New style presentation template.

basics/basics.tex

 \documentclass[slidestop]{beamer}
 
+\author{Jeroen F.J. Laros}
 \title{Git Basics}
+\providecommand{\mySubTitle}{}
 \providecommand{\myConference}{Git course}
-\providecommand{\myDate}{Monday, June 23, 2014}
-\author{Jeroen F. J. Laros}
-\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myGroup}{}
 \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}
-}
+
+\input{../shared/shared.tex}
 
 \usetheme{lumc}
 
@@ -26,102 +17,82 @@
 % This disables the \pause command, handy in the editing phase.
 %\renewcommand{\pause}{}
 
-% Make the title page.
-\bodytemplate
+% Make the title slide.
+\makeTitleSlide{\includegraphics[width=3.5cm]{git_logo}}
 
 % First page of the presentation.
 \section{Initialisation}
-\begin{frame}[fragile]
-  \frametitle{Starting a project.}
-
+\subsection{Starting a project}
+\begin{pframe}
   Creating a new repository is easy. You do not need a server, no registration,
   etc.
-  \bigskip
- 
   \begin{lstlisting}[language=none, caption=Make a new repository.]
     $ cd ~/projects
     $ git init
     Initialized empty Git repository in <path>/.git/
   \end{lstlisting}
-  \bigskip
   \pause
 
   Or you can ``clone'' an existing repository.
-  \bigskip
-
   \begin{lstlisting}[language=none, caption=Clone an existing repository.]
     $ git clone <path-to-repository>
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Starting a project.}
+\end{pframe}
 
+\begin{pframe}
   You can see a hidden directory in a Git repository.
-  \bigskip
-
   \begin{lstlisting}[language=none, caption=A hidden directory is added.]
     $ ls -a
     .  ..  .git
   \end{lstlisting}
-  \bigskip
 
   This directory contains almost everything that Git stores and manipulates.
-\end{frame}
+\end{pframe}
 
 \section{Manipulation}
-\begin{frame}
-  \frametitle{Local operations.}
-
+\subsection{Local operations}
+\begin{pframe}
   \begin{figure}[]
     \begin{center}
-      \includegraphics[height=0.8\textheight]{pics/18333fig0106-tn}
+      \includegraphics[height=0.7\textheight]{18333fig0106-tn}
     \end{center}
     \caption{Working directory, staging area, and Git directory.}
-    \label{}
   \end{figure}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Checking the status of your files.}
+\end{pframe}
 
+\subsection{Checking the status of your files}
+\begin{pframe}
   \begin{lstlisting}[language=none, caption=Check status.]
     $ git status
     nothing to commit (working directory clean)
   \end{lstlisting}
-  \bigskip
 
-  ``\bt{git status}'' can tell you whether your files are:
+  ``\lstinline{git status}'' can tell you whether your files are:
   \begin{itemize}
     \item Untracked.
     \item Unmodified.
     \item Modified.
     \item Staged.
   \end{itemize}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Checking the status of your files.}
+\end{pframe}
 
+\begin{pframe}
   \begin{figure}[]
     \begin{center}
-      \includegraphics[height=0.8\textheight]{pics/18333fig0201-tn}
+      \includegraphics[height=0.7\textheight]{18333fig0201-tn}
     \end{center}
     \caption{The lifecycle of the status of your files.}
-    \label{}
   \end{figure}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Adding, removing, renaming.}
+\end{pframe}
 
+\subsection{Adding, removing, renaming}
+\begin{pframe}
   \begin{lstlisting}[language=none, caption=This file is not tracked.]
     $ echo First version. > README
     $ git status
     # Untracked files:
     #       README
   \end{lstlisting}
-  \bigskip
   \pause
 
   \begin{lstlisting}[language=none, caption=Now the file will be tracked.]
@@ -130,19 +101,16 @@
     # Changes to be committed:
     #       new file:   README
   \end{lstlisting}
-  \bigskip
 
-  To rename a file, use ``\bt{git mv}'', to remove, use ``\bt{git rm}''.
-\end{frame}
+  To rename a file, use ``\lstinline{git mv}'', to remove, use
+  ``\lstinline{git rm}''.
+\end{pframe}
 
 \section{Working with versions}
-\begin{frame}[fragile]
-  \frametitle{commit}
-
+\subsection{commit}
+\begin{pframe}
   Once you have modified your files and added them to the \emph{staging area},
   you can commit them (add them to the repository).
-  \bigskip
-
   \begin{lstlisting}[language=none, caption=Commit a new version.]
     $ git commit
   \end{lstlisting}
@@ -152,20 +120,16 @@
   \begin{itemize}
     \item Useful when you want to search.
   \end{itemize}
-  \bigskip
   \pause
 
   \begin{lstlisting}[language=none, caption=Commit a new version.]
     $ git commit -m "Solved the counting bug."
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Undoing changes.}
+\end{pframe}
 
+\subsection{Undoing changes}
+\begin{pframe}
   Sometimes you will accidentally add a file.
-  \bigskip
-
   \begin{lstlisting}[language=none, caption=Adding a new version of a file.]
     $ echo Second version. > README
     $ git add README
@@ -173,63 +137,50 @@
     # Changes to be committed:
     #       modified:   README
   \end{lstlisting}
-  \bigskip
   \pause
 
-  If you want to undo this, you can use ``\bt{git reset}''.
-  \bigskip
-
+  If you want to undo this, you can use ``\lstinline{git reset}''.
   \begin{lstlisting}[language=none, caption=Unstage a file.]
     $ git reset README
     $ git status
     # Changes not staged for commit:
     #       modified:   README
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Undoing changes.}
+\end{pframe}
 
-  Keep in mind that ``\bt{git reset}'' by default sets a staged file back to unstaged.
+\begin{pframe}
+  Keep in mind that ``\lstinline{git reset}'' by default sets a staged file
+  back to unstaged.
   \begin{lstlisting}[language=none, caption=Unstage a file.]
     $ git reset README
     $ git status
     # Changes not staged for commit:
     #       modified:   README
   \end{lstlisting}
-  \bigskip
   \pause
 
-  To discard all changes in an unstaged file, you can use ``\bt{git checkout}''
+  To discard all changes in an unstaged file, you can use
+  ``\lstinline{git checkout}''
   \begin{lstlisting}[language=none, caption=Discarding changes.]
     $ git checkout -- .
     $ git status
     nothing to commit, working directory clean
   \end{lstlisting}
-  
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Undoing changes.}
+\end{pframe}
 
+\begin{pframe}
   For now, let's commit our change and move on.
-  \bigskip
-
   \begin{lstlisting}[language=none, caption=Adding a new version of a file.]
     $ echo Second version. > README
     $ git commit
     $ git status
     nothing to commit, working directory clean
   \end{lstlisting}
-  \bigskip
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Viewing the history.}
-
-  To see the history of your project, use ``\bt{git log}''.
-  \bigskip
+\end{pframe}
 
+\subsection{Viewing the history}
+\begin{pframe}
+  To see the history of your project, use ``\lstinline{git log}''.
   \begin{lstlisting}[language=none, caption=The log of our project.]
     $ git log
     commit cc61ee7cd72590f3bebcc9e1ff3e9435c7f7dd28
@@ -244,36 +195,29 @@
 
         First version.
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Undo a commit.}
+\end{pframe}
 
+\subsection{Undo a commit}
+\begin{pframe}
   Sometimes we want to undo an entire commit. This is done with
-  ``\bt{git revert}''.
-  \bigskip
-
+  ``\lstinline{git revert}''.
   \begin{lstlisting}[language=none, caption=Revert a commit.]
-    $ git revert cc61ee7cd72590f3bebcc9e1ff3e9435c7f7dd28
+    $ git revert cc61ee7cd7
     $ cat README
     First version.
   \end{lstlisting}
-  \bigskip
 
-  The hash can be found with ``\bt{git log}''.
+  The hash can be found with ``\lstinline{git log}''.
   \bigskip
   \pause
 
   You can also use a unique prefix of this hash, usually six characters is
   enough.
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Viewing changes in detail.}
-
-  If you want to see what has changed, use ``\bt{git diff}''.
-  \bigskip
+\end{pframe}
 
+\subsection{Viewing changes in detail}
+\begin{pframe}
+  If you want to see what has changed, use ``\lstinline{git diff}''.
   \begin{lstlisting}[language=none, caption=Difference between the working copy
     and the staging area.]
     $ echo Third version. > README
@@ -284,24 +228,18 @@
     -First version.
     +Third version.
   \end{lstlisting}
-  \bigskip
   \pause
 
-  For staged files, use the ``\bt{--cached}'' or ``\bt{--staged}'' option.
-  \bigskip
-
+  For staged files, use the ``\lstinline{--cached}'' or
+  ``\lstinline{--staged}'' option.
   \begin{lstlisting}[language=none, caption=Difference between the staging area
     and the last commit.]
     $ git diff --cached
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Viewing changes in detail.}
+\end{pframe}
 
+\begin{pframe}
   You can see the differences between any two versions.
-  \bigskip
-
   \begin{lstlisting}[language=none, caption=Difference between the working copy
     and an other commit.]
     $ git diff cc61ee
@@ -311,30 +249,28 @@
     -Second version.
     +Third version.
   \end{lstlisting}
-  \bigskip
   \pause
 
   \begin{lstlisting}[language=none, caption=Difference between two committed
     versions.]
     $ git diff 8e10be cc61ee
   \end{lstlisting}
-\end{frame}
+\end{pframe}
 
 \section{Extras}
-\begin{frame}[fragile]
-  \frametitle{Explicit no tracking.}
-
+\subsection{Explicit no tracking}
+\begin{pframe}
   Sometimes you do not want to track certain files:
   \begin{itemize}
     \item Executables.
-    \item \bt{pdf} files (if you still have the \LaTeX\ source).
-    \item Python bytecode (\bt{.pyc}) files.
+    \item PDF files (if you still have the \LaTeX\ source).
+    \item Python bytecode (\lstinline{.pyc}) files.
     \item Files containing passwords.
   \end{itemize}
-  \bigskip
+  \medskip
   \pause
 
-  Use the special ``\bt{.gitignore}'' file.
+  Use the special ``\lstinline{.gitignore}'' file.
   \begin{lstlisting}[language=none, caption=Ignoring certain files.]
     $ touch notrack.txt
     $ echo notrack.txt > .gitignore
@@ -343,46 +279,35 @@
     $ git status
     nothing to commit, working directory clean
   \end{lstlisting}
-\end{frame}
-
-\begin{frame}[fragile]
-  \frametitle{Help.}
-
-  With the ``\bt{help}'' command get the manual of a particular subcommand.
-  \bigskip
+\end{pframe}
 
+\subsection{Help}
+\begin{pframe}
+  With the ``\lstinline{help}'' command get the manual of a particular
+  subcommand.
   \begin{lstlisting}[language=none, caption=Get the full manual.]
     $ git help <command>
   \end{lstlisting}
-  \bigskip
   \pause
 
   Example.
-  \bigskip
   \begin{lstlisting}[language=none, caption=Get the manual for the diff
     subcommand.]
     $ git help diff
   \end{lstlisting}
-\end{frame}
-
-\section{Questions?}
-\lastpagetemplate
-\begin{fframe}
-  \begin{center}
-    Acknowledgements:
-    \bigskip
-    \bigskip
+\end{pframe}
 
-    Martijn Vermaat
-
-    Zuotian Tatum
-
-    Wibowo Arindrarto
+\makeAcknowledgementsSlide{
+  \begin{tabular}{l}
+    \acknowledgements
+  \end{tabular}
+  \bigskip
 
-  \end{center}
+  \hfill\includegraphics[width=3.5cm]{git_logo}
 
-  \vfill
-  \permfoot{http://git-scm.com/book}
-\end{fframe}
+  \begin{tabular}{l}
+    \small\url{http://git-scm.com/book}\\
+  \end{tabular}
+}
 
 \end{document}

basics/gen2phen_logo.eps

-../presentation/gen2phen_logo.eps
\ No newline at end of file

basics/git_logo.png

+../shared/git_logo.png
\ No newline at end of file

basics/lgtc_logo.eps

-../presentation/lgtc_logo.eps
\ No newline at end of file

basics/logos

+../presentation/logos/
\ No newline at end of file

basics/lumc_logo.eps

-../presentation/lumc_logo.eps
\ No newline at end of file

basics/lumc_logo_small.eps

-../presentation/lumc_logo_small.eps
\ No newline at end of file

basics/nbic_logo.eps

-../presentation/nbic_logo.eps
\ No newline at end of file

basics/ngi_logo.eps

-../presentation/ngi_logo.eps
\ No newline at end of file

basics/nwo_logo_en.eps

-../presentation/nwo_logo_en.eps
\ No newline at end of file

basics/pics

-../pics/
\ No newline at end of file

basics/ul_logo.eps

-../presentation/ul_logo.eps
\ No newline at end of file

branching/gen2phen_logo.eps

-../presentation/gen2phen_logo.eps
\ No newline at end of file

branching/git_logo.png

+../shared/git_logo.png
\ No newline at end of file

branching/lgtc_logo.eps

-../presentation/lgtc_logo.eps
\ No newline at end of file

branching/logos

+../presentation/logos/
\ No newline at end of file

branching/lumc_logo.eps

-../presentation/lumc_logo.eps
\ No newline at end of file

branching/lumc_logo_small.eps

-../presentation/lumc_logo_small.eps
\ No newline at end of file

branching/nbic_logo.eps

-../presentation/nbic_logo.eps
\ No newline at end of file

branching/ngi_logo.eps

-../presentation/ngi_logo.eps
\ No newline at end of file

branching/nwo_logo_en.eps

-../presentation/nwo_logo_en.eps
\ No newline at end of file

branching/ul_logo.eps

-../presentation/ul_logo.eps
\ No newline at end of file

introduction/18333fig0101-tn.png

-../pics/src/18333fig0101-tn.png
\ No newline at end of file

introduction/18333fig0102-tn.png

-../pics/src/18333fig0102-tn.png
\ No newline at end of file

introduction/18333fig0103-tn.png

-../pics/src/18333fig0103-tn.png
\ No newline at end of file

introduction/gen2phen_logo.eps

-../presentation/gen2phen_logo.eps
\ No newline at end of file

introduction/git_logo.png

+../shared/git_logo.png
\ No newline at end of file

introduction/introduction.tex

 \documentclass[slidestop]{beamer}
 
+\author{Jeroen F. J. Laros}
 \title{Introduction to Version Control}
+\providecommand{\mySubTitle}{}
 \providecommand{\myConference}{Git course}
-\providecommand{\myDate}{Tuesday, December 1, 2015}
-\author{Jeroen F. J. Laros}
-\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myGroup}{}
 \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}
-}
+
+\input{../shared/shared.tex}
 
 \usetheme{lumc}
 
@@ -27,7 +18,7 @@