rarely.

• You do git init at most once per project.

• You do git clone at most once per project on each computer you want to use for development.

• You create an SSH key at most once per computer you buy or get an account on (or after each reinstall of the operating system that blows away your account, if any).

• You tell GitHub about the SSH key once per SSH key.

• You tell Git your name and e-mail address similarly, at most once per per each computer you buy or get an account on.

Now we are ready to talk about everyday use of Git.

8.11 Everyday Git: One Computer, No Collaboration

8.11.1 Commits

What Git remembers is commits created by the git subcommand git commit.

If you never commit, then Git never does anything.

A Git commit consists of exactly what you say it does. Git allows precise control over what it does.

Most of the time you do not want such precise control. You just want Git to do the obvious. It can do that too.

So first the hard way, and then the easy way.

8.11.1.1 The Edit, Add, Commit Cycle.

There is no need to commit unless the Git repo has changed. So you edit some file in the repo so it is different from what Git remembers (in a previous commit).

Now if you want Git to remember the new version, you tell it first that you want it to remember the new version and second to do the commit. For example, if the file is foo.R, then

git add foo.R
git commit -m "A message about what the changes are"

does these two steps. If there are multiple files that have been edited, then you must do git add for each one you want changes remembered in the commit.

The -m argument to git commit is not necessary if you have told either UNIX or git what editor you use.

git config --global core.editor vim

or whatever editor you use instead of vim will do that job (this too is only done once per computer account you have). Then

git commit

will pop up an editor instance to type in the commit message.

8.11.1.2 The Cycle without Add Most of the Time

Doing a bunch of git add commands before each commit is what allows precise control of what you want the commit to remember.

But usually, you want the commit to remember all the changes to files Git is already tracking. One command does this:

git commit -a

(the -a flag tells Git to add all files it is already tracking).

When you use this pattern, you only need to say git add filename for new files either created since the last commit or not tracked before (not added in any previous commit).

8.11.1.3 Using RStudio

The edit-add-commit cycle can also be done entirely with RStudio.

One can edit the file in the upper left window and commit in the upper right window. Clicking the button labeled “Commit” will pop up a window in which you can select files to add, provide a commit message, and commit.

8.11.2 Status

Before doing a commit, it is often useful to do

git status

This tells you what would be committed (either with or without -a) if you were to do a commit. It also lists untracked files that will not be committed unless you do git add on them.

8.11.3 The File .gitignore

The file .gitignore in the top directory of the repo list files that git status and other git subcommands should ignore.

It uses wildcards (the gitignore documentation explains). For example, a .gitignore file that contains

*.html
*.Rout
*.pdf

ignores all files with those extensions (the character * is the wildcard character: it matches any string).

RStudio provides a .gitignore file in any Git repo it creates, but you may want to add to it.

8.11.4 Log

The command

git log

lists all commits that have been done, showing (by default) all the commit messages, the date and time, and the committer.

It provides an overview of the whole history of the repo.

8.11.5 Diff

The command

git diff

shows (by default) all of the changes between the “staging area,” which contains any results of git add that you may have done, and the working directory.

If have not done any git add since the last commit, then it shows all of your edits to tracked files since the last commit.

This can be very useful.

• If working with collaborators, this is Git’s competitor to “track changes” in Microsoft Office or Libre Office. It allows you to just look at changes.

• Even if there are no collaborators, it is often useful just to look at changes you made, especially just before a commit (to look even harder for mistakes).

8.12 Everyday Git: GitHub or Multiple Computers

If you made the repo by cloning a GitHub repository, then

git push origin master

will copy the latest commit to the GitHub repo. Now it is backed up there.

If you are using multiple computers, then you can use GitHub for communication between them. To start working on another computer, do all of the one time stuff (tell Git your name and e-mail address, make SSH keys, and put the public key on GitHub (there is a different public key for each computer, or at least for each computer account if different computers share file storage)).

Then clone (with git clone) the GitHub repo on this computer.

And you are ready to work on this other computer.

When you are finished working on this computer, do a commit, then

git push origin master

to push the changes to GitHub. Then on another computer (assuming no changes have been made to the working directory since the last commit on this computer; git status will tell you)

git pull origin master

will get all of the changes from GitHub.

Warning: Either of these (git push or git pull) can fail because you did effectively simultaneous (as far as Git can tell) editing on the two computers. Then you have to figure out how to fix the issue. The commands git merge and git stash may help. The former will be discussed below, but the latter we will skip. Most of the time, there will be no trouble (there is only trouble when you make changes on both computers with no commits; then you have to somehow reconcile the changes).

8.13 Everyday Git: Collaboration

8.13.1 Setup

When working with collaborators, the simplest workflow is for each collaborator to have their own GitHub repository and for everyone to pull from everyone else.

Suppose you are working with one collaborator https://github.com/jfmuggs who has an already existing GitHub repo named blurfle.

You clone it

git clone git://github.com/jfmuggs/blurfle.git

Now you have the blurfle repo on your computer. You have all of the code and all of the history. But you want to be able to push changes to where your collaborator (J. Fred Muggs, call him Fred) can see them. So you need a GitHub repo in your account.

So create an empty public repo (using the button labeled “New”). Don’t put a “README” file or a Gitignore file or anything. Then follow GitHub’s instructions to push the local repo to GitHub

git remote add origin https://github.com/cjgeyer/blurfle.git
git push -u origin master

except that doesn’t work because there is already a remote repository name origin (in the jfmuggs account). So let’s change that, and while we are at it, call neither of the GitHub repos origin.

git remote rename origin fred
git remote add me https://github.com/cjgeyer/blurfle.git
git push -u me master

Now there are two GitHub repos, both exactly the same (one in the jfmuggs account and one in the cjgeyer account). Of course, if you were doing this, you would replace my account name with yours.

Now Fred and I each have two repos, one local and one remote (on GitHub) that we can commit and push to. I also have another remote repo named (locally) fred that I can pull from. Fred should also give my GitHub repo a name; say he does

git remote add charlie https://github.com/cjgeyer/blurfle.git

8.13.2 Workflow

I make some changes and do a commit, then I push them

git push me master

Then I tell Fred “pull from me” (either by e-mail or by a GitHub pull request).

Then Fred can pull my changes

git pull charlie master

As always git push and git pull should only be done in a clean repo (just after a commit).

It gets complicated when we both make changes simultaneously. Then someone may have to reconcile any incompatible changes.

I get a “Pull from me” from Fred. I have uncommitted changes, so I do a commit (never pull when there are uncommitted changes). Then I do

git pull fred master

and it doesn’t work. Git says

Auto-merging foo.txt
CONFLICT (content): Merge conflict in foo.txt
Automatic merge failed; fix conflicts and then commit the result.

(if the file in which merge conflicts exist is named foo.txt and there may be multiple such files).

When we edit this file we see something like this

<<<<<<< HEAD
Foo that Foos is not static Foo.
=======
Foo! Bar! Baz! Qux!
>>>>>>> a26ce42b351548fb0efd61f7902358b1f69d3266

Schematically, this is

<<<<<<< HEAD

then some text that was my version of what goes here, then

=======

then some text that was Fred’s version of what goes here, then

>>>>>>> [some very long hexadecimal string, the SHA1 hash for the remote commit]

I edit the file, replacing all of this with what I think the text should be here (naturally, I think I’m right, although not always), in this case just the one line

Foo that Foos is not static Foo.

and then I have to do a commit (because the pull that failed with merge conflicts did not do a commit)

git commit -a

accepting the default commit message that Git suggests

Merge branch 'master' of github.com/jfmuggs/blurfle

Then I push and tell Fred to “Pull from me”.

Most pulls will work. If changes are made to two different parts of the file, Git just makes them automatically and commits the merge. It is only overlapping changes that must be fixed manually.

8.14 Wrapup

The Git subcommands

git init
git clone
git add
git commit
git diff
git status
git log
git help
git push
git pull
git remote

Allow you to do most of what Git can do for you. There are many other subcommands and a huge number of options to all subcommands, including the ones listed above (and we only discussed one such option, the -a option to git commit).

So there is a lot more to learn about Git. But this is enough for a start.