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| Checkout out the main branch: ||'''cvs'''||{{{cvs checkout dev}}}|| ||'''git'''||{{{git clone /space/freesurfer/repo/freesurfer}}}|| |
#acl LcnGroup:read,write,delete,revert All: |
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| Checkout the stable branch: ||'''cvs'''||{{{cvs checkout -r stable6 dev}}}|| ||'''git'''||{{{git clone -b stable6 /space/freesurfer/repo/freesurfer}}}|| |
This page is provided for !FreeSurfer developers to assist in the CVS -> git transition. |
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| Commit a modified source code file: | 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 == 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 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|git-clone]] == 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: [[https://www.atlassian.com/git/tutorials/syncing/git-pull|git-pull]] === Commit a modified source code file === 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. You always need to issue a |
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| ||{{{git push .}}}|| | ||{{{git push}}}|| |
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| Commit a modified data file: | Modify and commit a data file: |
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| ||<|3>'''git'''||{{{git annex unlock <file_name>}}}|| | ||<|5>'''git'''||{{{git annex unlock <file_name>}}}|| ||{{{git annex add <file_name>}}}|| |
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| ||{{{git push}}}|| | |
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| 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>}}}|| |
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| ||{{{git reset --soft HEAD~1}}}|| | ||'''git'''||{{{git reset --soft HEAD~1}}}|| |
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| ||{{{git reset --soft HEAD~2}}}|| | ||'''git'''||{{{git reset --soft HEAD~2}}}|| |
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 information and examples:
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.txtAdditional information and examples:
Commit a modified source code file
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. You always need to issue a
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> |
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git commit <file_name> |
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git push |
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git annex copy --to origin <file_name> |
Add a data file:
cvs |
cvs add <file_name> |
cvs commit <file_name> |
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git |
git annex add <file_name> |
git commit <file_name> |
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git push |
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git annex copy --to origin <file_name> |
Remove data file:
cvs |
rm <file_name> |
cvs rm <file_name> |
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cvs commit -m "Removing <file_name>" <file_name> |
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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 |