| Deletions are marked like this. | Additions are marked like this. |
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| Checkout the stable branch: | If you wanted to check out a specific branch, you could do that in a couple different ways: |
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| $> git clone -b stable6 /space/freesurfer/repo/freesurfer <optional_directory_name> | $> git clone -b stable6 /space/freesurfer/repo/freesurfer |
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Additional examples: [[https://git-scm.com/book/en/v2/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository|Cloning-an-Existing-Repository]] [[https://www.atlassian.com/git/tutorials/setting-up-a-repository/git-clone|git-clone]] |
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
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 examples of git specifics setting (e.g. default editor, color settings), see the following page: https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration
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:
$> git clone /space/freesurfer/repo/freesurfer
If you wanted to check out a specific branch, you could do that in a couple different ways:
$> git clone /space/freesurfer/repo/freesurfer $> cd freesurfer $> git checkout stable6 or, $> git clone -b stable6 /space/freesurfer/repo/freesurfer
Additional examples: Cloning-an-Existing-Repository
Daily Workflow
Commit a modified source code file:
cvs |
cvs commit -m "Added new capabilities." <file_name> |
git |
git commit -m "Added new capabilities." <file_name> |
git push |
Modify and commit a data file:
cvs |
cvs commit <file_name> |
git |
git annex unlock <file_name> |
git annex add <file_name> |
|
git commit <file_name> |
|
git push |
|
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 |