Note: this tutorial is based (mostely blantently copied), and therefore owes a lot, to the excellent materials offered in:
That notbook owed a lot to the following (including these notes for completeness):
There is also J.R. Johansson's tutorial on version control that is also written as a fully reproducible notebook and is also aimed at a scientific audience. It has a similar spirit to this one, and is part of his excellent series Lectures on Scientific Computing with Python that is entirely available as IPython Notebooks.
If we're running short on time, we'll do the simple guide
From What Is Version Control? Why Is It Important For Due Diligence?
Version control systems are essential for any form of distributed, collaborative development. Whether it is the history of a wiki page or large software development project, the ability to track each change as it was made, and to reverse changes when necessary can make all the difference between a well managed and controlled process and an uncontrolled ‘first come, first served’ system. It can also serve as a mechanism for due diligence for software projects.
From Wikipedia
“Revision control, also known as version control, source control or software configuration management (SCM), is the management of changes to documents, programs, and other information stored as computer files.”
Reproducibility?
What do (good) version control tools give you?
Because that's what folks were using when I came into programming... ¯\(ツ)/¯
I don't know, really. Here are some reasons though:
I am not going to be upset if you use something else, but using a system that is decentralized is important. If you need to pick, check out wikipedia.
This tutorial is structured in the following way: we will begin with a brief overview of key concepts you need to understand in order for git to really make sense. We will then dive into hands-on work: after a brief interlude into necessary configuration we will discuss 5 "stages of git" with scenarios of increasing sophistication and complexity, introducing the necessary commands for each stage:
In reality, this tutorial only covers stages 1-4, since for #5 there are many software develoment-oriented tutorials and documents of very high quality online. But most scientists start working alone with a few files or with a small team, so I feel it's important to build first the key concepts and practices based on problems scientists encounter in their everyday life and without the jargon of the software world. Once you've become familiar with 1-4, the excellent tutorials that exist about collaborating on github on open-source projects should make sense.
In [5]:
ls
A repository: a group of linked commits
And this is pretty much the essence of Git!
The minimal amount of configuration for git to work without pestering you is to tell it who you are:
In [6]:
%%bash
git config --global user.name "Jeremy S. Perkins"
git config --global user.email "jeremyshane@gmail.com"
And how you will edit text files (it will often ask you to edit messages and other information, and thus wants to know how you like to edit your files):
In [7]:
%%bash
# Put here your preferred editor. If this is not set, git will honor
# the $EDITOR environment variable
git config --global core.editor /usr/bin/nano # Yes, I still use nano
# On Windows Notepad will do in a pinch, I recommend Notepad++ as a free alternative
# On the mac, you can set nano or emacs as a basic option
# And while we're at it, we also turn on the use of color, which is very useful
git config --global color.ui "auto"
Set git to use the credential memory cache so we don't have to retype passwords too frequently. On OSX, you should run the following (note that this requires git version 1.7.10 or newer):
In [8]:
%%bash
git config --global credential.helper osxkeychain
# Set the cache to timeout after 2 hours (setting is in seconds)
git config --global credential.helper 'cache --timeout=7200'
Simply type git to see a full list of all the 'core' commands. We'll now go through most of these via small practical exercises:
In [9]:
!git
In [10]:
%%bash
rm -rf test
git init test
Note: all these cells below are meant to be run by you in a terminal where you change once to the test directory and continue working there.
Since we are putting all of them here in a single notebook for the purposes of the tutorial, they will all be prepended with the first two lines:
%%bash
cd test
that tell IPython to do that each time. But you should ignore those two lines and type the rest of each cell yourself in your terminal.
Let's look at what git did:
In [11]:
%%bash
cd test
ls
In [12]:
%%bash
cd test
ls -la
In [13]:
%%bash
cd test
ls -l .git
Now let's edit our first file in the test directory with a text editor... I'm doing it programatically here for automation purposes, but you'd normally be editing by hand
In [14]:
%%bash
cd test
echo "My first bit of text" > file1.txt
In [15]:
%%bash
cd test
git add file1.txt
We can now ask git about what happened with status:
In [16]:
%%bash
cd test
git status
For now, we are always going to call git commit either with the -a option or with specific filenames (git commit file1 file2...). This delays the discussion of an aspect of git called the index (often referred to also as the 'staging area') that we will cover later. Most everyday work in regular scientific practice doesn't require understanding the extra moving parts that the index involves, so on a first round we'll bypass it. Later on we will discuss how to use it to achieve more fine-grained control of what and how git records our actions.
In [17]:
%%bash
cd test
git commit -a -m"This is our first commit"
In the commit above, we used the -m flag to specify a message at the command line. If we don't do that, git will open the editor we specified in our configuration above and require that we enter a message. By default, git refuses to record changes that don't have a message to go along with them (though you can obviously 'cheat' by using an empty or meaningless string: git only tries to facilitate best practices, it's not your nanny).
In [18]:
%%bash
cd test
git log
Let's do a little bit more work... Again, in practice you'll be editing the files by hand, here we do it via shell commands for the sake of automation (and therefore the reproducibility of this tutorial!)
In [19]:
%%bash
cd test
echo "And now some more text..." >> file1.txt
And now we can ask git what is different:
In [20]:
%%bash
cd test
git diff
In [21]:
%%bash
cd test
git commit -a -m"I have made great progress on this critical matter."
First, let's see what the log shows us now:
In [22]:
%%bash
cd test
git log
Sometimes it's handy to see a very summarized version of the log:
In [23]:
%%bash
cd test
git log --oneline --topo-order --graph
Git supports aliases: new names given to command combinations. Let's make this handy shortlog an alias, so we only have to type git slog and see this compact log:
In [24]:
%%bash
cd test
# We create our alias (this saves it in git's permanent configuration file):
git config --global alias.slog "log --oneline --topo-order --graph"
# And now we can use it
git slog
While git add is used to add fils to the list git tracks, we must also tell it if we want their names to change or for it to stop tracking them. In familiar Unix fashion, the mv and rm git commands do precisely this:
In [25]:
%%bash
cd test
git mv file1.txt file-newname.txt
git status
Note that these changes must be committed too, to become permanent! In git's world, until something hasn't been committed, it isn't permanently recorded anywhere.
In [26]:
%%bash
cd test
git commit -a -m"I like this new name better"
echo "Let's look at the log again:"
git slog
And git rm works in a similar fashion.
What is a branch? Simply a label for the 'current' commit in a sequence of ongoing commits:
There can be multiple branches alive at any point in time; the working directory is the state of a special pointer called HEAD. In this example there are two branches, master and testing, and testing is the currently active branch since it's what HEAD points to:
Once new commits are made on a branch, HEAD and the branch label move with the new commits:
This allows the history of both branches to diverge:
But based on this graph structure, git can compute the necessary information to merge the divergent branches back and continue with a unified line of development:
Let's now illustrate all of this with a concrete example. Let's get our bearings first:
In [27]:
%%bash
cd test
git status
ls
We are now going to try two different routes of development: on the master branch we will add one file and on the experiment branch, which we will create, we will add a different one. We will then merge the experimental branch into master.
In [28]:
%%bash
cd test
git branch experiment
git checkout experiment
In [29]:
%%bash
cd test
echo "Some crazy idea" > experiment.txt
git add experiment.txt
git commit -a -m"Trying something new"
git slog
In [30]:
%%bash
cd test
git checkout master
git slog
In [31]:
%%bash
cd test
git status
In [32]:
%%bash
cd test
echo "fixed this little bug" >> file-newname.txt
git commit -a -m"The mainline keeps moving"
git slog
In [33]:
%%bash
cd test
ls
In [34]:
%%bash
cd test
git merge experiment
git slog
We are now going to introduce the concept of a remote repository: a pointer to another copy of the repository that lives on a different location. This can be simply a different path on the filesystem or a server on the internet.
For this discussion, we'll be using remotes hosted on the GitHub.com service, but you can equally use other services like BitBucket or Gitorious as well as host your own.
In [35]:
%%bash
cd test
ls
echo "Let's see if we have any remote repositories here:"
git remote -v
Since the above cell didn't produce any output after the git remote -v call, it means we have no remote repositories configured. We will now proceed to do so. Once logged into GitHub, go to the new repository page and make a repository called test. Do not check the box that says Initialize this repository with a README, since we already have an existing repository here. That option is useful when you're starting first at Github and don't have a repo made already on a local computer.
We can now follow the instructions from the next page:
In [36]:
%%bash
cd test
git remote add origin https://github.com/kialio/test.git
In [37]:
%%bash
cd test
git push -u origin master
Let's see the remote situation again:
In [45]:
%%bash
cd test
git remote -v
We can now see this repository publicly on github.
Let's see how this can be useful for backup and syncing work between two different computers. I'll simulate a 2nd computer by working in a different directory...
In [47]:
%%bash
# Here I clone my 'test' repo but with a different name, test2, to simulate a 2nd computer
git clone https://github.com/kialio/test.git test2
cd test2
pwd
git remote -v
Let's now make some changes in one 'computer' and synchronize them on the second.
In [48]:
%%bash
cd test2 # working on computer #2
echo "More new content on my experiment" >> experiment.txt
git commit -a -m"More work, on machine #2"
Now we put this new work up on the github server so it's available from the internet
In [49]:
%%bash
cd test2
git push
Now let's fetch that work from machine #1:
In [50]:
%%bash
cd test
git pull
While git is very good at merging, if two different branches modify the same file in the same location, it simply can't decide which change should prevail. At that point, human intervention is necessary to make the decision. Git will help you by marking the location in the file that has a problem, but it's up to you to resolve the conflict. Let's see how that works by intentionally creating a conflict.
We start by creating a branch and making a change to our experiment file:
In [51]:
%%bash
cd test
git branch trouble
git checkout trouble
echo "This is going to be a problem..." >> experiment.txt
git commit -a -m"Changes in the trouble branch"
And now we go back to the master branch, where we change the same file:
In [52]:
%%bash
cd test
git checkout master
echo "More work on the master branch..." >> experiment.txt
git commit -a -m"Mainline work"
So now let's see what happens if we try to merge the trouble branch into master:
In [53]:
%%bash
cd test
git merge trouble
Let's see what git has put into our file:
In [54]:
%%bash
cd test
cat experiment.txt
At this point, we go into the file with a text editor, decide which changes to keep, and make a new commit that records our decision. I've now made the edits, in this case I decided that both pieces of text were useful, but integrated them with some changes:
In [55]:
%%bash
cd test
cat experiment.txt
Let's then make our new commit:
In [56]:
%%bash
cd test
git commit -a -m"Completed merge of trouble, fixing conflicts along the way"
git slog
Note: While it's a good idea to understand the basics of fixing merge conflicts by hand, in some cases you may find the use of an automated tool useful. Git supports multiple merge tools: a merge tool is a piece of software that conforms to a basic interface and knows how to merge two files into a new one. Since these are typically graphical tools, there are various to choose from for the different operating systems, and as long as they obey a basic command structure, git can work with any of them.
Single remote with shared access: we are going to set up a shared collaboration with one partner (the person sitting next to you). This will show the basic workflow of collaborating on a project with a small team where everyone has write privileges to the same repository.
Note for SVN users: this is similar to the classic SVN workflow, with the distinction that commit and push are separate steps. SVN, having no local repository, commits directly to the shared central resource, so to a first approximation you can think of svn commit as being synonymous with git commit; git push.
We will have two people, let's call them Alice and Bob, sharing a repository. Alice will be the owner of the repo and she will give Bob write privileges.
We begin with a simple synchronization example, much like we just did above, but now between two people instead of one person. Otherwise it's the same:
Next, we will have both parties make non-conflicting changes each, and commit them locally. Then both try to push their changes:
alice.txt to the repo and commits.bob.txt and commits.The problem is that Bob's changes create a commit that conflicts with Alice's, so git refuses to apply them. It forces Bob to first do the merge on his machine, so that if there is a conflict in the merge, Bob deals with the conflict manually (git could try to do the merge on the server, but in that case if there's a conflict, the server repo would be left in a conflicted state without a human to fix things up). The solution is for Bob to first pull the changes (pull in git is really fetch+merge), and then push again.
There are lots of good tutorials and introductions for Git, which you can easily find yourself; this is just a short list of things I've found useful. For a beginner, I would recommend the following 'core' reading list, and below I mention a few extra resources:
The smallest, and in the style of this tuorial: git - the simple guide contains 'just the basics'. Very quick read.
The concise Git Reference: compact but with all the key ideas. If you only read one document, make it this one.
In my own experience, the most useful resource was Understanding Git Conceptually. Git has a reputation for being hard to use, but I have found that with a clear view of what is actually a very simple internal design, its behavior is remarkably consistent, simple and comprehensible.
For more detail, see the start of the excellent Pro Git online book, or similarly the early parts of the Git community book. Pro Git's chapters are very short and well illustrated; the community book tends to have more detail and has nice screencasts at the end of some sections.
If you are really impatient and just want a quick start, this visual git tutorial may be sufficient. It is nicely illustrated with diagrams that show what happens on the filesystem.
For windows users, an Illustrated Guide to Git on Windows is useful in that it contains also some information about handling SSH (necessary to interface with git hosted on remote servers when collaborating) as well as screenshots of the Windows interface.
Cheat sheets : Two different cheat sheets in PDF format that can be printed for frequent reference.
At some point, it will pay off to understand how git itself is built. These two documents, written in a similar spirit, are probably the most useful descriptions of the Git architecture short of diving into the actual implementation. They walk you through how you would go about building a version control system with a little story. By the end you realize that Git's model is almost an inevitable outcome of the proposed constraints:
Git ready : A great website of posts on specific git-related topics, organized by difficulty.
QGit: an excellent Git GUI : Git ships by default with gitk and git-gui, a pair of Tk graphical clients to browse a repo and to operate in it. I personally have found qgit to be nicer and easier to use. It is available on modern linux distros, and since it is based on Qt, it should run on OSX and Windows.
Git Magic : Another book-size guide that has useful snippets.
The learning center at Github : Guides on a number of topics, some specific to github hosting but much of it of general value.
A port of the Hg book's beginning : The Mercurial book has a reputation for clarity, so Carl Worth decided to port its introductory chapter to Git. It's a nicely written intro, which is possible in good measure because of how similar the underlying models of Hg and Git ultimately are.
Intermediate tips : A set of tips that contains some very valuable nuggets, once you're past the basics.