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\documentclass[slidestop]{beamer}

\title{Combining changes by merging}
\providecommand{\myConference}{Git course}
\providecommand{\myDate}{Tueday, December 1, 2015}
\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}
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\usetheme{lumc}

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

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

\begin{document}

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

% Make the title page.
\bodytemplate


\section{The Git commit graph}

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

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

\begin{frame}
  \frametitle{Committing moves the current branch pointer}
  \begin{itemize}
    \item Committing moves the current branch to the new commit.
    \item (Of course, \bt{HEAD} moves with it.)
  \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}
    \item The commit graph can become non-linear.
    \item Usually by committing from the same commit twice.
  \end{itemize}
\end{frame}

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

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


\section{Inspecting the commit graph}

\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{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}

\begin{frame}
  \frametitle{Remote branches}
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  In this course, we don't really discuss branches, except:
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  \begin{itemize}
    \item Commits from a remote show up as a remote branch.
    \item Even with only a \bt{master} branch, remotes might still diverge.
    \item Merging remote branches is just like merging local branches.
  \end{itemize}
  \bigskip
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  \includegraphics[width=10cm]{images/example-hue}
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\end{frame}


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\section{Merging from remotes}
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\begin{frame}
  \frametitle{An example repository}
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  \includegraphics[width=10cm]{images/example-hue}\\
  \bigskip
  Branch \bt{master} on \bt{hue} is one commit ahead of our \bt{master} and we
  have already seen how to merge \bt{hue/master} into \bt{master}:
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  \begin{itemize}
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    \item \bt{git merge hue/master}
    \item This was easy: Git just moves \bt{master} (and \bt{HEAD}) to point
      to \bt{hue/master}.
    \item It is called a {\em fast forward merge}.
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  \end{itemize}
\end{frame}

\begin{frame}[fragile]
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  \frametitle{Fast forward merging: \bt{git merge}}
  If a remote branch is ahead of us, it can be merged easily:
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  \bigskip
  \begin{lstlisting}
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$ git merge hue/master
Updating c7f3bd9..251a51b
Fast-forward
testlib.py |    2 +
1 file changed, 2 insertions(+)
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  \end{lstlisting}
  \bigskip
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  \includegraphics[width=10cm]{images/example-hue-merged}
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\end{frame}


\begin{frame}
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  \frametitle{An example repository}
  \includegraphics[width=8cm]{images/example-hue-diverged}\\
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  \bigskip
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  Branch \bt{master} on \bt{hue} and our \bt{master} have diverged and merging
  now seems less straightforward.
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  \begin{itemize}
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    \item \bt{git merge hue/master}
    \item Git will create a new commit in which it combines both changes.
    \item It is called a {\em three-way merge}.
    \item The {\em merge commit} has two parents.
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  \end{itemize}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Three-way merging: \bt{git merge}}
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  Let's merge the remote work on \bt{master} back into our local \bt{master}:
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  \bigskip
  \begin{lstlisting}
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$ git merge hue/master
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Merge made by the 'recursive' strategy.
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 FACTS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
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  \end{lstlisting}
  \bigskip
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  \includegraphics[width=9cm]{images/example-hue-merged2}
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\end{frame}

\begin{frame}[fragile]
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  \frametitle{The other way around}
  \bt{git push} also does an implicit \bt{git merge} on the remote.
  \begin{itemize}
    \item We send our local commits to the remote.
    \item They are merged into the remote branch.
    \item But only if this is a fast-forward merge.
    \item Diverging commits {\em cannot be pushed directly}.
  \end{itemize}
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  \bigskip
  \bigskip
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  \includegraphics[width=10cm]{images/example-hue-pushed}
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\end{frame}


\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}
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* 5edaf08 (hue/master, hue/HEAD) State character preference
| * f1ef19c (HEAD, master) State character preference
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|/
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* 1f6d2ab Initial commit
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  \end{lstlisting}
  \bigskip
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  We'd like to merge branch \bt{hue/master} into \bt{master}.
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\end{frame}

\begin{frame}[fragile]
  \frametitle{Setting the stage (2/3)}
  The last commit on \bt{master}:
  \bigskip
  \begin{lstlisting}
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f1ef19c State character preference
diff --git a/FACTS.md b/FACTS.md
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index de15194..ef40359 100644
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--- a/FACTS.md
+++ b/FACTS.md
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@@ -1,2 +1,4 @@
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Facts about television series
=============================
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+
+My favorite character is Eric Cartman.
  \end{lstlisting}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Setting the stage (3/3)}
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  The last commit on \bt{hue/master}:
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  \bigskip
  \begin{lstlisting}
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$ git show --oneline hue/master
5edaf08 State character preference
diff --git a/FACTS.md b/FACTS.md
index de15194..5e69508 100644
--- a/FACTS.md
+++ b/FACTS.md
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@@ -1,2 +1,4 @@
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Facts about television series
=============================
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+
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+My favorite character is Milhouse.
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  \end{lstlisting}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Creating a merge conflict}
  \begin{lstlisting}
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$ git merge hue/master
Auto-merging FACTS.md
CONFLICT (content): Merge conflict in FACTS.md
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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)
#
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#              both modified:      FACTS.md
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#
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}
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$ cat FACTS.md
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Facts about television series
=============================

<<<<<<< HEAD
My favorite character is Eric Cartman.
=======
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My favorite character is Milhouse.
>>>>>>> hue/master
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  \end{lstlisting}
  \bigskip
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  What we had is under \bt{HEAD}, what \bt{hue/master} had is above
  \bt{hue/maser}.
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  \pause
  \bigskip
  \begin{lstlisting}
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$ nano FACTS.md
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  \end{lstlisting}
\end{frame}

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

My favorite characters are Eric Cartman
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and Milhouse.
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  \end{lstlisting}
  \pause
  \bigskip
  And can now finish the merge commit.
  \bigskip
  \begin{lstlisting}
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$ git add FACTS.md
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$ git commit
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[master 1e496cb] Merge remote-tracking branch 'hue/master'
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  \end{lstlisting}
\end{frame}

\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}
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$ git merge hue/master
Auto-merging FACTS.md
CONFLICT (content): Merge conflict in FACTS.md
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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}

\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:
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FACTS.md
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Normal merge conflict for 'FACTS.md':
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  {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}


\section{Questions?}
\lastpagetemplate
\begin{frame}
  \begin{center}
    Acknowledgements:
    \bigskip
    \bigskip

    Jeroen Laros

    Zuotian Tatum

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

\end{document}