Martin Luessi (mluessi at nmr.mgh.harvard.edu)
Martinos Center Why N How, April 5, 2012
..imagine the following scenario:
- You write a data analysis script
- You want to share it with others and collaborate on it
How do you do it?
- Send around e-mails?
- Put the file on a shared drive / dropbox?
Potential problems:
- It is difficult to track changes (someone needs to coordinate)
- What if two collaborators make incompatible changes?
- What if you later find that an earlier version was better?
- Widely used for software development
- Allow multiple people to work on the same files
- Keep track of file changes
- Provide a structured way of integrating changes (branching and merging)
- Work with any type of text file (not binary files like .doc etc.)
Potential uses for scientists:
- Software development
- Data analysis scripts (Python, BASH, Matlab, ...)
- Papers (if they are plain text files, e.g., LaTex)
- Presentations (like this one)
- git is a free and open source, distributed version control system
- Originally created by Linus Torvalds in 2005 (Creator of the Linux Kernel)
- It is designed to be fast
Unique features:
- Every git clone is a full repository with complete history etc.
- It does not have to rely on a centralized server (unlike CVS or SVN)
- Branching and merging are easy to do and fast
A repository contains:
- Files and directories
- A historical record of changes
- A set of commit objects
- A set of heads (references to commit objects)
Either create a new repository:
[$] cd ~/mycode
[$] git init
Initialized empty Git repository in /home/martin/mycode/.git/Or clone a repository:
[$] git clone git://github.com/schacon/simplegit.git
Initialized empty Git repository in /home/martin/simplegit/.git/
remote: Counting objects: 100, done.
remote: Compressing objects: 100% (86/86), done.
remote: Total 100 (delta 35), reused 0 (delta 0)
Receiving objects: 100% (100/100), 9.51 KiB, done.
Resolving deltas: 100% (35/35), done.
[$] ls -al simplegit
total 24
drwxr-xr-x 4 martin martin 4096 Apr 4 14:41 .
drwxr-xr-x 9 martin martin 4096 Apr 4 14:41 ..
drwxr-xr-x 7 martin martin 4096 Apr 4 14:41 .git
-rw-r--r-- 1 martin martin 125 Apr 4 14:41 README
-rw-r--r-- 1 martin martin 592 Apr 4 14:41 Rakefile
drwxr-xr-x 2 martin martin 4096 Apr 4 14:41 libNotice: The .git directory contains the git repository
See the status
[$] cd ~/mycode
[$] git status
# On branch master
#
# Initial commit
#
nothing to commit (create/copy files and use "git add" to track)- We are on the master branch
- The repository is empty
Let's add a file
[$] echo "hello git" >> test.txt
[$] git add test.txtSee the status again
[$] git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
# (use "git rm --cached <file>..." to unstage)
#
# new file: test.txtcommit all changes
[$] git commit -a -m "my first file"
[master (root-commit) cb2ff46] my first file
Committer: martin <martin@think.(none)>
1 files changed, 1 insertions(+), 0 deletions(-)
create mode 100644 test.txSee the log
[$] git log
commit cb2ff4663bdc3bf3d38a0ad534dd770656c45f0d
Author: martin <martin@think.(none)>
Date: Wed Apr 4 15:10:42 2012 -0400
my first fileMake modifications to the file
[$] echo "new content" >> test.txtSee the difference
[$] git diff
diff --git a/test.txt b/test.txt
index 8d0e412..ab04ca9 100644
--- a/test.txt
+++ b/test.txt
@@ -1 +1,2 @@
hello git
+new contentAnd again commit the changes
[$] git commit -a -m "more changes"
[master cb7fe4f] more changes
Committer: martin <martin@think.(none)>
1 files changed, 1 insertions(+), 0 deletions(-)- Use git init to create a new repository
- Use git clone to clone an existing repository
- Use git status to see the status
- Use git add to add a file/directory to version control
- Use git diff to see the changes you made
- Use git commit to commit your changes
- Use git log to see the log
- So far we have been working on the master branch
- You usually want to make changes in a separate branch
Let's see what branches are available
[$] git branch
* masterso far we only have the master branch
Including our previous two commits (A and B) our repo looks like this:
(A) --- (B)
|
master
|
HEADCreate a new branch
[$] git branch my_branchSwitch to the new branch
[$] git checkout my_branchChange the file again and commit the changes (commit C)
[$] echo "even more content" >> test.txt
[$] git commit -a -m "more content"Now our repository looks like this
(A) --- (B) ---- (C)
| |
master my_branch
|
HEADLet's switch back to the master branch
[$] git checkout masterand look at the file
[$] cat test.txt
hello git
new contenthere the file is still the same. The changes we made are in my_branch
We can checkout my_branch again and make more changes.
Finally, we can merge the changes into the master branch
[$] git checkout master
[$] git merge my_branch
Updating cb7fe4f..6354500
Fast-forward
test.txt | 1 +
1 files changed, 1 insertions(+), 0 deletions(-)Now, the master branch includes the changes we made in my_branch
[$] cat test.txt
hello git
new content
even more contentOur repository looks like this
(A) --- (B) ---- (C) -------(D)
| |
my_branch master
|
HEAD- How do you share a git repo with multiple people?
- You could put it on an shared drive / dropbox etc.
Still:
- Managing permissions can be difficult
- It is difficult to keep track of who changes what
- You still need e-mail, IRC, etc. to coordinate and discuss changes
- github is a company that specializes in git hosting
- It combines git with social networking
- Free for open source projects
- 1.3 million users, 2 million git repos (as of 2/2012)
- You can follow coders and projects
- The news feed shows you what is going on
- Create an account on https://www.github.com
- Set up SSH keys see http://help.github.com/set-up-git-redirect
- Set your name and e-mail address
- Either create a new git repository
- Or find a project you want to contribute to and fork the repo
- Clone the repository
[$] git clone git@github.com:mluessi/gitexample.git- Set your name and e-mail address
[$] cd gitexample
[$] git config user.name "Firstname Lastname"
[$] git config user.email myemail@mail.comImportant: Use the same e-mail and name you use on github
- Start changing things, as we did before
- Remember: don't make changes in the master branch
- To keep your local repo up to date, pull changes from github
[$] git pull- Fork the repo on github and clone it to your machine (prev. slides)
- Create a new branch and check it out
[$] git branch alg_optimization
[$] git checkout alg_optimizationTip: You can do the same using git checkout -b alg_optimization
- Make your changes, commit them to the branch
- So far, all your changes are local, github does not know about them
- You need to push the branch to github
[$] git push origin alg_optimizationNote: origin is an alias for a remote repo, you can configure them using git remote
- Go to your repo on github
- Switch to your feature branch
- Make a Pull Request (PR)
This will:
- Send an e-mail notification to all authors
- The PR can be discussed
- You can discuss changes in individual lines
- You can keep pushing changes to your branch until everyone is happy
- Finally, the owners of the original repo can merge your changes
To learn more
- On git http://git-scm.com/documentation
- A good tutorial http://www.eecs.harvard.edu/~cduan/technical/git
- WIRED: Lord of the Files: How GitHub Tamed Free Software
- Details on how to contribute to a project on github
- Trick: show the current branch in your BASH prompt
If you did not like this talk, fork it, improve it, and create a PR
https://github.com/mluessi/intro-to-git-and-github