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\documentclass[slidestop]{beamer}

\title{Working with branches in Git}
\providecommand{\myConference}{Git course}
\providecommand{\myDate}{Monday, October 14, 2013}
\author{Martijn Vermaat}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\providecommand{\lastCenterLogo}{
  \raisebox{-0.1cm}{
    \includegraphics[height=1cm]{lgtc_logo}
    %\includegraphics[height=0.7cm]{ngi_logo}
  }
}
\providecommand{\lastRightLogo}{
  %\includegraphics[height=0.7cm]{nbic_logo}
  %\includegraphics[height=0.8cm]{nwo_logo_en}
  %\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
}

\usetheme{lumc}

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\lstset{
  basicstyle=\ttfamily,
  language=none,
  frame=none,
  numbers=none,
  numbersep=0
}

\AtBeginSection[]
{
  \begin{frame}
    \frametitle{Table of contents}
    \tableofcontents[currentsection]
  \end{frame}
}

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\begin{document}

% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}

% Make the title page.
\bodytemplate

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\section{The Git commit graph}
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\begin{frame}
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  \frametitle{A linear history}
  \includegraphics[width=10cm]{images/linear}
  \begin{itemize}
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    \item Every commit has a parent.
    \item {\em Committing} creates a new commit on top of the current one.
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  \end{itemize}
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\end{frame}

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\begin{frame}
  \frametitle{The default \bt{master} branch}
  \includegraphics[width=10cm]{images/master}
  \begin{itemize}
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    \item A {\em branch} is a pointer to a commit.
    \item By default there is one branch: \bt{master}.
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  \end{itemize}
\end{frame}

\begin{frame}
  \frametitle{The current commit: \bt{HEAD}}
  \begin{itemize}
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    \item The current commit is called \bt{HEAD} (shown in blue here).
    \item \bt{HEAD} is actually a pointer to the current branch.
    \item (Or to the current commit if there is no current branch -- this is
      called detached head state.)
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  \end{itemize}
  \vspace{1cm}
  \includegraphics[width=10cm]{images/head}
\end{frame}

\begin{frame}
  \frametitle{Committing moves \bt{HEAD} and the current branch}
  \begin{itemize}
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    \item Committing moves the current branch to the new commit.
    \item Of course, \bt{HEAD} moves with it.
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    \item (In detached head state, only \bt{HEAD} moves.)
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  \end{itemize}
  \vspace{1cm}
  \includegraphics[width=10cm]{images/commit}
\end{frame}

\begin{frame}
  \frametitle{A non-linear history}
  \includegraphics[width=10cm]{images/nonlinear}
  \begin{itemize}
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    \item The commit graph can become non-linear.
    \item Usually by committing from the same commit twice.
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  \end{itemize}
\end{frame}

\begin{frame}
  \frametitle{Use branches to keep track of different code paths}
  \begin{itemize}
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    \item Branch names are easier to remember than commit hashes.
    \item Branch names make it clear what commits are about.
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  \end{itemize}
  \vspace{0.5cm}
  \includegraphics[width=6cm]{images/branches}
\end{frame}

\begin{frame}
  \frametitle{Different code paths may later join}
  \begin{itemize}
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    \item Commits from different branches can be brought together.
    \item We call this {\em merging}.
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  \end{itemize}
  \vspace{0.5cm}
  \includegraphics[width=6cm]{images/merge}
\end{frame}


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\section{Inspecting the commit graph}
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\begin{frame}
  \frametitle{An example repository}
  \includegraphics[width=8cm]{images/example}
  \begin{itemize}
    \item Branches \bt{license} and \bt{interface} diverged from \bt{master}.
    \item Only \bt{license} has been merged back into \bt{master}.
    \item Current branch is \bt{master}.
  \end{itemize}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Showing the current branch: \bt{git status}}
  \begin{lstlisting}
$ git status
# On branch master
nothing to commit (working directory clean)
  \end{lstlisting}
  \bigskip
  Remember: you cannot type \bt{git status} enough!
\end{frame}

\begin{frame}[fragile]
  \frametitle{Listing branches: \bt{git branch}}
  \begin{lstlisting}
$ git branch
  interface
  license
* master
  \end{lstlisting}
  \bigskip
  Three branches, current branch is \bt{master}.
  \pause
  \bigskip
  \begin{lstlisting}
$ git branch -v
  interface 8fc25c1 Trivial Python interface
  license   0fbe3e3 Add MIT license
* master    c7f3bd9 Add .gitignore file
  \end{lstlisting}
  \bigskip
  \bt{-v}: Shows the commit each branch points to.
\end{frame}

\begin{frame}[fragile]
  \frametitle{The commit log: \bt{git log}}
  \begin{lstlisting}
$ git log --oneline --decorate
c7f3bd9 (HEAD, master) Add .gitignore file
4a44c4e Merge branch 'license'
64af1ee Add course teachers to README
0fbe3e3 (license) Add MIT license
d1c7fd7 Initial commit with README
  \end{lstlisting}
  \bigskip
  \bt{--oneline}: Shows commit summary on one line.

  \bt{--decorate}: Adds branch information.
\end{frame}

\begin{frame}[fragile]
  \frametitle{The commit log as a graph: \bt{git log}}
  \begin{lstlisting}
$ git log --oneline --decorate --graph --all
* 8fc25c1 (interface) Trivial Python interface
| * c7f3bd9 (HEAD, master) Add .gitignore file
|/
*   4a44c4e Merge branch 'license'
|\
| * 0fbe3e3 (license) Add MIT license
* | 64af1ee Add course teachers to README
|/
* d1c7fd7 Initial commit with README
  \end{lstlisting}
  \bigskip
  \bt{--graph}: Shows the commit graph.

  \bt{--all}: Includes all branches instead of just the current.
\end{frame}
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\begin{frame}[fragile]
  \frametitle{Switching to another branch: \bt{git checkout}}
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  \begin{lstlisting}
$ git checkout interface
Switched to branch 'interface'
  \end{lstlisting}
  \bigskip
  This points \bt{HEAD} to the named branch and updates your working
  directory.
  \pause
  \bigskip
  \begin{lstlisting}
$ git status
# On branch interface
nothing to commit (working directory clean)
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  \end{lstlisting}
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\end{frame}


\section{Manipulating the commit graph}

\begin{frame}
  \frametitle{An example repository}
  \includegraphics[width=8cm]{images/example}
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  \begin{itemize}
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    \item Branches \bt{license} and \bt{interface} diverged from \bt{master}.
    \item Only \bt{license} has been merged back into \bt{master}.
    \item Current branch is \bt{master}.
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  \end{itemize}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Creating a new branch: \bt{git branch}}
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  \begin{lstlisting}
$ git branch lib
  \end{lstlisting}
  \bigskip
  Creates branch \bt{lib} at \bt{HEAD}.
  \pause
  \bigskip
  \begin{lstlisting}
$ git checkout lib
Switched to branch 'lib'
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  \end{lstlisting}
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  \pause
  \bigskip
  Or, for Git pro's, in one command:
  \bigskip
  \begin{lstlisting}
$ git checkout -b lib
Switched to a new branch 'lib'
  \end{lstlisting}
  \bigskip
  At this point, \bt{lib} is just a label to the same commit as \bt{master}.
\end{frame}

\begin{frame}
  \frametitle{Our example repository}
  \includegraphics[width=8cm]{images/example-branched}\\
  \vspace{0.5cm}
  Created branch \bt{lib} from \bt{master}.
\end{frame}

\begin{frame}[fragile]
  \frametitle{Working on a branch: \bt{git commit}}
  We can extend the \bt{lib} branch by adding commits.
  \bigskip
  \begin{lstlisting}
$ echo 'VERSION=1' > testlib.py
$ git add testlib.py
$ git commit -m 'Add empty testlib'
  \end{lstlisting}
  \pause
  \bigskip
  \begin{lstlisting}
$ git log --oneline --decorate --graph --all
* 251a51b (HEAD, lib) Add empty testlib
* c7f3bd9 (master) Add .gitignore file
| * 8fc25c1 (interface) Trivial Python interface
|/
*   4a44c4e Merge branch 'license'
|\
| * 0fbe3e3 (license) Add MIT license
...
  \end{lstlisting}
\end{frame}

\begin{frame}
  \frametitle{Our example repository}
  \includegraphics[width=8cm]{images/example-committed}\\
  \vspace{0.5cm}
  Extended branch \bt{lib}.
\end{frame}

\begin{frame}[fragile]
  \frametitle{Fast forward merging: \bt{git merge}}
  Let's merge our work on \bt{lib} back into \bt{master}.
  \bigskip
  \begin{lstlisting}
$ git checkout master
Switched to branch 'master'
$ git merge lib
Updating c7f3bd9..251a51b
Fast-forward
 testlib.py |    1 +
 1 file changed, 1 insertion(+)
 create mode 100644 testlib.py
  \end{lstlisting}
  \bigskip
  This merge was easy:
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  \begin{itemize}
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    \item \bt{lib} was directly upstream of \bt{master}.
    \item Git just moves \bt{HEAD} and \bt{master} to point to \bt{lib}.
    \item This is called a {\em fast forward merge}.
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  \end{itemize}
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\end{frame}

\begin{frame}
  \frametitle{Our example repository}
  \includegraphics[width=8cm]{images/example-merged-ff}\\
  \vspace{0.5cm}
  Merged branch \bt{lib} into \bt{master} (fast forward).
\end{frame}

\begin{frame}[fragile]
  \frametitle{Three-way merging: \bt{git merge}}
  Let's merge our work on \bt{interface} back into \bt{master}.
  \bigskip
  \begin{lstlisting}
$ git merge interface
Merge made by the 'recursive' strategy.
 interface.py |    3 +++
 1 file changed, 3 insertions(+)
 create mode 100755 interface.py
  \end{lstlisting}
  \bigskip
  This merge was harder:
  \begin{itemize}
    \item \bt{interface} and \bt{master} had diverged.
    \item Git determines changes in \bt{interface} and \bt{master} since their
      most recent common ancestor and creates a new commit from that.
    \item This is called a {\em recursive three-way merge} and the resulting
      merge a {\em merge commit}.
  \end{itemize}
\end{frame}

\begin{frame}
  \frametitle{Our example repository}
  \includegraphics[width=8cm]{images/example-merged}\\
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  \vspace{0.5cm}
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  Merged branch \bt{interface} into \bt{master}.
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\end{frame}

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\begin{frame}[fragile]
  \frametitle{Deleting branches: \bt{git branch}}
  Old branches that have been merged can be deleted.
  \bigskip
  \begin{lstlisting}
$ git branch -d interface
Deleted branch interface (was 8fc25c1).
  \end{lstlisting}
  \bigskip
  \begin{lstlisting}
$ git branch -d lib license
Deleted branch lib (was 251a51b).
Deleted branch license (was 0fbe3e3).
  \end{lstlisting}
  \bigskip
  No history is lost, just labels removed.
\end{frame}


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\section{Basic merge conflicts}

\begin{frame}
  \frametitle{Merge conflicts}
  Git is pretty good at merging:
  \begin{itemize}
    \item The changes might have been in different files.
    \item Or in different parts of the same file.
    \item Git tries to figure out a sensible result.
  \end{itemize}
  \pause
  \bigskip
  Sometimes this is not possible:
  \begin{itemize}
    \item The changes might be incompatible.
    \item When we try \bt{git merge}, Git gives up.
    \item This situation is called a {\em merge conflict}.
  \end{itemize}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Setting the stage (1/3)}
  \begin{lstlisting}
$ git log --oneline --decorate --graph --all
* 9d2ad27 (HEAD, master) State character preference
| * 374ab60 (simpsons) State character preference
|/
* 4012f4f Initial commit
  \end{lstlisting}
  \bigskip
  We'd like to merge branch \bt{simpsons} into \bt{master}.
\end{frame}

\begin{frame}[fragile]
  \frametitle{Setting the stage (2/3)}
  The last commit on \bt{master}:
  \bigskip
  \begin{lstlisting}
$ git show --oneline
9d2ad27 State character preference
diff --git a/README b/README
index de15194..ef40359 100644
--- a/README
+++ b/README
@@ -1,2 +1,4 @@
 Facts about television series
 =============================
+
+My favorite character is Eric Cartman.
  \end{lstlisting}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Setting the stage (3/3)}
  The last commit on \bt{simpsons}:
  \bigskip
  \begin{lstlisting}
$ git show --oneline simpsons
374ab60 State character preference
diff --git a/README b/README
index de15194..9dd729b 100644
--- a/README
+++ b/README
@@ -1,2 +1,4 @@
 Facts about television series
 =============================
+
+My favorite character is Homer Simpson.
  \end{lstlisting}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Creating a merge conflict}
  \begin{lstlisting}
$ git merge simpsons
Auto-merging README
CONFLICT (content): Merge conflict in README
Automatic merge failed; fix conflicts and then
commit the result.
  \end{lstlisting}
  \bigskip
  \begin{lstlisting}
$ git status
# On branch master
# Unmerged paths:
#   (use "git add/rm <file>.." as appropriate to
#    mark resolution)
#
#              both modified:      README
#
no changes added to commit (use "git add" and/or
"git commit -a")
  \end{lstlisting}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Resolving a merge conflict (1/2)}
  \begin{lstlisting}
$ cat README
Facts about television series
=============================

<<<<<<< HEAD
My favorite character is Eric Cartman.
=======
My favorite character is Homer Simpson.
>>>>>>> simpsons
  \end{lstlisting}
  \bigskip
  What we had is under \bt{HEAD}, what \bt{simpsons} had is above
  \bt{simpsons}.
  \pause
  \bigskip
  \begin{lstlisting}
$ emacs README
  \end{lstlisting}
\end{frame}

\begin{frame}[fragile]
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  \frametitle{Resolving a merge conflict (2/2)}
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  We resolve the conflict by hand.
  \bigskip
  \begin{lstlisting}
$ cat README
Facts about television series
=============================

My favorite characters are Eric Cartman
and Homer Simpson.
  \end{lstlisting}
  \pause
  \bigskip
  And can now finish the merge commit.
  \bigskip
  \begin{lstlisting}
$ git add README
$ git commit
[master 1e496cb] Merge branch 'simpsons'
  \end{lstlisting}
\end{frame}

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\begin{frame}[fragile]
  \frametitle{Aborting a merge}
  If you don't feel like resolving the merge conflict, you can go back with
  \bt{git merge --abort}.
  \bigskip
  \begin{lstlisting}
$ git merge simpsons
Auto-merging README
CONFLICT (content): Merge conflict in README
Automatic merge failed; fix conflicts and then
commit the result.
  \end{lstlisting}
  \bigskip
  \begin{lstlisting}
$ git merge --abort
  \end{lstlisting}
  \bigskip
  \begin{lstlisting}
$ git status
# On branch master
nothing to commit (working directory clean)
  \end{lstlisting}
\end{frame}

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\begin{frame}[fragile]
  \frametitle{Resolving conflicts with \bt{git mergetool}}
  We can also use graphical merge tools such as {\em Meld}.
  \bigskip
  \begin{lstlisting}
$ git mergetool
merge tool candidates: meld opendiff kdiff3 ...
Merging:
README

Normal merge conflict for 'README':
  {local}: modified file
  {remote}: modified file
Hit return to start merge resolution tool (meld):
  \end{lstlisting}
\end{frame}

\begin{frame}
  \frametitle{Meld example}
  \includegraphics[width=11cm]{images/meld}\\
  \vspace{0.5cm}
  Tools like Meld provide an editable three-way diff.
\end{frame}
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\section{Questions?}
\lastpagetemplate
\begin{frame}
  \begin{center}
    Acknowledgements:
    \bigskip
    \bigskip

    Jeroen Laros

    Zuotian Tatum

  \end{center}
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  \vfill
  \permfoot{http://git-scm.com/book}\\
  \permfoot{https://www.atlassian.com/git}
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\end{frame}

\end{document}