Git

<!DOCTYPE html> <html> <head> <title>Git</title> <meta charset="utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=3" /> <meta content="ImageJ Wiki" property="og:site_name"> <meta content="Git" property="og:title"> <meta content="article" property="og:type"> <meta content="The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants, including ImageJ2, Fiji, and others." property="og:description"> <meta content="https://imagej.github.io/develop/git/index" property="og:url"> <meta content="https://imagej.github.io/media/icons/imagej2.png" property="og:image"> <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png"> <link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png"> <link rel="icon" type="image/png" sizes="16x16" href="/favicon-16x16.png"> <link rel="manifest" 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href="/events/conferences">Conferences</a></li> <li><a href="/events/hackathons">Hackathons</a></li> <li><a href="/events">More...</a></li> </ul></details></li>  <li><details><summary><a href="/libs">Libraries</a></summary><ul> <li><a href="/libs/imagej-ops">ImageJ Ops</a></li> <li><a href="/libs/imagej-common">ImageJ Common</a></li> <li><a href="/libs/imagej-legacy">ImageJ Legacy</a></li> <li><a href="/libs/scijava">SciJava</a></li> <li><a href="/libs/scifio">SCIFIO</a></li> <li><details><summary><a href="/libs/imglib2">ImgLib2</a></summary><ul> <li><a href="/libs/imglib2/getting-started">Getting Started</a></li> <li><a href="/libs/imglib2/accessors">Accessors</a></li> <li><a href="/libs/imglib2/accessibles">Accessibles</a></li> <li><a href="/libs/imglib2/examples">Examples</a></li> <li><a href="/libs/imglib2/workshop-introductory">Introductory Workshop</a></li> <li><a href="/libs/imglib2/workshop-advanced">Advanced Workshop</a></li> <li><a href="/libs/imglib2/matlab">ImgLib2 images in MATLAB</a></li> <li><a href="/libs/imglib2/benchmarks">Benchmarks</a></li> <li><a href="/libs/imglib2/faq">FAQ</a></li> <li><a href="/libs/imglib2/developing">Developing ImgLib2</a></li> <li><a href="/libs/imglib2/discussion">ImgLib2 Discussion</a></li> </ul></details></li>  <li><a href="/libs">More...</a></li> </ul></details></li>  <li><details><summary><a href="/software">Software</a></summary><ul> <li><a href="/software/nih-image">NIH Image</a></li> <li><a href="/software/imagej">ImageJ</a></li> <li><a href="/software/imagej2">ImageJ2</a></li> <li><a href="/software/fiji">Fiji</a></li> <li><a href="/software">More...</a></li> </ul></details></li>  </ul></details></li>  </ul> </div> </section> <section id="right-column" class="sidebar dock">   <div id="toc" class="toc menu dockable"> <div class="drag-handle"></div> <h3>Page contents</h3> <ul data-toc="#content" data-toc-headings="h1,h2,h3,h4,h5,h6"></ul> </div> </section>  <div class="container"> <header class="major special"> <h1>Git</h1> </header> </div>   <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> <div class="notice" style="font-size: 2; background: #ebf2f8; border-left: 10px solid #67a1fe"><div class="notice-icon"><img src="/media/icons/info.svg" width="32" /></div><div class="notice-content"><p>If Git is completely new to you, read:</p> <ul> <li><a href="https://try.github.io/">TryGit 15-minute interactive tutorial</a></li> <li><a href="http://pcottle.github.io/learnGitBranching/">Learn Git Branching interactive tutorial</a></li> <li>“Git for dummies” tutorial below</li> </ul> <p>If you are passingly familiar with Git, but wish it was less arcane, check out:</p> <ul> <li><a href="http://think-like-a-git.net/">Think Like (a) Git - A Guide for the Perplexed</a></li> </ul> </div> </div> <p>Development of ImageJ and related software relies heavily on <a href="http://git-scm.com/">Git</a>. See the <a href="/develop/source">source code</a> page for information on where the Git repositories reside.</p> <h2 id="why-do-we-use-git">Why do we use Git?</h2> <ul> <li>Git is a first-class <a href="https://en.wikipedia.org/wiki/Distributed_version_control">distributed</a> <a href="https://en.wikipedia.org/wiki/Version_control">version control</a> system, so we use it to keep a record of changes to avoid loss-of-work and to appropriately explain/document changes as projects develop.</li> <li>Git history, which is composed of “snapshots” of the source code, can be used to go back at any point in time, which leads to reproducible science.</li> </ul> <h2 id="git-tutorials">Git tutorials</h2> <p>This website has lots of tutorials on Git; see the left sidebar.</p> <h2 id="rewriting-history">Rewriting history</h2> <p>One of the most powerful things Git can do is rewrite a series of patches after the fact. This is a powerful technique worth learning. There are many guides available here and elsewhere:</p> <ul> <li><a href="https://learngitbranching.js.org/">Learn Git Branching</a> is an interactive web tool where you can work through exercises covering a range of topics, including rebasing and rewriting history.</li> <li><a href="/develop/improving-the-code#modifying-your-commits">Modifying your commits</a> section of the <a href="/develop/improving-the-code">Contributing to a plugin</a> page</li> <li><a href="/develop/git/topic-branches#advanced-topic-branch-editing-ka-rebase-on-drugs">Advanced topic branch editing</a> section of the <a href="/develop/git/topic-branches">Git topic branches</a> tutorial</li> <li><a href="https://www.atlassian.com/git/tutorials/rewriting-history/">Rewriting history</a> tutorial from Atlassian</li> <li><a href="https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History">7.6 Git Tools - Rewriting History</a> from the Git book</li> <li><a href="https://help.github.com/articles/about-git-rebase/">About Git rebase</a> article from GitHub</li> <li><a href="https://help.github.com/articles/using-git-rebase/">Using Git rebase</a> article from GitHub</li> </ul> <h2 id="git-for-dummies">Git for dummies</h2> <h1 id="what-is-git">What is Git?</h1> <p>Git is a distributed Version Control System (“VCS”), or Source Code Management tool (“SCM”). The purpose is to track the development of source code through time, along with useful side information: Who did it? When? Why?</p> <h1 id="principles-of-git">Principles of Git</h1> <p>The source code lives in a <em>working directory</em>, where you have <em>tracked</em> files (i.e. files which are version-controlled) and <em>untracked</em> files (for example, <em>.class</em> files; they are generated from the source code, so they are uninteresting).</p> <p>The timeline of the development is made up of <em>revisions</em> (<em>commits</em> in Git speak) of the source code. Each commit knows about its predecessors. In the common case, commits form something like a perl of revisions. By comparing a commit to its <em>parent commit</em> (i.e. comparing a revision to the previous one), one can see the changes introduced by the “child” commit.</p> <p>Commits contain the names and contents of the tracked files, information about the author (and the committer, who does not need to be the author), the time of the commit, and a <em>commit message</em> where the author should say what the reasons for the changes are.</p> <p>To make a new commit, you first tell Git what changed contents you want to be part of the new commit by <em>adding</em> (or <em>staging</em>) them, and then performing the commit itself, which will open an editor in which you can type the commit message.</p> <p>All Git-specific things, such as revisions, are stored in the <em>repository</em>, which lives in the subdirectory <em>.git/</em> in your project’s root directory.</p> <p>To collaborate with others, there are also <em>remote repositories</em> from where you can <em>clone</em>, and with which you can synchronize by <em>fetching</em> and <em>pushing</em>.</p> <h1 id="why-do-i-need-git">Why do I need Git?</h1> <p>Git makes it not only to record what you did, it makes it easy to follow the development of other developers, and integrate those changes (<em>merge</em> in Git speak).</p> <p>Even if we are all brilliant developers, from time to time the program appears to be completely broken by our work. Git can tell you which changes you made relative to the current commit—quickly!</p> <p>Further benefits:</p> <ul> <li>Study the history of a project to understand not only <em>what</em> the developers did <em>when</em>, but also <em>why</em> by reading their commit messages (i.e., the log of changes).</li> <li>Recover any past revision, such as when the latest version suffers from a bug (i.e., a <em>regression</em>) not present in an older version.</li> <li>Easily <a href="/develop/git/pinpoint-regressions">find the commit which introduced such a regression</a>.</li> <li>Ensure the code and history is never lost, even if your machine fails—anyone with a <em>clone</em> of the repository has a copy of the entire history.</li> <li>Work on multiple new features or bug-fixes simultaneously, easily organizing and switching between them using <em>branches</em>.</li> </ul> <p>The only negative to Git is the activation barrier of learning it. Once you become proficient, Git is a huge asset to any development project.</p> <p>If you feel comfortable in using the commandline but you are still not familiar with Git the <strong><a href="/develop/git/workshop">Git workshop</a></strong> page might be a perfect entry point for you.</p> <p>If the commandline is not your favorite playground you can have a look at the Git integration <strong><a href="/develop/git/eclipse">EGit</a></strong> in the <strong><a href="/develop/eclipse">Eclipse</a></strong> IDE.</p> <h1 id="essential-git-commands">Essential Git commands</h1> <p>Except for the <em>clone</em> command, this follows the common workflow:</p> <ul> <li> <p><code class="language-plaintext highlighter-rouge">git diff HEAD</code> will show you the changes of your working directory relative to the current commit.</p> </li> <li> <p><code class="language-plaintext highlighter-rouge">git add <file>...</code> tells Git that you want the next commit to contain the current version of that file/these files.</p> </li> <li> <p><code class="language-plaintext highlighter-rouge">git commit</code> tells Git that you want to commit a new revision with all staged changes.</p> </li> <li> <p><code class="language-plaintext highlighter-rouge">git fetch origin</code> synchronizes the local copy of the default remote repository.</p> </li> <li> <p><code class="language-plaintext highlighter-rouge">git merge origin/master</code> integrates the default remote repository’s changes into your local repository and working directory (<u>never</u> do this when you have uncommitted changes!).</p> </li> <li> <p><code class="language-plaintext highlighter-rouge">git push origin HEAD</code> publish your changes in the remote repository.</p> </li> </ul> <p>Initially, you need to start from somewhere:</p> <ul> <li><code class="language-plaintext highlighter-rouge">git clone <URL></code> will make a new local repository and initialize it from a remote one.</li> </ul> <p>See also the more verbose <a href="/develop/git/mini-howto">Git mini howto</a>.</p> <h1 id="substantial-differences-to-other-version-control-systems">Substantial differences to other version control systems</h1> <p>If you know CVS or Subversion, you are in for some surprises:</p> <ul> <li>In Git, each repository is local. To publish your changes, you need to have a remote repository, too, and <em>push</em> your work there.</li> <li>In Git, <a href="/develop/git/topic-branches">branches</a> are easy and fast.</li> <li>In Git, you <code class="language-plaintext highlighter-rouge">git add</code> <u>content</u>, not files. In other words, when the file <em>README</em> is already tracked, <code class="language-plaintext highlighter-rouge">git add README</code> will tell Git that you want the changes in said file to be part of the next commit.</li> <li>In Git, you <u>never, ever</u> try to integrate remote changes into an uncommitted state. In other words, if you have uncommitted changes, you <u>always</u> commit them before calling <code class="language-plaintext highlighter-rouge">git fetch origin; git merge origin/master</code>.</li> </ul> </div> </div> </section>  <section id="footer"> <ul class="icons"> <li><a href="https://forum.image.sc/tag/imagej" class="icon alt"><img src="/media/icons/image-sc.png" width="24" style="vertical-align: middle; margin-top: -10px"><span class="label">Forum</span></a></li> <li><a href="https://twitter.com/hashtag/ImageJ" class="icon brands alt fa-twitter"><span class="label">Twitter</span></a></li> <li><a href="https://github.com/imagej" class="icon brands alt fa-github"><span class="label">GitHub</span></a></li> </ul> <ul class="copyright"> <li>Design: <a href="http://html5up.net">HTML5 UP</a></li> </ul> </section>  <nav role="navigation"> <div id="ham-toggle"> <input type="checkbox" /> <span></span>  <span></span>  <span></span>  <ul id="ham-menu"> <div class="menu"><h3>ImageJ 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