Merge remote-tracking branch 'origin/branching'

README.md

-# Git Introduction Course
+# Git introduction course
 
 This course aims at everyone who works in the Bioinformatics field. We cover a
-*version control system* named **git**. This system is widely used by software
+*version control system* named *Git*. This system is widely used by software
 developers, but can also be used for project management. By keeping track of
 all versions, history, etc. collaboration with colleagues is easy and your
 analysis will be reproducible.
 
-The presentations are made in LaTeX, for the template and stylesheet, go
+The presentations are made in *LaTeX*, for the template and stylesheet, go
 [here](https://humgenprojects.lumc.nl/svn/presentation/trunk/).

branching/Makefile

+/local/projects/presentation/trunk/Makefile
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branching/beamerthemelumc.sty

+/local/projects/presentation/trunk/beamerthemelumc.sty
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branching/branching.tex

+\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}
+
+\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}.
+  \end{itemize}
+\end{frame}
+
+\begin{frame}
+  \frametitle{The current commit: \bt{HEAD}}
+  \begin{itemize}
+    \item The current commit is called \bt{HEAD} (shown in blue).
+    \item \bt{HEAD} normally points to the current branch.
+    \item Or to a commit if there is no current branch.
+  \end{itemize}
+  \vspace{1cm}
+  \includegraphics[width=10cm]{images/head}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Committing moves \bt{HEAD} and the current branch}
+  \begin{itemize}
+    \item Committing moves the current branch to the new commit.
+    \item Of course, \bt{HEAD} moves with it.
+    \item If there is no current branch, only \bt{HEAD} moves.
+  \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{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}
+
+\begin{frame}[fragile]
+  \frametitle{Switching to another branch: \bt{git checkout}}
+  \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)
+  \end{lstlisting}
+\end{frame}
+
+
+\section{Manipulating 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{Creating a new branch: \bt{git branch}}
+  \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'
+  \end{lstlisting}
+  \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:
+  \begin{itemize}
+    \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}.
+  \end{itemize}
+\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}\\
+  \vspace{0.5cm}
+  Merged branch \bt{interface} into \bt{master}.
+\end{frame}
+
+\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}
+
+
+\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]
+  \frametitle{Resolving a merge conflict (1/2)}
+  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}
+
+\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}
+
+
+\section{Questions?}
+\lastpagetemplate
+\begin{frame}
+  \begin{center}
+    Acknowledgements:
+    \bigskip
+    \bigskip
+
+    Jeroen Laros
+
+    Zuotian Tatum
+
+    % https://www.atlassian.com/git
+
+  \end{center}
+\end{frame}
+
+\end{document}

branching/gen2phen_logo.eps

+/local/projects/presentation/trunk/gen2phen_logo.eps
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