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| #acl LcnGroup:read,write,delete,revert All: 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 [[https://www.atlassian.com/git/tutorials/what-is-git|Atlassian]] and [[https://git-scm.com/doc|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: [[https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration|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: [[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|Cloning-an-Existing-Repository]] == Daily Workflow == {{attachment:git-image-50.jpeg}} === 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 ## git $> git pull $> git status deleted: README.txt modified: configure.in $> git checkout README.txt }}} Additional information and examples: [[https://www.atlassian.com/git/tutorials/syncing/git-pull|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: [[https://www.atlassian.com/git/tutorials/saving-changes|Saving changes]] [[https://git-scm.com/book/en/v2/Git-Basics-Recording-Changes-to-the-Repository|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: [[https://www.atlassian.com/git/tutorials/saving-changes/git-add|git-add]] [[https://git-scm.com/book/en/v2/Git-Basics-Recording-Changes-to-the-Repository#Tracking-New-Files|Tracking-New-Files]] === Start working here === ||{{{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}}}|| |
- Diff for "Freesurfer_git"