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Brian Wandell edited this page Jan 16, 2018 · 16 revisions

VISTASOFT is on github. The GIT model we have adopted for vistalab is this.

  • Obtain a free github account
  • Clone the github to your computer
  • Before editing, create a branch. (You can push the branch back to github, if you like).
    git push -u origin <branchName>
  • If the edits are useful, issue a pull request at github. This is an email message asking others to check your edits and agree to merge them into the master branch
In addition to vistasoft, the vistlab github account includes other public repositories. Projects under development are also there, but they are not yet public. These include projects on diffusion, fMRI modeling, and computational modeling.

To learn more about git usage

Table of Contents

Overview

Get a git account by going to github or go to directly get a free account. If you want an account where you can have a private repository - say you are developing code for a class - then you can make a request here.

Git and github can be used in two different modes: if you wish to use git from the command line, you will need to make sure that your computer runs git. You can also download and install the most recent version from here. Alternatively, there are a variety of gui tools you can use to interface with git and github, Github software download. The tortoisegit software seems pretty good.

Learning how to use git

The web has a lot of resources for getting started with git. You should probably try to understand what git is doing first. There are also a bunch of online tutorials you can go through.

A good cognitive map of that territory is provided by the git parable. Ariel thinks you should go read it. Seriously.

We recommend learning how to use git command lines to interact with the repository. You can download git for all major platforms.

The github folks have grahical interfaces to git and to github-hosted repositories for some popular operating systems. GIT itself is then part of the distribution.

Download the github software. This will be a form that is specific to your operating system.

Working on Vistalab repositories

Clone the vistalab repository on your local machine

  • Go to a folder where you want to keep the code (for example, ~/matlab/git/)
  • Use the following command to clone your forked vistalab repository onto your local machine
 git clone http://github.com/vistalab/vistasoft.git

Editing the code in your repository

  • When you want to make a change to the code, create a branch to make your changes 
 git branch [new branch name]
  • Move into your new branch 
 git checkout [new branch name]
  • Edit on your branch
  • Commit your changes to your branch

Sharing your branch and changes with others

  • To share the changes on your branch, push it to github where others can see it
 git push origin [your branch name]
  • You can now see your branch and all of your changes on github!
  • If you think the changes are ready to be integrated into the main distribution, issue a pull request.

Working with Git Day to Day

Each operating system has different tools and ways to add a repository. We describe our current experiences here.

Make a new repository

If you already have code you want to put in your repository, go to the root directory of the code. Type 

 git init

If you type 

 git status

It will announce what files are there but they will not yet be added. To add everything you can type 

 git add *

This will add everything recursively. To check try 

 git status

To commit these, you can type 

 git commit -a

starting your default text editor. To get around this, use 

 git commit -am "Your commit message goes here"

This completes making the local repository on your machine.

Go to your github web site and sign in. Then create a repository on the github, following the instructions provided here. When you visit the web-page of the newly-created repository, it will contain the complete constructions of adding your branch to github. After you have added it (the first time), you can easily push any new changes that you have committed with the next line. 

 git push origin [branch name]

GIT tips

Git commands for users of SVN

Look at the bottom of this web page for information about how to avoid typing your password every time you push or pull.

A good resource

Configure 

 git config --global user.name

 git config --global core.editor

Show the remote URL (on github, usually) 

  git remote show origin

Pushing a local branch to github

Suppose you created a local branch, 'yourBranch', and you want to expose to others through your GitHub repository. You can push that branch into the github repository using the command 

 git push -u origin yourBranch

It is useful to set a global default for how you push data to github. The recommended default for our lab is 

 git config --global push.default simple

This option pushes your local branch (but not others) to github. Thus, you can change thisBranch and thatBranch. But only the changes in thisBranch will be pushed. Furthermore, the push will only occur if the name of the branch you are tracking on github matches the name of your local branch. (It is possible for myBranch to track otherNameBranch on github). Ugh.

The list of options (instead of simple) are described on this page.

Track a github branch locally

Suppose there is a branch called camera on github. You don't have a local version. To get it 

 git branch --track localName origin/remoteName

For example, to track dev on github with a local branch also named dev, type 

 git branch --track dev origin/dev

Commit and add in one command

Rather than git add XXX and git commit XXX you can use 

 git commit -a

To also type a comment use 

 git commit -am "YOUR COMMENT HERE"

Viewing the commit history

This is a nice way to set an alias to show commits 

 git config --global alias.hist 'log --pretty=format:"%h %ad | %s%d [%an]" --graph --date=short'

From this page

Restore a deleted file

Restore deleted file 

 git rev-list -n 1 HEAD -- <file_path>

Then checkout the version at the commit before, using the caret (^) symbol: 

 git checkout <deleting_commit>^ -- <file_path>

Get file from branch

Link 

 git checkout master               # first get back to master
 git checkout experiment -- app.js # then copy the version of app.js 
                                   # from branch "experiment"

Delete a branch 

  git branch -D branchName               % Local branch
  git push origin --delete branchName    % Remote branch

Override local changes with repository

Provided that the remote repository is origin, and that you're interested in master:

Get the origin and then 

 git fetch origin
 git reset --hard origin/master

This tells to fetch the commits from the remote repository, and position your working copy to the tip of its master branch. All your local commits not in the remote will be gone.

Revisiting a previous commit

Use git checkout to set the files to a previous commit. For example, suppose you know the SHA number of a commit. Then 

  git checkout SHA-NUMBER

will keep your repository in place but bring you back to the state at the time of that earlier commit. When you make this change, you will be told you are in a 'detached HEAD' state that lets you look around. To return to the HEAD, you can use git checkout <branchname></branchname>, or, I think git checkout HEAD.

There are related commands (reset and revert). But they do something more scary.

Stashing your work

Sometimes you are doing something and need to change to another branch. You aren't ready for a commitment. So, you want to stash your work. You can use 

 git stash

To see the list of things you have stashed you can use 

 git stash list

This shows you what has been stashed on all your branches. When you change back to the branch and want to get the stashed stuff back type 

 git stash apply

Revert a merge

Sometimes you merge and then want to undo it. This is straightforward if you have not yet pushed to the repository. In that case you can revert by the command 

 git revert commit_sha

This puts you back to the commit with the sha number commit_sha. You can see the different commit_sha values and their messages with the command 

 git log

If you have NOT pushed to github and you just want to go back 1 commit, you can use 

 git revert HEAD~1

See what you are about to push

If you want to see the differences between your local branch and the one on github, to understand what will happen if you execute a push, you can use 

  git diff --stat [remote/branch]

For example, 

  git diff --stat origin/master

Add a tag (label) to a commit

Label a commit (e.g., version 2.3) 

 git tag (shows the tags)
 git tag -a v1.4 -m 'my version 1.4' (Adds a tag and a message for this tag)

 <a href="http://git-scm.com/book/en/Git-Basics-Tagging" target="_blank">From the book</a>

Tips and tricks

Add branch name to terminal prompt

Once you start having many different branches of your repo, you will want to avoid getting confused about which branch you are currently working on. One way to do that is to make your terminal "git aware", by entering the following lines in your bashrc: 

  # Set the prompt to show the current git branch:
  function parse_git_branch {
    ref=$(git symbolic-ref HEAD 2> /dev/null) || return
    echo "("${ref#refs/heads/}")" 
  }
  PS1="\h:\W$RED \$(parse_git_branch)$NO_COLOR $"

Add global git account information

Git needs to recognize your name and email address to be able to access your online account.

If you do not specify them in the global configuration file they are configured automatically based on your username and hostname on the local computer.

You can set them explicitly as follows: 

    git config --global user.name "Your Name"
    git config --global user.email [email protected]

After doing this, you may fix the identity used for this commit with: 

    git commit --amend --reset-author
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