Merge branch 'master' of git.lumc.nl:courses/scriptingcourse

README.md

@@ -19,14 +19,11 @@ course before.
 
 ## Coordinates
 
-- Date: 9-10 May, 2019
-- Time: 9:00 - 17:00
-- Location: J1-84
+- Date: TBA
+- Time: TBA
+- Location: TBA
 - Teachers:
-  - Mihai Lefter
-  - Jonathan Vis
-  - Yassene Mohammed
-  - Magnus Palmblad
+  - TBA
 
 - Registration via www.medgencentre.nl. Direct access to the 
 [registration form](https://forms.lumc.nl/lumc2/SCRIPTINGcourse).
@@ -55,12 +52,12 @@ course before.
 | 09:00 | [Processes](https://git.lumc.nl/courses/scriptingcourse/wikis/files-most-recent/processes.pdf)   |
 | 09:30 | [Practical 4](https://git.lumc.nl/courses/scriptingcourse/wikis/files-most-recent/processes_practical.pdf)   |
 | 10:00 | Coffee break   |
-| 10:15 | [Regular expressions](https://git.lumc.nl/courses/scriptingcourse/raw/master/regex/regular_expressions_lecture_20180528_v5_all_slides_y.pdf)   |
+| 10:15 | [Regular expressions](https://git.lumc.nl/courses/scriptingcourse/raw/master/regex/regular_expressions_lecture_20190509_v6_stud_slides_y.pdf)   |
 | 11:00 | Practical 5   |
 | 12:00 | Lunch   |
 | 13:00 | Practical 6   |
-| 13:30 | [AWK](https://git.lumc.nl/courses/scriptingcourse/wikis/files-most-recent/awk.pdf)   |
-| 14:15 | [Practical 7](https://git.lumc.nl/courses/scriptingcourse/wikis/files-most-recent/awk_practical.pdf)   |
+| 13:30 | [AWK](https://git.lumc.nl/courses/scriptingcourse/blob/master/website/Introduction_to_AWK_2019_handouts.pdf)   |
+| 14:15 | [Practical 7](https://git.lumc.nl/courses/scriptingcourse/blob/master/website/Introduction_to_AWK_2019_handouts.pdf)   |
 | 15:45 | Wrap-up and Q&A   |
 | 16:00 | Closing   |
 

basic_scripting/Makefile

+../.submodules/presentation/Makefile
\ No newline at end of file

basic_scripting/basic_scripting.tex

@@ -4,6 +4,9 @@
 \usepackage{minted}
 \usepackage{tikz}
 \usepackage[many]{tcolorbox}
+
+\usepackage[inkscapelatex=false,inkscapearea=page]{svg}
+
 \definecolor{scriptback}{HTML}{CDECF0}
 
 \newenvironment{scriptfile}[1]
@@ -79,7 +82,7 @@
 %\renewcommand{\pause}{}
 
 % Make the title slide.
-\makeTitleSlide{\includegraphics[width=4cm]{../images/course_logo.pdf}}
+\makeTitleSlide{\includesvg[width=4cm]{../images/course_logo.svg}}
 
 % First page of the presentation.
 \section{Introduction}
@@ -597,7 +600,8 @@ $ ./quiz1.sh
   \item \textbf{((expression)) - detailed next}
  \end{itemize}
   \begin{tikzpicture}[remember picture,overlay]
-    \node[xshift=-3.3cm,yshift=-5.4cm] at (current page.north east) {\includegraphics[width=3.8cm]{../images/arithmetic.pdf}};
+    \node[xshift=-3.3cm,yshift=-5.4cm] at (current page.north east)
+{\includesvg[width=3.8cm]{../images/arithmetic.svg}};
   \end{tikzpicture}
 
 \end{pframe}

basic_scripting/beamerthemelumc.sty

+../.submodules/presentation/beamerthemelumc.sty
\ No newline at end of file

basic_scripting/logos

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

introduction/Makefile

+../.submodules/presentation/Makefile
\ No newline at end of file

introduction/beamerthemelumc.sty

+../.submodules/presentation/beamerthemelumc.sty
\ No newline at end of file

introduction/introduction.tex

@@ -5,6 +5,9 @@
 \usepackage{framed}
 \usepackage{booktabs}
 
+\usepackage[inkscapelatex=false,inkscapearea=page]{svg}
+
+
 \author{Mihai Lefter}
 \title{\courseTitle}
 \providecommand{\mySubTitle}{Introduction}
@@ -39,7 +42,7 @@
 %\renewcommand{\pause}{}
 
 % Make the title slide.
-\makeTitleSlide{\includegraphics[width=4cm]{../images/course_logo.pdf}}
+\makeTitleSlide{\includesvg[width=4cm]{../images/course_logo.svg}}
 % \makeTitleSlide
 
 \section{Why learning scripting?}
@@ -59,7 +62,7 @@
   \item Far more useful functions through command substitution.
  \end{itemize}
  \begin{center}
-  \includegraphics[width=0.6\textwidth]{../images/motivation_comics.pdf}\\
+  \includesvg[width=0.6\textwidth]{../images/motivation_comics.svg}\\
   \tiny{https://xkcd.com/974/}
  \end{center}
 \end{pframe}
@@ -68,7 +71,7 @@
 \begin{pframe}
 \vspace{-1.2cm}
 \begin{center}
- \includegraphics[width=0.7\textwidth]{../images/program.pdf}
+ \includesvg[width=0.7\textwidth]{../images/program.svg}
 \end{center}
 \vspace{-0.9cm}
 \begin{center}
@@ -102,44 +105,45 @@
   \end{itemize}
  \end{itemize}
  \begin{tikzpicture}[remember picture,overlay]
-  \node[xshift=-3.5cm,yshift=-6.0cm] at (current page.north east) {\includegraphics[width=4.5cm]{../images/aristocrat-tux.pdf}};
+  \node[xshift=-3.5cm,yshift=-6.0cm] at (current page.north east)
+{\includesvg[width=4.5cm]{../images/aristocrat-tux.svg}};
  \end{tikzpicture}
 \end{pframe}
 
 \section{Terminal, Shell, and Kernel}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/cli_overview.pdf}
+  \includesvg[width=0.95\textwidth]{../images/cli_overview.svg}
  \end{center}
 \end{pframe}
 
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/terminal_shell_overview_00.pdf}
+  \includesvg[width=0.95\textwidth]{../images/terminal_shell_overview_00.svg}
  \end{center}
 \end{pframe}
 
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/terminal_shell_overview_01a.pdf}
+  \includesvg[width=0.95\textwidth]{../images/terminal_shell_overview_01a.svg}
  \end{center}
 \end{pframe}
 
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/terminal_shell_overview_01b.pdf}
+  \includesvg[width=0.95\textwidth]{../images/terminal_shell_overview_01b.svg}
  \end{center}
 \end{pframe}
 
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/terminal_shell_overview_01c.pdf}
+  \includesvg[width=0.95\textwidth]{../images/terminal_shell_overview_01c.svg}
  \end{center}
 \end{pframe}
 
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/terminal_shell_overview_02.pdf}
+  \includesvg[width=0.95\textwidth]{../images/terminal_shell_overview_02.svg}
  \end{center}
 \end{pframe}
 
@@ -147,54 +151,54 @@
 \subsection{Everything is a file}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_00.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_00.svg}
  \end{center}
 \end{pframe}
 
 \subsection{Special directories}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_01.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_01.svg}
  \end{center}
 \end{pframe}
 
 \subsection{Absolute paths}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_02.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_02.svg}
  \end{center}
 \end{pframe}
 
 \subsection{Relative paths}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_03.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_03.svg}
  \end{center}
 \end{pframe}
 
 \subsection{Quiz 1 - Q1}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_04.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_04.svg}
  \end{center}
 \end{pframe}
 
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_05.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_05.svg}
  \end{center}
 \end{pframe}
 
 \subsection{Quiz 1 - Q2}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_06.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_06.svg}
  \end{center}
 \end{pframe}
 
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.95\textwidth]{../images/filesystem_07.pdf}
+  \includesvg[width=0.95\textwidth]{../images/filesystem_07.svg}
  \end{center}
 \end{pframe}
 
@@ -643,7 +647,7 @@
   \end{itemize}
  \end{itemize}
  \begin{center}
-  \includegraphics[width=0.8\textwidth]{../images/redirection_00.pdf}
+  \includesvg[width=0.8\textwidth]{../images/redirection_00.svg}
  \end{center}
 %   \item There are 3 files open:
 %   \begin{itemize}
@@ -673,7 +677,7 @@
   \item Redirect a command output as input to another command.
  \end{itemize}
  \begin{center}
-  \includegraphics[width=0.8\textwidth]{../images/redirection_01.pdf}
+  \includesvg[width=0.8\textwidth]{../images/redirection_01.svg}
  \end{center}
 \end{pframe}
 
@@ -738,7 +742,7 @@
 \subsection{Going deeper - file descriptors}
 \begin{pframe}
  \begin{center}
-  \includegraphics[width=0.7\textwidth]{../images/redirection_02.pdf}
+  \includesvg[width=0.7\textwidth]{../images/redirection_02.svg}
  \end{center}
 
  \textcolor{command-color}{\lstinline{command}} \textcolor{redirection}{\lstinline{[file_description_number]redirection_operator}} \textcolor{argument-color}{\lstinline{file}}

introduction/logos

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