Moved common parts to shared and started basics update

basics/basics.tex

@@ -2,13 +2,13 @@
 
 \input{../shared/shared.tex}
 
-\author{Jeroen F.J. Laros}
+\author{}
 \title{\courseTitle}
 \providecommand{\mySubTitle}{Git Basics}
 \providecommand{\myConference}{\courseTitle}
 \providecommand{\myGroup}{}
 \providecommand{\myDepartment}{Department of Human Genetics}
-\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\myCenter}{}
 
 \usetheme{lumc}
 
@@ -18,62 +18,97 @@
 %\renewcommand{\pause}{}
 
 % Make the title slide.
-\makeTitleSlide{\includegraphics[width=3.5cm]{git_logo}}
+\makeTitleSlide{\includegraphics[width=3.5cm]{../shared/git_logo.pdf}}
 
 % First page of the presentation.
-\section{Initialisation}
-\subsection{Starting a project}
+\section{Starting a project}
+\subsection{You can either}
 \begin{pframe}
-  Creating a new repository is easy. You do not need a server, no registration,
-  etc.
-  \begin{lstlisting}[language=none, caption=Make a new repository.]
-    $ cd ~/projects
-    $ git init
-    Initialized empty Git repository in <path>/.git/
-  \end{lstlisting}
+  1. Start from scratch on your own:
+  \vspace{-0.3cm}
+  \begin{framed}
+   \prompt\ \cmd{mkdir}\ \cmdarg{my\_project}\\
+   \prompt\ \cmd{cd}\ \cmdarg{my\_project}\\
+   \prompt\ \gitcmd\ \cmd{init}\\
+   \cliout{Initialized empty Git repository in \{current-directory\}\/.git\/}
+  \end{framed}
   \pause
 
-  Or you can ``clone'' an existing repository.
-  \begin{lstlisting}[language=none, caption=Clone an existing repository.]
-    $ git clone <path-to-repository>
-  \end{lstlisting}
+  2. Or you can \cmd{clone} an existing remote (or local) repository:
+  \vspace{-0.3cm}
+  \begin{framed}
+   \prompt\ \gitcmd\ \cmd{clone}\ \cmdarg{\<path-to-repository\>}\\
+   \cliout{Cloning into \{repo-name\} ...}
+  \end{framed}
 \end{pframe}
 
+\subsection{Where does git store its repository information?}
 \begin{pframe}
   You can see a hidden directory in a Git repository.
-  \begin{lstlisting}[language=none, caption=A hidden directory is added.]
-    $ ls -a
-    .  ..  .git
-  \end{lstlisting}
+  \vspace{-0.3cm}
+  \begin{framed}
+   \prompt\ \cmd{ls}\ \cmdopt{-a}\\
+   \cliout{. .. .git}
+  \end{framed}
+
+  This is where git stores the files necessary to track your progress. You
+  rarely need to edit the contents of this directory.
+  \bigskip
 
-  This directory contains almost everything that Git stores and manipulates.
+  \important{Removing this directory means removing your repository!}
 \end{pframe}
 
-\section{Manipulation}
-\subsection{Local operations}
+\section{Git Operations}
 \begin{pframe}
-  \begin{figure}[]
-    \begin{center}
-      \includegraphics[height=0.7\textheight]{18333fig0106-tn}
-    \end{center}
-    \caption{Working directory, staging area, and Git directory.}
-  \end{figure}
+  \vspace{-0.9cm}
+  Operations can be local or remote.\\
+  Most importantly, they track files around these three areas
+  \footnote[1]{\scriptsize{Adapted from
+  \href{http://git-scm.com/book/en/v2/Getting-Started-Git-Basics}
+  {Pro Git Book}.}}:
+  \begin{center}
+    \includegraphics[width=0.7\textwidth]{images/git_areas.pdf}\\
+  \end{center}
 \end{pframe}
 
-\subsection{Checking the status of your files}
+\subsection{Prelude: quick setup}
 \begin{pframe}
-  \begin{lstlisting}[language=none, caption=Check status.]
-    $ git status
-    nothing to commit (working directory clean)
-  \end{lstlisting}
+  If you have never used \gitcmd\ before you need to tell it who you are. This
+  information is saved in \cmdarg{.gitconfig}\ and used to mark each commit.
+  \vspace{-0.4cm}
+  \begin{framed}
+   \prompt\ \gitcmd\ \cmd{config}\ \cmdopt{--global user.name}\
+   \cmdarg{\{your-name-or-nick-name\}}\\
+   \prompt\ \gitcmd\ \cmd{config}\ \cmdopt{--global user.email}\
+   \cmdarg{\{your-email-address\}}
+  \end{framed}
+  \pause
+  \vspace{-0.2cm}
+
+  Local configuration for each repository is possible as well.
+  \vspace{-0.4cm}
+  \begin{framed}
+   \prompt\ \gitcmd\ \cmd{config}\ \cmdopt{--local user.name}\
+   \cmdarg{\{your-name-or-nick-name\}}\\
+   \prompt\ \gitcmd\ \cmd{config}\ \cmdopt{--local user.email}\
+   \cmdarg{\{your-email-address\}}
+  \end{framed}
+  \vspace{-0.2cm}
+  \pause
 
-  ``\lstinline{git status}'' can tell you whether your files are:
-  \begin{itemize}
-    \item Untracked.
-    \item Unmodified.
-    \item Modified.
-    \item Staged.
-  \end{itemize}
+  You would like colored output?
+  \vspace{-0.4cm}
+  \begin{framed}
+   \prompt\ \gitcmd\ \cmd{config}\ \cmdopt{--global color.ui}\ \cmdarg{auto}
+  \end{framed}
+\end{pframe}
+
+\subsection{Checking the status of your files}
+\begin{pframe}
+  \begin{framed}
+   \prompt\ \gitcmd\ \cmd{status}\\
+   \cliout{nothing to commit (working directory clean)}
+  \end{framed}
 \end{pframe}
 
 \begin{pframe}

commit_graph/commit_graph.tex

@@ -12,25 +12,6 @@
 \providecommand{\myDepartment}{Department of Human Genetics}
 \providecommand{\myCenter}{Center for Human and Clinical Genetics}
 
-\definecolor{cblack}{rgb}{0,0,0}
-\definecolor{cwhite}{rgb}{1,1,1}
-\definecolor{command-color}{rgb}{0,0.5,0}
-\definecolor{git-color}{rgb}{0.94,0.23,0.18}
-\definecolor{option-color}{rgb}{0.9,0.2,0.11}
-\definecolor{argument-color}{rgb}{0.11,0.27,0.7}
-\definecolor{pattern-color}{rgb}{0,0.5,0.5}
-\definecolor{wildcard-color}{rgb}{0.75,0.3,0}
-\definecolor{cli-text}{rgb}{0.15,0.15,0.15}
-\definecolor{important-note}{rgb}{0.69,0.13,0.13}
-\definecolor{redirection}{rgb}{0.99,0.13,0.13}
-\definecolor{shadecolor}{rgb}{0.9,0.9,0.9}
-\definecolor{one-dot}{rgb}{0.9,0.2,0.0}
-\definecolor{two-dots}{rgb}{0.11,0.11,0.8}
-\definecolor{slash}{rgb}{0.3,0.3,0.3}
-
-\definecolor{head}{HTML}{B22222}
-\definecolor{branch}{HTML}{20b2aa}
-\definecolor{commit-id}{HTML}{b8860b}
 
 \usetheme{lumc}
 
@@ -297,7 +278,7 @@
   Creates branch \textcolor{branch}{\lstinline{lib}} at \textcolor{head}{\lstinline{HEAD}}.
   \pause
   \medskip
-  
+
   How can I see that it worked?
   \pause
   \vspace{-0.3cm}
@@ -311,17 +292,17 @@
   \end{framed}
   \vspace{-0.2cm}
   \pause
-  
+
   How can I switch to the new \textcolor{branch}{\lstinline{lib}} branch?
 \end{pframe}
-  
+
 \begin{pframe}
   \begin{framed}
     \lstinline{$} \textcolor{git-color}{\lstinline{git}} \textcolor{command-color}{\lstinline{checkout}} \textcolor{argument-color}{\lstinline{lib}}\\
     \lstinline{Switched to branch '}\textcolor{branch}{\lstinline{lib}}\lstinline{'}
   \end{framed}
 \end{pframe}
-  
+
 \begin{pframe}
   For Git pro's, in one command:
   \begin{framed}
@@ -441,7 +422,7 @@
 \begin{pframe}
   Make sure that the working directory is clean before merging.
   \medskip
-  
+
   Otherwise:
   \vspace{-0.3cm}
   \begin{framed}
@@ -513,7 +494,7 @@
    \lstinline{* }\textcolor{commit-id}{\lstinline{5edaf08}}\lstinline{ (}\textcolor{branch}{\lstinline{hue}}\lstinline{) State character ...}\\
    \lstinline{| * }\textcolor{commit-id}{\lstinline{f1ef19c}}\lstinline{ (}\textcolor{head}{\lstinline{HEAD}}\lstinline{, }\textcolor{branch}{\lstinline{master}}\lstinline{) State character ...}\\
    \lstinline{|/}\\
-   \lstinline{* }\textcolor{commit-id}{\lstinline{1f6d2ab}}\lstinline{ Initial commit} 
+   \lstinline{* }\textcolor{commit-id}{\lstinline{1f6d2ab}}\lstinline{ Initial commit}
   \end{framed}
 
   We'd like to merge branch \textcolor{branch}{\lstinline{hue}} into \textcolor{branch}{\lstinline{master}}.

shared/shared.tex

+\usepackage{framed}
+
 \providecommand{\courseTitle}{Code and data management with Git}
 \providecommand{\myDate}{22-11-2017}
 \providecommand{\acknowledgements}{
@@ -6,3 +8,31 @@
   Szymon Kie{\l}basa\\
   Jeroen Laros\\
 }
+
+\definecolor{cblack}{rgb}{0,0,0}
+\definecolor{cwhite}{rgb}{1,1,1}
+\definecolor{command-color}{rgb}{0,0.5,0}
+\definecolor{git-color}{rgb}{0.94,0.23,0.18}
+\definecolor{option-color}{HTML}{483d8b}
+\definecolor{argument-color}{rgb}{0.11,0.27,0.7}
+\definecolor{pattern-color}{rgb}{0,0.5,0.5}
+\definecolor{wildcard-color}{rgb}{0.75,0.3,0}
+\definecolor{cli-text}{rgb}{0.15,0.15,0.15}
+\definecolor{important-note}{rgb}{0.69,0.13,0.13}
+\definecolor{redirection}{rgb}{0.99,0.13,0.13}
+\definecolor{shadecolor}{rgb}{0.9,0.9,0.9}
+\definecolor{one-dot}{rgb}{0.9,0.2,0.0}
+\definecolor{two-dots}{rgb}{0.11,0.11,0.8}
+\definecolor{slash}{rgb}{0.3,0.3,0.3}
+
+\definecolor{head}{HTML}{B22222}
+\definecolor{branch}{HTML}{20b2aa}
+\definecolor{commit-id}{HTML}{b8860b}
+
+\newcommand{\gitcmd}{\textcolor{git-color}{\lstinline{git}}}
+\newcommand{\prompt}{\lstinline{$}}
+\newcommand{\cmd}[1]{\textcolor{command-color}{\lstinline{#1}}}
+\newcommand{\cmdarg}[1]{\textcolor{argument-color}{\lstinline{#1}}}
+\newcommand{\cmdopt}[1]{\textcolor{option-color}{\lstinline{#1}}}
+\newcommand{\cliout}[1]{\textcolor{cli-text}{\lstinline{#1}}}
+\newcommand{\important}[1]{\textbf{\textcolor{important-note}{#1}}}