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This page is provided for !FreeSurfer developers to assist in the CVS -> git transition. Git is a feature loaded version control system which at times can be a bit of a hurdle to learn. However, when used in its simplest form it is very similar to most all other version control systems, including CVS. This page will give the basic CVS commands used by most !FreeSurfer developers the git equivalent of that command.

== 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
}}}



Checkout the stable branch:
{{{
$> git clone -b stable6 /space/freesurfer/repo/freesurfer

$> cvs checkout -r stable6 dev
}}}

== Daily Workflow ==


Commit a modified source code file:
||'''cvs'''||{{{cvs commit -m "Added new capabilities." <file_name>}}}||
||<|2>'''git'''||{{{git commit -m "Added new capabilities." <file_name>}}}||
||{{{git push}}}||

Modify and commit a data file:
||'''cvs'''||{{{cvs commit <file_name>}}}||
||<|5>'''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:
||<|2>'''cvs'''||{{{cvs add <file_name>}}}||
||{{{cvs commit <file_name>}}}||
||<|4>'''git'''||{{{git annex add <file_name>}}}||
||{{{git commit <file_name>}}}||
||{{{git push}}}||
||{{{git annex copy --to origin <file_name>}}}||


Remove data file:
||<|3>'''cvs'''||{{{rm <file_name>}}}||
||{{{cvs rm <file_name>}}}||
||{{{cvs commit -m "Removing <file_name>" <file_name>}}}||
||<|2>'''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}}}||