• Freesurfer_git

This page is provided for FreeSurfer developers to assist in the CVS -> git transition.

This page is not meant to be a comprehensive guide for using git. Git is a feature loaded version control system which at times can be a bit of a hurdle to learn. The following site However, when used in its simplest form it is very similar to most all other version control systems, including CVS. Below are many of the basic CVS commands used by FreeSurfer developers the git equivalent of that command. The Atlassian and git-scm are great resources for those who want to dig deeper and and learn more about git and its features.

Initial Git Setup

Very first thing to do. Add the following line to your .cshrc or .bashrc file.

## bash
export PATH=/usr/pubsw/packages/git-annex/current/bin:$PATH

## csh
setenv PATH "/usr/pubsw/packages/git-annex/current/bin":"$PATH"

When we start out using git we want to set a few of our configuration settings. We only need to do this one time:

$> cd ~
$> git config --global user.name "Zeke Kaufman"
$> git config --global user.email zkaufman@nmr.mgh.harvard.edu
$> git config --global color.ui true

For additional git specifics setting:

Customizing-Git

Checkout out the main branch

When working with CVS, we would checkout out the FreeSurfer repository using the cvs checkout dev command. In git we 'clone' repositories. This gives us a local version of the repository which we can work with:

## CVS 
$> cvs checkout dev

## git
$> git clone /space/freesurfer/repo/freesurfer

Or check out a specific branch:

## CVS
$> cvs checkout -r stable6 dev

## git
$> git clone -b stable6 /space/freesurfer/repo/freesurfer

Additional information and examples:

Cloning-an-Existing-Repository

Cloning-an-Existing-Repository

Daily Workflow

Updating your code

In CVS, when we want the most up-to-date version of the code, we issue a cvs update command. This will update our files to the latest version, restore any missing files, and warn us of any conflicts. The nearest equivalent in git is the git pull command. This will update our local repository and update all the necessary files to the most recent version. It is good practice to always issue a git pull command before starting to work on any files.

## CVS
$> cvs update

## git
$> git pull

One major difference between cvs update and git pull command is that git pull will not restore any missing files (i.e. files that we deleted locally). In git, if we want to restore locally deleted files, we need to take the additional step of issuing a git checkout command. For example:

Example:

## CVS
$> cvs update
  cvs update: warning: README was lost
  U README
  M configure.in

## git
$> git pull
$> git status

    deleted:    README.txt
    modified:   configure.in

$> git checkout README.txt

Additional information and examples:

Git Pull

Viewing differences

Generating diffs between your working copy of the code, and the repository version, is also very similar with git and cvs. For example, say we want to look at the differences in the README file:

## CVS
$> cvs diff README
  Index: README
  ===================================================================
  RCS file: /space/repo/1/dev/dev/README,v
  retrieving revision 1.13
  diff -r1.13 README
  20a21
  > An example line of added text.

In git this looks like:

## git
$> git diff README
  diff --git a/README b/README
  index 95ec88a..d4686af 100644
  --- a/README
  +++ b/README
  @@ -18,3 +18,4 @@
  +An example line of added text.

View log information

Again, this is nearly identical with cvs and git:

Commit a change

Git and CVS can be virtually identical when it comes to committing changes. The primary difference is that git requires the additional step of pushing to the central repository. This means issuing the git push command after committing all your changes:

## CVS 
$> git commit -m "Fixed a bug." <file_name>
$> git commit -m "More debug information" <file_name> 

## git
$> git commit -m "Fixed a bug." <file_name>
$> git commit -m "More debug information" <file_name> 
$> git push   ## DON'T FORGET TO DO THIS!!

Always issue a git push command after committing all your changes

Additional information and examples:

Saving changes

Recording changes to the repository

Adding/Removing a file

Adding and removing files in CVS and git is also a very similar operation. Use the git rm and git add command in the same way you would use the cvs rm and cvs add command. Just remember to commit the change, followed by a git push. For example,

Adding a file:

$> git add <file_name>
$> git commit -m "initial add of new file." <file_name>
$> git push

Removing a file:

$> git rm <file_name>
$> git commit -m "Removing obsolete file." <file_name>
$> git push

Additional information and examples:

git-add

Tracking-New-Files

Start working here

Add a data file:

Remove data file:

Undo 1 commit (before push):

Undo 2 commits: