Version Control with Git

If you're like most scientists, you spend a fair amount of your "computer time" just trying to organize and keep track track of all of the files associated with your research projects. Among the many logistical headaches that you likely deal with on a daily basis are:

Updating files, like scripts or papers, without losing copies of your old version (Myfile_2014_01_v2_Sent_Final_FINAL_Submitted.doc)
Figuring out what changed between two versions of a file (When was the last time I updated the regression model?)
Maintaining multiple versions of files that started off the same but then diverged (I need to make a lab meeting version and a poster version of Figure 1, which are mostly the same but not exactly.)
Merging two divergent copies of a file (I want to add the Figure 1 changes from the poster into the file that makes the figures for my paper, but without losing all of the new stuff that I've added to the latter file.)
Sharing your files (and their history) with the world - or just a few collaborators.
Syncing versions of your project files across multiple computers and collaborating with colleagues on projects.

We've all developed various habits and protocols that we use (consciously or unconsciously) to manage these issues. The usual practice is often some combination of nested folders, file naming conventions, emailing files, cutting and pasting, and lots of opening-two-files-side-by-side and reading line by line.

In this lesson, we're going to look at a tool known as a version control system (VCS) that provides an integrated means of dealing with all of the above logistical issues. Specifically, we're going to learn the basics of git, which is rapidly becoming the most popular version control system in scientific software development.

The practice of using version control will pay dividends immediately from an organizational perspective, even if your projects are relatively small and you work on them alone. However, version control really starts to show its importance as the size of your projects grow. When you write a program that will be maintained on an ongoing basis (rather than just a one-off script for a single project) and when you try to start collaborating with other computational scientists, version control becomes a virtual requirement. Knowing how to work with version control systems will also be necessary if you ever want to contribute to existing open source scientific software packages, including IPython, numpy, and many of the other tools that we've been discussing.

Before we get started, we'll make sure you have all of the software and accounts that you'll need for this lesson and then discuss some basic background and terminology. We'll then proceed through each of the seven "headaches" above and see how we can make these less painful through judicious use of git. Finally, we'll close with a brief discussion of the difference between plain text and binary files, as these relate to version control, and talk through a few tips for writing papers.

The lessons below are really just an entry point into the world of git. For more information, and more detailed explanations of all that follows, have a look at the excellent free book Pro Git.

Installing and configuring git

To confirm that git is installed on your computer, open a terminal window and run the command

$ git --version

If this prints something like git version 1.8.3.4 (or any other version number), then you're ready to go. If you see git: command not found then you need to install git.

The easiest way to install git is to use one of the installers here. On Windows, you might want to instead install mysysgit which will also give you a bash-like command line environment. On Linux or a Mac, you can also install git through your package manager (on a Mac, you might be interested in trying homebrew).

Once git is installed, we will need to configure a few global options. The most important are to tell git your name and your email address, which will be used to identify your actions. To do this, run the following commands in a terminal session (using your name and email address):

$ git config --global user.name "John Doe"
$ git config --global user.email johndoe@example.com

Additionally, we want to make sure that git is going to use a useful text editor when necessary. If you're on a Mac or have installed nano using the Software Carpentry Windows installation instructions, you should run

$ git config --global core.editor "nano"

Before doing the above, you should try running the command nano in your shell to make sure that it opens. If you're on Linux (or otherwise prefer to use a different text editor like emacs or vim), you can enter something different here.

Note that this configuration information isn't sent anywhere - it's just saved in a file on your computer (specifically, a file named .gitconfig that is located in your home directory).

For the later parts of this lesson where we begin working with remote copies of our files, we'll need a non-local account to hold our uploaded files. The most popular site for doing this is Github, which is what we'll use here. To create an account on Github, simply go to http://github.com and sign up (it's free). A similar, though not quite a widely used, service is Bitbucket, which you may want to check out for your own uses later.

Getting started with git

The first step in using git is to select a project (i.e., a set of files in a directory that accomplish a defined research task) that you wish to manage with version control. You'll then create what's known as a git repository to contain and manage these files.

To start off, let's imagine that we have a project in which we're analyzing data from camera traps that have photographed the wildlife in a particular area. Our basic tasks are to read in the raw data, run a regression analysis, make a table, and make a figure. In practice, we would likely manage a simple analysis like this by placing all of our code into a single file, probably a hundred lines long or so, which is what we'll model here.

To keep things simple in this lesson, we won't actually write the code to perform these tasks - instead, we'll create the script file and add simple lines of pseudo-code to describe each action. (Incidentally, we'll actually review some real code to do this in a later lesson.)

To start off, our script file will contain the following text.

# Camera trap script

Read data file

Run analysis

Exercise 1

Using the terminal, navigate to a convenient location on your computer and make a directory called wildphoto. Inside this folder, create a text file called script.py that contains the text above.

Now, we'll set up a git repository for this folder by running the following command within that directory. Again, make sure that you're in the wildphoto directory before running this command.

$ git init
Initialized empty Git repository in /Users/jkitzes/wildphoto/.git/

As you can tell by the output of the git init command, initializing a repository involves creating a hidden folder, called .git, inside of the wildphoto folder. This hidden folder will contain all of the tracking information about your files. If you ever want to delete the git repository, so that you're back where you started without any version control history, it's actually as simple as just deleting this folder.

Now that you have your repository initialized, it's time to start tracking files. At this point, git is not paying specific attention to any files in this directory - if you'd like git to track a file, you have to tell git to track it. Any files that you don't tell git about will remain untracked.

To track a file, we need to add it to the repository. Once we've added a file once, git will watch it from then forward as we make changes to it. To add a file to a repository, we first need to review the three possible "locations" that a file can be in. These are

Workspace - a new file, or a change to a file that's already tracked (more on this later), that's sitting in your folder
Staging area (or index) - a temporary holding state where you line up all of the files or changes that you want to commit to your repository
Repository (or repo, for short) - git's "memory bank" that holds and tracks your files and changes to your files

Basically, the process of using git involves making edits in our workspace, adding these edits to our staging area (this is known as "staging"), then saving everything in the staging area to the git repository (this is known as "committing").

To get started, it's often a good idea to check in on git to see what it thinks is going on. To do this, we run the simple command

$ git status
# On branch master
#
# Initial commit
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#   script.py
nothing added to commit but untracked files present (use "git add" to track)

This information returned by this command tells us what git is thinking at the moment. In this case, git is telling us that we have an untracked file called script.py and that nothing is currently present in our commit (this is another way of saying that nothing is in our staging area). We'll talk about the meaning of "branch master" later on.

To add the file script.py to the staging area, we run the command

$ git add script.py

This command doesn't seem to do anything, but if we run git status again, we'll see its effect.

$ git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
#   (use "git rm --cached <file>..." to unstage)
#
#   new file:   script.py
#

Now we have the new file script.py in our staging area. If we wanted to, we could add other files, or make other changes, and add them all to the staging area as well. Remember, the staging area is a way of collecting any number of changes that you'd like to commit to the repository all at once.

A logical question at this point is why git bothers to have a staging area at all - why don't you just commit everything that's changed all at once to the repository? This boils down to a question of workflow. It is often the case that you'll make a bunch of changes to a bunch of files (possibly screwing up all sorts of things), but you don't necessarily want to add all of these permanently to the repository all at once. You may want to add them a few at a time, so as to better keep track of their history. Or you may not want to add some of them at all. The staging area basically helps you organize all of the changes that you've made into commits that you add to your repo, one by one, in some logical fashion that will be useful to you later on.

Finally, we end by committing our changes that are currently in the staging area to the git repository. To do this we run

$ git commit

When you do this, you will appear to be suddenly transported somewhere else in your terminal window (or a graphical text editor of some kind might pop up). Don't worry - all that has happened is that git has opened a text editor for you to enter a commit message. This is one of the most useful features of a version control system - each time you commit some set of changes to your repo, you get to enter a short description of what the change was and perhaps why you made it. This helps to track the history of the updates to your project files.

It's good practice to start by entering a short one line sentence to describe the commit in general terms. Often this is all that you'll need. If you want to capture more ideas, you can press Return twice to enter a blank line below the first sentence and then type as much information as you'd like.

You'll see that git has added some lines starting with # symbols to your commit message. Since anything starting with # is considered to be a comment and not included in your commit message, these lines are just for your information and you can safely ignore them.

So, in this case, a useful message might just be "Initial commit of script to analyze camera data". Go ahead and type that line at the top of the text editor, then save the file and exit the editor. In nano, you can just press Ctrl-x to exit, after which nano will ask you if you want to save the file. Press Y for yes and press Enter to accept the file name/location that it suggests.

Now you'll magically be dropped back into your terminal window, and you'll see that your command has printed output like the following.

$ git commit
[master (root-commit) beda5b7] Initial commit of script to analyze camera 
data
 1 file changed, 9 insertions(+)
 create mode 100644 script.py

The key information here is that we've successfully changed 1 file (script.py) by making 9 insertions (that's one for each new line of text in the file). You'll learn about the other information here as we go along.

So, what was the point of all that? The upshot is that the exact state of the file script.py that was in the staging area at the moment of our commit is now permanently stored and tracked in our version control system. No matter what changes we make to this file in the future, we can always easily come back to this version at any time, as we'll see later. We can also easily compare this version to other future versions.

To see a record of our previous commits, we can run the command git log, which will show us a history of our commits (so far, just this one initial commit).

$ git log
commit beda5b7b6fa4c3b8642c7d26b87f691fd6bcd8dc
Author: Justin Kitzes <jkitzes@berkeley.edu>
Date:   Mon Jan 13 16:07:01 2014 -0800

    Initial commit of script to analyze camera data

As before, we can check git status to see what git thinks is going on (typing these two words will soon become like a reflex).

$ git status
# On branch master
nothing to commit, working directory clean

Once again, we'll talk about the meaning of "branch master" later on. The second line, though, tells us that our working directory is "clean" (i.e., it matches the repository exactly), and as such there's nothing available to commit. In other words, we haven't changed anything since our last commit.

Having made our initial commit to track script.py, we can now get on with our actual research work of writing more code to perform more analysis. As we do so, our workflow will now include periodically committing our changes to the git repository so that we save a historical record of everything that we've done.

Now that you've got the basics down, we'll turn to our seven "headaches" and see how git can help us alleviate each of these.

1. Keeping version history

Probably the most basic logistical headache of computational research (or, really, any kind of research) is keeping track of old and new versions of files as they're updated. Whether you primarily work with Word documents or computer code, you probably have folders sitting around on your computer containing files like Analysis_v3.doc, Analysis_v4.doc, Analysis_v5_final.doc, etc. Or, if you like to live dangerously, maybe you only have file and rely on a backup system (like Time Machine or Dropbox) to retain snapshots of the file and pre-set time intervals, so that you can (in theory) got back to any moment in time and see what your file contained.

Rather than constantly using "Save As" on our files or relying on a backup system, we can instead use git to hold both old and new copies of our files for us. To see how this works, let's make a few updates to our file.

Exercise 2

Update this file two times, each time adding a new line to the script. For the first update, add a blank line under Run analysis and then a line reading Make table. Save this change, stage this change using git add, and then commit it, adding a useful commit message. Then, add another blank line under Make table followed by another line Make small figure, and commit this change as well. Run git log to see your three commits.

After making both of these changes, your script.py file should look like this.

# Camera trap script

Read data file

Run analysis

Make table

Make small figure

If we run git log again, we should see something like this.

$ git log
commit 89f54453b748131b87cee9d5742dd4412cd8183d
Author: Justin Kitzes <jkitzes@berkeley.edu>
Date:   Mon Jan 13 16:08:44 2014 -0800

    Add initial code to make small figure

commit 97e349856f3b3ee2647c327d3a609ff1dc9fae6f
Author: Justin Kitzes <jkitzes@berkeley.edu>
Date:   Mon Jan 13 16:08:20 2014 -0800

    Add code to make table

commit beda5b7b6fa4c3b8642c7d26b87f691fd6bcd8dc
Author: Justin Kitzes <jkitzes@berkeley.edu>
Date:   Mon Jan 13 16:07:01 2014 -0800

    Initial commit of script to analyze camera data

Pretty soon, our log of commits is going to start getting longer, and it will be helpful to have a better way of viewing our commit history. To help visualize our history better, try running the version of git log below, which adds some additional arguments.

$ git log --oneline --graph --decorate --all
* 89f5445 (HEAD, master) Add initial code to make small figure
* 97e3498 Add code to make table
* beda5b7 Initial commit of script to analyze camera data

You'll note that new version of our command this gives a simple list of our three commits, each represented by a * symbol. Following the * is a strange list of characters, which is known as a hash. A hash is a random string that is used as an identifier for each commit and can be used to reference the commit (we'll use these in just a moment). Note that your hashes will be different from these, as they're randomly generated for each individual commit. Finally, you'll see the first line of each commit message.

Before your most recent commit, you'll see two additional words in parentheses, HEAD and master. These labels provide a useful way of navigating around your history and of knowing where you are in your history at any time. HEAD is particularly important - git uses the special label HEAD to refer to the location of your workspace with regard to your git history. In other words, if HEAD points to the commit labeled 89f5445, as it does here, it means that when you actually open the wildphoto folder on your computers, you'll be looking at all of your files as they were at commit 89f5445. As we'll see in a moment, we can move HEAD around so that we see different versions of our files in our wildphoto folder, or our workspace. The word master refers to a branch called master, which once again we'll discuss later.

As you've probably gathered by now, each of these commits is storing the exact state of our file script.py, as present in the staging area, at the moment of the commit. In that sense, git is retaining an exact history of our file for us over time. (If we had more than one file, it would be storing the exact state of our entire workspace folder at each commit.)

Before we move on, it turns out that the above version of git log is going to be very useful, so let's quickly create an alias for it.

$ git config --global alias.lg "log --oneline --graph --decorate --all"

If you now type git lg, you'll see that does the same thing as the long line that we entered above.

Moving on, one of the simplest things that we might want to do with our history is to pull up and examine older version of our file, perhaps to run it again to compare its analysis results to a different version. There are a few ways to do this - we'll discuss the most important here, and you'll see a few others later.

In this case, let's say that we want to roll back our entire workspace to a previous state, say the state of the folder at the time of our initial commit. Recall, at this point, that our script did not yet have the lines to make the table or figure.

To roll back our entire workspace, we use the command git checkout followed by the hash for the commit that we want to go back to (be sure to use the hash for your initial commit in your own repository, as found by running the git lg command described above).

$ git checkout beda5b7
Note: checking out 'beda5b7'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at beda5b7... Initial commit of script to analyze camera data

Wow, that was kind of a lot of output. The important line is the last one, starting with "HEAD is now at...". If we run our special git lg command again, we'll see that HEAD has in fact moved.

$ git lg
* 89f5445 (master) Add initial code to make small figure
* 97e3498 Add code to make table
* beda5b7 (HEAD) Initial commit of script to analyze camera data

This tells us that our workspace, that is our actual wildphoto folder on our computer, now is showing us our files exactly as they were at the moment of this initial commit. Hop over to your wildphoto folder and open the file script.py. Miraculously, it has reverted back to it's state as of your original commit!

It can be a little disconcerting to see your files update like this "in place" - it may give you the feeling that you're losing or overwriting information. Rest assured that git has a history of all of your file versions that you've ever committed and that you can get back to any spot at any time.

The rest of that git checkout command output mentioned a detached HEAD state. Fortunately, a detached HEAD in git is not nearly as frightening as it sounds. All it means is that you shouldn't start editing files from this place in history and committing them, because you'll lose those changes. This is probably the only major danger that you'll run across using git - make sure not to commit new changes in a detached head state, because you may lose them! We'll talk later on about how you would correctly "go back in time" and then start making new versions of your files beginning from this older location. For now, though, since we just want to look at our old files, we won't be running into this problem.

Let's say you've looked around at this old version and want to come back now to your most recent version. Looking at the output of the previous git lg, we can see that the label master is attached to our most recent commit regarding the figure. To get back to this spot, just run another git checkout command.

$ git checkout master
Previous HEAD position was beda5b7... Initial commit of script to analyze camera data
Switched to branch 'master'

Be careful here not to use git checkout followed by the hash for the most recent commit - that will leave you in a detached HEAD state and just move you around. The command above, on the other hand, places you on something called a branch that has the name "master". This is where you want to be (on a branch) before you start committing more changes - we'll explain that more in a minute.

You can run the git lg command above again to see that, in fact, your HEAD has returned to the most recent commit.

A final word about using commit hashes to check out versions. Aside from using a hash, git gives us an easy way to label particularly important commits so that we can easily get to them later on. To do this, we use a command called git tag my-tag-name. For example, you can tag our current commit with the name lab_mtg by running the command

$ git tag lab_mtg

Running our git lg command, we now see

$ git lg
* 89f5445 (HEAD, tag: lab_mtg, master) Add initial code to make small figure
* 97e3498 Add code to make table
* beda5b7 Initial commit of script to analyze camera data

In addition to HEAD and master, we now see that the commit 89f5445 is labeled by a tag lab_mtg. We can now use this label instead of the commit hash to work with this commit from here forward.

2. Comparing two versions of a file

In the previous section, we saw how we could roll back our entire project to a previous state. While this is great for reviewing the history of our project, it doesn't help us much if we want to compare versions of a file from two particular points in that history (for example, compare our current version to a version a few commits back). For this, we can use two different techniques.

Comparing files 1

If the file that you want to compare is simply a plain text file, like our script.py, then we can use an easy command called git diff.

$ git diff beda5b7:script.py 89f5445:script.py
diff --git a/script.py b/script.py
index b60af41..b4c75da 100644
--- a/script.py
+++ b/script.py
@@ -3,3 +3,8 @@
 Read data file

 Run analysis
+
+Make table
+
+Make small figure

In the above command, we entered the hash for the earlier commit (here, our initial commit) followed by the hash for the later commit (here, our most recent commit). The command git diff actually calls an external command line program called diff and runs it on the versions of script.py found in those two commits. After a few cryptic lines (that you might be able to interpret if you stare hard), you'll see that this command prints out the file script.py with some + signs to show the lines that were added between these two commits. If lines were deleted, you'd see - signs, and if lines were changed you'd see something a bit more complicated that indicated the in-place change.

Two quick tips. First, you'll want to be sure to enter the earlier commit first to get the order of changes correct. Second, if you leave off the : and file names from the git diff command, you'll see the differences between all files that changed between two commits.

For large files, the output of git diff can be less than helpful. If you want to use this command in "real life", check out the command git difftool and how to set up an external, graphical viewer for diff-ing. Still, this is a reasonable place to start for identifying changes to plain text files.

Exercise 3

Consider the command git diff lab_mtg HEAD. See if you can guess what the output will be, and then run it and see the actual output. Were you right?

Comparing files 2

There are two cases in which a diff tool is not going to be very helpful for comparing file versions. First, if your files are not plain text but are instead binary or some other complicated text format (see section at end of this lesson), the output of diff will be essentially nonsensical. Second, sometimes you just want to compare two files visually side by side (i.e., just opening them both and reading them at the same time) rather than relying on a tool.

In both of these cases, you need to go back in time, grab a copy of a specific file from an earlier commit, and bring it into your present workspace so that you can actually open the current version and the older version at the same time. You can do this fairly easily with a command called git show.

$ git show beda5b7:script.py > old_script.py

Now, if you look into your folder, you'll see a new file called old_script.py. If you open this, you'll see that it gives you the version of the script.py file that you had at the commit beda5b7. You can use the syntax above to get back a copy of any file from any commit. Recall that the > symbol is a redirect, a shell command that takes the output of the git command and saves it in the file with the name following this symbol.

Keep in mind that using git show generates temporary files that are copies of old versions. You'll want to delete these after you're done looking at them, or else your repo will just end up with a whole bunch of copies of different versions of your files all mushed together, which is exactly the confusion that we're trying to avoid by using version control in the first place.

A final note - if you write your papers in Word, you can use this git show approach to approximate the git diff command above. Simply use git show to bring an old copy of your Word doc into your workspace and then use the Word (Compare and Merge Documents)[http://support.microsoft.com/kb/306484] feature.

3. Maintaining multiple project branches

So far, the techniques that we've looked at provide a unified way of replacing the "Save As..." technique that you may be using now to save and review old copies of files. This next lesson is where the power of version control really starts to make our lives more efficient.

To get started, we'll introduce the concept of a branch. Branches work sort of like they sound - imagine a tree with a big trunk growing upward, with a branch coming out to one side. Both the trunk and the branch are growing from the tips (from the apical meristem, for you biologists), so the newest wood is always at the tip of the branch and the tip of the trunk.

Now, apply this analogy to the development of a file. Let's say we're working on script.py for some time, and at some point we need to create a version of our analysis that's specifically for a seminar presentation. While we work on adjusting our script for the presentation, we also may want to keep working on the main version of our file, which runs the analysis for our dissertation. To do this, we'll create a separate branch for the "presentation version" of our script and allow it to grow, on its own, independently of the trunk. At any time, we can switch back and forth between the tip of the branch and the tip of the trunk, depending on whether we want to "add new wood" to the presentation or the dissertation branch.

Let's walk through this process, which should make the above example more clear. First, we can run our git lg command again to see where we are.

$ git lg
* 89f5445 (HEAD, tag: lab_mtg, master) Add initial code to make small figure
* 97e3498 Add code to make table
* beda5b7 Initial commit of script to analyze camera data

Direct your attention now to the label "master" that's associated with our most recent commit. Whenever you create a new git repository, a branch called "master" is automatically created, and this is the branch where all of your commits are added unless you specify otherwise. Master is thus the trunk from our tree analogy above. So far, we've just been growing our trunk upwards.

Now, however, let's introduce a second branch (aside from the main branch "master"). To do this, we use our old friend the git checkout command, but with a new additional option.

$ git checkout -b presentation
Switched to a new branch 'presentation'
$ git lg
* 89f5445 (HEAD, tag: lab_mtg, presentation, master) Add initial code to 
  make small figure
* 97e3498 Add code to make table
* beda5b7 Initial commit of script to analyze camera data

The option -b in this command tells git to create a new branch with the subsequent name. We only need to use this option once - from now on, to switch between branches, we can just use git checkout branch-name. As you can see, we now have a new branch called presentation that points to the commit that we were just on. At the moment, the presentation and master branches point to the same place.

It's important to keep track of which branch you're on at all times, since that branch is where any new commits will be appended (i.e., whether the new commit will grow the trunk or a branch of our tree). To check what branch you're on, you can always run

$ git branch
  master
* presentation

The branch with the * symbol is, logically, the one that you're currently on.

Now, let's try adding some commits that will cause the two branches to start growing apart.

Exercise 4

Now that we're on the presentation branch, let's start making a few updates to our analysis specifically for our presentation. First off, we'll want the lines in our figure to be red so they can be seen better. Change the line "Make small figure" to "Make small figure, red line" and commit this change. Run git lg and review the output. What has happened?

Here's a tip for commit messages. If you just want to add the opening sentence of a commit, without a longer description, you can run git commit -m "My message" directly from the command line so that you don't have to drop into and out of a text editor every time.

From running git lg, you can see that we've added a commit (i.e., some new growth) to the presentation branch, while the master branch has stayed where it was. Now, let's imagine that while we're waiting for the presentation to happen, we had a new idea about our table. We don't need to change the table for the presentation, but we do want to make the change so that it will be reflected later on in our dissertation.

Exercise 5

Switch back to the master branch by running git checkout master. Run git lg and review your wildphoto folder to make sure you understand where you are now - is the edit to make the figure line red present here? Open script.py and add the line "Make header bold" underneath the "Make table" line. Commit this change. Run git lg and examine the output - does it remind you of a tree trunk with a branch?

The more that you play around with branches, the more that you'll realize how incredibly useful they are. Another great use of branches is to create a branch for some experimental change that you'd like to make that might take a while to complete and could really mess up your results in the mean time. If you make all of those messy edits in a branch, you can always git checkout master to get back to your last clean, working copy of your files. You can even do something like wake up in the morning, git checkout messy-change, work on your experimental stuff, have lunch, git checkout master, and then go back to plodding along slowly but surely towards your dissertation.

One final note. Now that we've discussed branches, we're better able to discuss the "detached HEAD" state that we saw earlier. A detached HEAD simply means that your HEAD (i.e., the commit that your project folder currently represents) is not linked to the tip of a branch. What this means is that if you add a commit, this commit will just be floating in space rather than glued on to the tip of an existing branch (imagine a tree adding 1 inch of new wood floating somewhere by itself in the sky). If we do this, we won't have any easy way of getting back to that new commit later on. To avoid this problem, you should only commit when you are at the tip of an existing branch (i.e., when your HEAD is attached). If you ever get completely lost, running git checkout master will always take you back to a safe, known location at the tip of your main trunk.

5. Merging two project branches together

We've now discussed how to use branches to develop your project along two parallel lines. Now, we'll discuss how to bring two branches back together after they've diverged (something a real tree doesn't do, most of the time) using an operation called a merge. Merging two branches is actually quite common, and applies most commonly when you've gone off and created some edits in a branch that you want to bring back to be a part of your canonical "master" branch going forward.

Merging two branches can range in difficulty from very easy to extremely difficult, with the difficulty depending on how many conflicting changes you've made in the two branches. Fortunately, many times merging a branch will introduce no specific conflicts, in which case merging is trivial. First we'll examine a merge with no conflicts, and then we'll try our hand at a merge with conflicts.

Merging with no conflicts

Let's say that we like the new red line in our figure that we made for the presentation and that we want to bring this change back into our master "trunk" so that we'll have it in our future development. To merge the branch presentation into the branch master, we do the following (note that when you run the second command, the git merge, you'll be asked to enter a commit message for the special commit that performs the merge itself).

$ git checkout master
Already on 'master'
$ git merge presentation
Auto-merging script.py
Merge made by the 'recursive' strategy.
 script.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

The first git checkout command is just to make extra sure that we're on the master branch - the branch that you're on when you run git merge is the one that the changes will come into. The second command actually performs the merge, and we can see that it succeeds with no problems. Running git log to see our current status shows us the following.

$ git lg
*   288f50d (HEAD, master) Merge branch 'presentation'
|\
| * df89527 (presentation) Make line red
* | 013b1af Make header bold
|/
* 89f5445 (tag: lab_mtg) Add initial code to make small figure
* 97e3498 Add code to make table
* beda5b7 Initial commit of script to analyze camera data

We can see that the presentation branch is still right where we left it, but now master has, as antecedents, both the "Make header bold" commit from earlier and merged in the "Make line red" commit from the presentation branch. That means that our current workspace, at the tip of master, will reflect the changes associated with both of these commits, even though they were originally on two separate branches. If you open script.py, you'll see that both of these changes are now in our workspace, which is showing us the new tip of our master branch.

Merging with conflicts

Unfortunately, some merges can be more difficult due to conflicts. Conflicts occur when you've made changes in both branches since they've diverged that conflict with each other. A merge with only a few conflicts is still relatively easy to handle, as we'll see below. If you routinely end up merging branches with a lot of conflicts, I would recommend that you look into setting up git mergetool to make your life easier.

To create a conflict, we could create another branch and start committing, but to save us some time, we'll instead just undo our last merge and start from there. To undo your last commit, completely nuking everything that you did in tha commit forever, run the following.

$ git reset --hard HEAD^1
HEAD is now at 013b1af Make header bold

You can run git lg again to see that our version history now looks just like it did before we merged. The above command is quite handy any time you make a mistake by committing. The notation "HEAD^1" is a shortcut way of saying "one commit before HEAD", where HEAD (as you recall) points to the commit that is currently present in our workspace. If you want to undo the commit but not nuke everything, you can use the --soft option instead - this will leave the changes that you made in the commit in your staging area, so that you can review, edit, and re-commit them, rather than destroying them entirely like --hard does.

Let's now create a conflict. Imagine that while you were working alternately on the presentation and the master versions, you checked out the master branch and decided that you wanted the lines in the figure to be thicker for your dissertation figures. To do so, you changed the line "Make small figure" in your script file in the master branch to "Make small figure, thick line". Go ahead and make and commit this change.

Now, let's once again try to merge the presentation branch into the master branch. Running git merge now gives us a little trouble.

$ git merge presentation
Auto-merging script.py
CONFLICT (content): Merge conflict in script.py
Automatic merge failed; fix conflicts and then commit the result.

Uh oh, now what's going on? We're actually currently paused in the middle of our merge, and git is waiting for us to resolve the merge conflict.

Again, a merge conflict occurs when we've made changes in the same location in a file in both branches since the point at which the branches diverged. In this example, we caused the conflict by editing the line "Make small figure" two different ways in the two branches - in one branch, we added "make line red" and in the other branch we added "thick line". Git has no automatic way of knowing which of these we want to keep (or if we want to combine these somehow), so it asks for our help.

If we run git status now to see what git is thinking, we'll see some new output.

$ git status
# On branch master
# You have unmerged paths.
#   (fix conflicts and run "git commit")
#
# Unmerged paths:
#   (use "git add <file>..." to mark resolution)
#
#   both modified:      script.py
#
no changes added to commit (use "git add" and/or "git commit -a")

This tells us that we have one file, script.py that is "unmerged" (i.e., we have to complete the merge ourselves).

To complete the merge, we start by opening the script.py file currently in our workspace to see what it looks like. When you do that, you'll see these funny lines in the middle of the file.

<<<<<<< HEAD
Make small figure, thick line
=======
Make small figure, red line
>>>>>>> presentation

The <<<< and >>>> symbols give the top and the bottom of the conflict area, and the ==== symbols separate the top version, which was the version in HEAD (where our workspace was pointed - this was the master branch that we were merging into), from the bottom version, which was the version in the presentation branch.

To settle this conflict, we just edit this section however we want. In this case, we'll make the line say "Make small figure, thick red line". Make sure to delete all of the other stuff (from the <<<< to the >>>>) added by the merge command, so that the file looks exactly how we want it to look after the merge is done. In other words, instead of that whole block of stuff above, our file should now just have

Make small figure, thick red line

in its place.

Now we can add this fix to our staging area using git add and then run git status to see what's going on.

$ git add script.py
$ git status
# On branch master
# All conflicts fixed but you are still merging.
#   (use "git commit" to conclude merge)
#
# Changes to be committed:
#
#   modified:   script.py
#

Git helpfully tells us that we've fixed all of our conflicts, but that we're still in the middle of our merge, and that we need to run git commit to complete the merge. Go ahead and do so, and run git lg once again to make sure that you've got the history that you would expect.

And with that, we conclude the main part of our lesson focused on working with git locally for your own projects. Next we'll turn somewhat briefly to the basics of using git remotely for syncing, sharing and collaboration. But before we do that, try your hand at the capstone exercise(s) below.

Exercise 6

To really hammer home everything that we've learned so far, try the following tasks.

Since you're so proud of your script, add a line that says "# All rights reserved" near the top and commit this change on your master branch.

Use git diff to compare the current version of your script to the one from the initial commit.

Use git show to bring a copy of your script version tagged lab_mtg into your current workspace and open it side by side with your most recent version. Don't forget to delete this temporary file when you're done.

Make a branch called experimental and commit a few changes there. Don't hold back - create conflicts if you dare!

Merge your experimental branch back into your master branch.

If you finish the above easily, here's a bonus exercise.

Exercise 7

Make a change to your script and add it to the staging area. Then make another additional change and, before running git add again, run git status. What does this output tell you about how git understands files versus changes to files? Can you think of practical applications of this behavior?

Before we move on to using git remotely, a final word about using git in practice. While it's important to understand the basics of how to use git from the command line, as we have here, there are certain operations that are much more easily done with a "modern" graphical program, including visualizing complex branching structures and dealing with difficult merges. There are many programs to choose from - on a Mac or Windows, I would suggest trying Sourcetree, which you can download and install here. If you're on Linux, you might try Smartgit or search for other alternatives.

6. Sharing a project

Once you have your research projects managed with version control, you will soon want to find ways to share your project and its history with the world (or at least with a few collaborators). We're going to walk through the very basics of how to do this using Github, which is rapidly becoming the most popular site for sharing scientific code. Working with so called remote repositories can get quite complicated, and here we'll only be able to scratch the surface of what's possible. Refer to the free online book Pro Git or talk to the instructors if you'd like more information or pointers.

Syncing your files across computers and sharing them with the world requires access to somewhere up in "the cloud" where you will upload and download files. For this, we're going to use Github. By now, you should have already created a user account on Github, and we're going to use that account to upload your wildphoto project to a remote repository.

To get started, we need to tell Github to create a remote repository space to hold your project. Head over to github.com and log in, if you haven't already. You'll then be taken to a page (currently mostly empty) where, on the right hand side, you will see a box with the title "Your repositories". Next to that box, you'll see a green button called "New repository". Click this button. On the next page, fill in wildphoto as the Repository name, leave the button checked to make the repository public, and do not check the box to Initialize the repository. Then click the button to Create repository.

In the future, you may want to create private repositories to hold code that you do not wish to make publicly available. To do this, you'll need to upgrade to a Micro account, which is free for students. Github will then give you the option of allowing only specific collaborators to view your private repositories.

Once you create the remote repository, Github will provide you with some helpful instructions on what to do next. Since we already have a local repository that we want to upload, we want to use the second set of instructions, Push an existing repository from the command line. You can think of the git push command as basically equivalent to uploading your current project directory as well as all of your project history. Later on, we'll use a command called git pull, which you can think of as equivalent to downloading. (Side note: git pull is actually a little more complicated, as it has to deal not only with downloading but with merging in any changes that have been made in the remote repository that you don't have. We'll discuss this more later on.)

Now that we've mentioned push and pull, there's one more concept that we need to consider right now, which is the idea of a remote. In git, a remote is essentially an internet address to which you can push, and from which you can pull, changes to your project. To tell our local wildphoto repository how to interact with our new Github remote repository, we thus have to "add a remote" to our local project.

To do this, as explained on the Github help page that you're now looking at, we can run the command

$ git remote add origin https://github.com/jkitzes/wildphoto.git

This tells git to add a remote address named origin, and to assign it the URL given at the end of the statement. origin is a special name that is usually reserved for the main remote repository that we're working with. As you might have gathered from the above, it's possible to work with multiple remote repositories for a single project. This is an important part of advanced collaborative workflows that are beyond the scope of this beginner tutorial. For now, we're only going to be working with this one remote, which now points to our main Github repo that we just set up.

Finally, we're ready to send our project and it's history to Github. To do this, we run our git push command. The argument -u is an option that you only need to use the first time you push to a remote repository, and the following words origin master indicate to push the master branch to the remote repository named origin.

$ git push -u origin master
Counting objects: 24, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (16/16), done.
Writing objects: 100% (24/24), 1.94 KiB | 0 bytes/s, done.
Total 24 (delta 8), reused 0 (delta 0)
To https://github.com/jkitzes/wildphoto.git
 * [new branch]      master -> master
Branch master set up to track remote branch master from origin.

You may need to enter your Github password after running this command, which you should do. Hopefully you will see something similar to the above, which indicates that everything completed successfully. The output here tells us that our data was compressed, written to our remote repository, and that git has set up our local master branch to track the remote repository branch also called master. This essentially means that when we later "download" our data using git pull, git will know where to put it.

If you're working on a Windows machine, that command may have failed with an error message like could not read Username for https:...: No such device or address. If you get this message, try entering the command env GIT_SSL_NO_VERIFY=true and then try again.

Now, head back over to your web browser and reload the page that you were just on (or head over to http://github.com/my-username/wildphoto), and you'll see that your script.py file is available for all the world to see. You've just published your first scientific software package!

Exercise 8

Take a few minutes to poke around the Github page for your project. In particular, try clicking on the link for the file script.py and the link in the header that says "7 commits". Ask your instructors any questions as they come up.

If you'd like to make sure that you've got this workflow down, create a README file in your local wildphoto directory, commit it to your local repo, then push it to Github.

As you begin to work with git remotes, you may notice that you have to enter your password every time you try to git push. One good way to avoid this is to set up and use SSH keys, but we won't go through that process here.

7. Syncing and collaborating

Syncing files across multiple computers and collaborating with colleagues on a project requires, at the most basic level, essentially the same operations - you need to be able to create local copies of your repository on many computers, make changes to your files on any computer, push these changes back to the remote repository, then re-sync each of the computers with the new changes found in the remote repository. Here, we'll walk through a simple example using two computers, one owned by you and one by your (lone) collaborator on your wildphoto project, in which you'll use the simplest possible collaborative workflow, called "shared repo". If you imagine that your collaborator is actually you working at your home computer (instead of your office computer), you'll see that the process for collaborating is actually identical to the process of keeping your two computers in sync.

Before we get started, to immediately answer the obvious question - yes, you can place your version controlled project folder in Dropbox and access it from different computers, as well as share it with others. And yes, this can sometimes lead to problems that can be hard to fix (Dropbox's syncing mechanism can have trouble with the file structure of the .git folder where your project history is stored), especially if you both start working on the same file at the same time. We're going to discuss the more formal and "official" way for syncing and collaborating for the rest of this lesson.

To get started, pair up with a partner seated near you. Elect one of you to be the main project "owner" and one to be the project "collaborator". (For the rest of our lesson, being the collaborator is going to be more work, so you may want to have the person who's feeling the most comfortable so far be the collaborator.) In real world collaboration, the distinction between these two is not that important - it basically just involves choosing whose account is going to host the wildphoto repository that you both work with.

To begin, have the collaborator navigate to a different location on his/her hard drive, away from his/her own copy of the wildphoto project. From here forward, the collaborator will be working with the owner's remote repository.

Now, the collaborator needs to get a copy of the owner's wildphoto repository. The command for getting a fresh copy of a remote repository is git clone, followed by the URL from which you want to download the project. Have the collaborator navigate to the owner's wildphoto project page on Github by going to http://github.com/owners-username/wildphoto. There, on the right hand side of the owner's wildphoto project page on Github, you'll see a little box with the title "HTTPS clone URL". Copy this URL, and use it in the below command (you can also just replace owners-username with the owner's actual username, which will give the same thing).

$ git clone https://github.com/owners-username/wildphoto.git
Cloning into 'wildphoto'...
remote: Counting objects: 24, done.
remote: Compressing objects: 100% (8/8), done.
remote: Total 24 (delta 8), reused 24 (delta 8)
Unpacking objects: 100% (24/24), done.
Checking connectivity... done

Now the collaborator has a complete, working copy of the owner's wildphoto repository on his/her computer, including the most current project files and the entire project history. Pretty easy, eh? Note that this was possible because the owner's Github repo was public - part of creating a public repo is allowing anyone, anywhere in the world, to clone a copy of your project and start working with it.

To follow our basic collaborative workflow (again, if you imagine that your collaborator is you at a different computer, then this is the workflow for syncing), we now need to complete the following three steps.

Have the collaborator make a change to the project and commit this change to his/her local repo
Have the collaborator push this change to the remote Github repo.
Have the owner download this change from the remote repo so that the owner's repo includes the collaborator's change.

You actually have almost all the tools to do this already. First, though, the owner will have to give the collaborator permission to push changes to the owner's repo (in a public repo, anyone can clone, but not everyone can push). To do this, the owner will need to go to the page for their repo on Github (http://github.com/owners-username/wildphoto), click on the Settings link on the right, click on the Collaborators link on the left, and add the collaborator's Github username on this page.

With that, you'll just need a few additional pieces of information to complete the three steps above. First, you should know that when the collaborator cloned the owner's repo, it automatically set up a remote called origin that points to the owner's Github repository (very convenient) - the collaborator can thus push changes to the remote master branch on Github using the same command that we saw before, git push origin master. Second, when it comes time for the owner to download and sync the new changes that the collaborator pushed to Github, the owner can just use the command git pull, which will download and merge in all changes in the Github remote master branch to your local master branch (assuming that the owner is on the master branch - run git checkout master if you're not sure).

Exercise 9

Complete the three steps described above for a simple collaborative workflow. The instructors will come around the room to help you.

And that pretty much covers the basics of simple collaborating and syncing. Congrats - you're now a certified git beginner!

While that last comment was a bit tongue in cheek, it is true that what we've been able to cover today has only introduced a few of the many things that git can do and the many ways in which git can be used. In particular, while we were able to fairly thoroughly cover the basics of using git on your local computer, we only scratched the surface of how to use git remotely and collaboratively. If you are interested in moving forward with using git remotely, there are three additional "bit topics" that you'll soon need to learn about.

The first of these is how to work remotely with branches. You'll note that in the above, we only discussed how to push and pull the master branch from a remote repository. For the most part, working with other branches just involves adding the branch name to the end of the end of the git push and git pull commands, but you'll probably shortly need to look up the definition of tracking branches among other things.

The second is how to deal with conflicts that collaborators create when they work on the same part of a file. On your local machine, we saw conflicts arise when trying to merge one branch into another. When working remotely, this same type of conflict can happen. What you need to know is that you run git pull, you are actually both downloading the remote changes to the repository as well as trying to merge them into the branch that you are currently on. If this creates a merge conflict, you'll have to address it. To gain a finer level of control over this process, most intermediate and advanced git users use the two commands git fetch and git merge, instead of git pull, and often make extensive use of temporary branches to hold different versions of the project so they can be merged in a logical fashion.

The third is how to use a "fork/pull" collaborative workflow instead of the "shared repo" model that we've described above. If you end up collaborating on larger projects, including, for example, the repository holding all of the core Software Carpentry bootcamp lessons, you'll find that most large projects don't allow all collaborators to have push access to the main repository, the model that we used above. Rather, each collaborator makes a "fork", or a copy of the main repository, on their local Github account. They then make changes in branches of their own forks and then submit a "pull request" back to the main repository, asking the maintainers of the core repository to pull in their changes. In addition to preventing mistakes in the core repository, this model also builds in the idea of code review, and the discussions surrounding pull requests are often extensive.

Once again, if you'd like to learn more about these or more about git in general, check out the book Pro Git.

Why plain text?

Now that we've discussed many of the things that git can do with files, here's a closing word about the difference between plain text and binary files. Plain text files are exactly what they sound like - files that contain nothing other than text, as in letters, numbers, and (some) basic symbols. Plain text files thus lack formatting like font sizes (or even font names), metadata such as margin sizes, and fancy features such as comment bubbles, embedded images, and anything else other than (you guessed it) text.

The file that we worked with in this lesson was a plain text file, as are most files that contain code, such as .m or .R files that contain code for Matlab or R respectively. Other common examples of plain text files include .txt files containing narrative text (like the README files that come with many programs), and .csv files, which are actually just plain text files in which each "column" of data is separated from the next by a comma (csv actually stands for "comma separated values").

Plain text files have two major advantages for our purposes. First, being a simple and standard format, plain text can be read by almost any program. As a corollary, the ubiquitous nature of plain text means that it is likely to outlive all of those other proprietary file formats in the future. Second, with specific regard to git, plain text files are very easy to compare to each other. In other words, it's relatively easy for a program (like the command line diff program that we used above) to open two plain text files and find the differences between them simply by comparing, line by line, the contents of each file. This is much harder, if not impossible, to do for more complex file formats.

This type of line-by-line comparison is not possible for binary files, which for these purposes is the "opposite" of a plain text file. Binary files are files, like an image, that cannot be converted into any sort of textual representation. Because they cannot be diff-ed, version control is somewhat less useful for binary files, although it can still help greatly with headaches 1, 3, 5, and 6 above.

Somewhere in between plain text and binary files are markup files like xml files, html files, the IPython notebook files, Microsoft's docx format, etc. These are technically plain text files, but ones that contain many other characters (beyond the actual important content, in an intellectual sense) that control how the content of the file is displayed and rendered. As plain text files, version control can "see inside" of these, but it often does a poor job at comparing them to each other due to the presence of all of those additional characters and how they are updated when you change the important content of the file.

A final note on writing papers

Personally, I've found that one of the most useful applications of version control is to manage revisions to my papers. Revising manuscripts represents a great example of a process in which you're likely to have multiple versions of parts of a file (i.e., the long and the short Methods version, the dissertation vs. the submission version) that you need to assemble repeatedly in different orders and combinations (i.e., as you submit your manuscript to the fourth journal). This makes papers a great candidate for version control. However, these benefits really become most apparent only when you're using plain text files - that it, when you've written your papers in plain text (not in Word).

If you already use LaTeX, then you're all set - go forth and use git! (Side tip: if you are planning to use LaTeX for your UC Berkeley dissertation, check out the ucbthesis class file and documentation).

If you usually write your papers in Word, but work in a field in which your papers really only involve text (i.e., no or very few figures, tables, or equations), then I would suggest trying out the very simple markup language called Markdown, which will allow you to write your manuscripts in plain text with some basic, minimum formatting tags. Overall, it's very easy to use Markdown for writing, and there's a great command line program called pandoc that will convert Markdown to Word (and other formats) when you need to.

If you don't fall into either of these camps, version control can still help you keep track of your manuscripts as "blobs" - this just means you won't be able to do the diff and merge work that we've discussed. If are willing to make an effort to switch your writing to plain text, and especially if you plan on writing lots of equations in the future, I would recommend that you invest the time to learn LaTeX - it has a somewhat steep learning curve, but you're very likely to be pleased with the results in the long term. LaTeX is especially good for managing and formatting large documents, like dissertations, which is an area where Word often falls short.