Deletions are marked like this. | Additions are marked like this. |
Line 12: | Line 12: |
Add this line to your {{{.cshrc}}} or {{{.bashrc}}} file. | Add the following line to your {{{.cshrc}}} or {{{.bashrc}}} file. |
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
For additional git specifics setting:
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.
$> 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:
$> rm README $> git pull $> git status deleted: README.txt $> git checkout README.txt
Additional information and examples:
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:
$> git commit -m "Fixed a bug." <file_name> $> git commit -m "More debug information" <file_name> $> git commit -m "Implemented a new feature." <file_name> $> git push
Always issue a git push command after committing all your changes
Additional information and examples:
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:
Start working here
git annex copy --to origin <file_name> |
Add a data file:
cvs |
cvs add <file_name> |
cvs commit <file_name> |
|
git |
git annex add <file_name> |
git commit <file_name> |
|
git push |
|
git annex copy --to origin <file_name> |
Remove data file:
cvs |
rm <file_name> |
cvs rm <file_name> |
|
cvs commit -m "Removing <file_name>" <file_name> |
|
git |
git rm <file_name> |
git commit -m "Removing <file_name>" <file_name> |
Undo 1 commit (before push):
git |
git reset --soft HEAD~1 |
Undo 2 commits:
git |
git reset --soft HEAD~2 |