Merge branch 'master' of gitlab.ethz.ch:thealternative/courses

.gitignore

+# LaTeX traces
+*.log
+*.toc
+*.aux
+*.out
+*-blx.bib
+*run.xml
+*.fdb_latexmk
+*.fls
+*.synctex.gz
+*.snm
+*.nav
+
+# Bibtex traces
+*.bak
+*.blg
+*.bbl
+
+# PythonTeX traces and binaries
+pythontex-*/
+*.pytxcode
+
+# Gedit
+*~

FOSS_course/header.tex → .style/header.tex

 \documentclass[aspectratio=169]{beamer}
-\usepackage[T1]{fontenc} %pipes don't display properly without this
+\usepackage[T1]{fontenc} % the pipe character doesn't display properly without this
 \usepackage[utf8]{inputenc}
 \usepackage{listings}
 \usepackage{color}
 \usepackage{datapie}
+\usepackage{minted} % COMPILE WITH `pdflatex -shell-escape`!
 \usepackage{multicol}
 \usepackage{upgreek}
-\usepackage{siunitx} %pretty measurement unit rendering
-\usepackage{hyperref} %enable hyperlink for urls
+\usepackage{siunitx} % pretty measurement unit rendering
+\usepackage{hyperref} % enable hyperlink for URLs
 \usepackage{lmodern}
 \usepackage{setspace}
+\usepackage[os=win]{menukeys} % by default keys are given for MacOS
 
 \usefonttheme[onlymath]{serif}
 \setcounter{MaxMatrixCols}{20}
@@ -26,9 +28,9 @@
 
 %Define generic colors
 \definecolor{slg}{gray}{0.25}
-\definecolor{lg}{gray}{0.55}
+\definecolor{lg}{gray}{0.53}
 \definecolor{vlg}{gray}{0.73}
-\definecolor{tlg}{gray}{0.9}
+\definecolor{tlg}{gray}{0.91}
 
 %Define data colors
 \definecolor{mygreen}{rgb}{0,0.6,0}

FOSS_course/compile.sh

 #!/usr/bin/env bash
 
-pdflatex slides.tex
+pdflatex -shell-escape slides.tex
 bibtex slides
-pdflatex slides.tex
-pdflatex slides.tex
+pdflatex -shell-escape slides.tex
+pdflatex -shell-escape slides.tex

FOSS_course/data/web_os.csv

 Name,percent
-Unix,70.5
-Windows,29.5
+Unix,71.4
+Windows,28.6

FOSS_course/data/web_servers.csv

 Name,percent
-Apache,44.0
-Nginx,30.7
-Cloudflare Server,11.2
-Microsoft-IIS,8.2
-other,5.9
+Apache,40.5
+Nginx,31.7
+Cloudflare Server,13.2
+Microsoft-IIS,7.8
+other,5.8

FOSS_course/slides.tex

-\input{header}
+\input{../.style/header}
 
 \title{Free and Open Source Software}
 \author{Horea Christian}
@@ -72,7 +72,7 @@
 				\textcolor{ldorange}{$\sim$1970-1980:}
 				\begin{itemize}
 					\item Increasingly easy to withold control (e.g. binary-only distribution)
-					\item United States vs. IBM (1969): “Bundled Software is anticompetitive”
+					\item United States vs. IBM (1969, dropped 1982): “Bundled Software is anticompetitive”
 					\item Computer Software Copyright Act (1980): “Software is patentable”
 				\end{itemize}
 			\end{frame}
@@ -193,6 +193,11 @@
 				% Proprietary Software is Often Malware https://www.gnu.org/proprietary/
 			\end{frame}
 			\begin{frame}{Sustainability}
+
+				\begin{center}
+					“the quality of being able to continue over a period of time“
+				\end{center}
+
 				The Software:
 				\begin{itemize}
 					\item depends on no single entity for its continuity.
@@ -335,7 +340,7 @@
 						\vspace{-0.75em}
 						\centering\tiny
 							\DTLpiechart{radius=0.235\textheight,variable=\quantity,innerlabel={\DTLpiepercent\%},outerlabel=\name,cutaway={1-2}}{server}{\name=Name,\quantity=percent}
-							\caption{Web Server Market Share 2019-10-04 via \href{http://w3techs.com/technologies/overview/web_server/all}{w3techs}}
+							\caption{Web Server Market Share 2020-02-26 via \href{http://w3techs.com/technologies/overview/web_server/all}{w3techs}}
 						\end{figure}
 					\column{0.5\linewidth}
 						\begin{figure}[htbp]
@@ -344,7 +349,7 @@
 	\DTLsetpiesegmentcolor{1}{green!40}
 	\DTLsetpiesegmentcolor{2}{red!40}
 							\DTLpiechart{radius=0.265\textheight,variable=\quantity,innerlabel={\DTLpiepercent\%},outerlabel=\name,cutaway={2}}{os}{\name=Name,\quantity=percent}
-							\caption{Website OS Market Share 2019-10-04 via \href{http://w3techs.com/technologies/overview/operating_system/all}{w3techs}}
+							\caption{Website OS Market Share 2020-02-26 via \href{http://w3techs.com/technologies/overview/operating_system/all}{w3techs}}
 						\end{figure}
 				\end{columns}
 			\end{frame}
@@ -385,7 +390,7 @@
 					\caption{\copyright Red Hat, Inc.}
 				\end{figure}
 				\begin{itemize}
-					\item Founded 1993 
+					\item Founded 1993, subsidiary of IBM since 2019
 					\item 2015--2018 stock price $\mathrm{\upbeta_{RHT}=1.16}$ (e.g. $\mathrm{\upbeta_{MSFT}=1.22}$)
 					\item Very diverse open source products, e.g. OpenStack, RHEL, CloudForms
 				\end{itemize}
@@ -431,7 +436,7 @@
 					\item Come to the next “Linux Days” events:
 					\textcolor{lg}{\url{http://thealternative.ch/}}
 					\item Join the next “Stammtisch”:\\
-					\textcolor{lg}{18:00 Thursday, March 12 - Learning Spaces on the E Floor of ETH Building CHN Universitätestrasse 16}
+					\textcolor{lg}{18:00 Thursday, March 5 - Katholische Hochschulgemeinde Zürich AKI, 2nd floor, Hirschengraben 86, 8001}
 					\item Give us feedback!\\
 					\textcolor{lg}{\url{https://feedback.thealternative.ch/}}
 				\end{itemize}

README.md

@@ -25,6 +25,8 @@ git clone https://gitlab.ethz.ch/thealternative/courses.git
 
 You can find the course materials in the various subdirectories of this repository.
 
+You need `git-lfs` installed for the larger files to download as expected.
+
 # For TheAlternative Members
 
 This repository is kept up to date by TheAlternative members. If you teach a course, please add your slides and supplementary material, such as exercise sheets, to this repo. Do not upload any private files, as this repository is publicly visible.

archive/HS19-debugging-on-linux/build.sh

+#!/bin/bash
+printf "Building Main Presentation... "
+pandoc -t beamer --template template.tex --listings pres.md -o pres.pdf --pdf-engine pdflatex 
+echo "Done"

archive/HS19-debugging-on-linux/code/bugtype/bo.c

+
+int
+main(int argc, char **argv) {
+  int arr[10];
+  arr[11] = 1;
+  return 0;
+}

archive/HS19-debugging-on-linux/code/bugtype/loi.c

+#include<pthread.h>
+
+pthread_mutex_t lock1 = PTHREAD_MUTEX_INITIALIZER;
+pthread_mutex_t lock2 = PTHREAD_MUTEX_INITIALIZER;
+
+void *
+thread1(void *arg __attribute__((unused))) {
+   pthread_mutex_lock(&lock1);
+   pthread_mutex_lock(&lock2); //Lock-Order-Inversion between here...
+   pthread_mutex_unlock(&lock2);
+   pthread_mutex_unlock(&lock1);
+   return NULL;
+}
+
+void *
+thread2(void *arg __attribute__((unused))) {
+   pthread_mutex_lock(&lock2);
+   pthread_mutex_lock(&lock1); // ... and here!
+   pthread_mutex_unlock(&lock1);
+   pthread_mutex_unlock(&lock2);
+   return NULL;
+}
+
+int
+main(int argc, char **argv) {
+  pthread_t t1, t2; 
+  pthread_create(&t1, NULL, thread1, NULL);
+  pthread_create(&t2, NULL, thread2, NULL);
+  pthread_join(t1, NULL);
+  pthread_join(t2, NULL);
+  return 0;
+}
+

archive/HS19-debugging-on-linux/code/bugtype/ms.c

+#include<stdlib.h>
+
+int
+main(int argc, char **argv) {
+  int *p;
+  p = malloc(sizeof(int));
+  return 0;
+}

archive/HS19-debugging-on-linux/code/bugtype/rc.c

+#include<pthread.h>
+
+volatile int inc;
+
+void *
+thread(void *arg __attribute__((unused))) {
+  for (int i = 0; i < 65536; i++) 
+	inc++;
+  return NULL;
+}
+
+int
+main(int argc, char **argv) {
+  pthread_t t1, t2;
+  pthread_create(&t1, NULL, thread, NULL);
+  pthread_create(&t2, NULL, thread, NULL);
+  pthread_join(t1, NULL);
+  pthread_join(t2, NULL);
+  return 0;
+}

archive/HS19-debugging-on-linux/code/bugtype/uaf.c

+#include<stdlib.h>
+
+int
+main(int argc, char **argv) {
+  int *ip;
+  ip = malloc(sizeof(int));
+  free(ip);
+  *ip = 3;
+  return 0;
+}

archive/HS19-debugging-on-linux/code/bugtype/ud.c

+int
+main(int argc, char **argv) {
+  int i = 32;
+  int j = 0xCAFFEE;
+  j = j << i;
+  return 0;
+}

archive/HS19-debugging-on-linux/code/bugtype/ui.c

+#include<stdio.h>
+
+int
+main(int argc, char **argv) {
+  int i;
+  if (i)
+	printf("Hui\n");
+  else
+	printf("Pfui\n");
+  return 0;
+}

archive/HS19-debugging-on-linux/code/gdb-examples/simple.c

+
+#include<stdio.h>
+#include<stdbool.h>
+#include<tgmath.h>
+
+bool
+is_prime(int number) {
+  int max = ((int) sqrt((double) number)) + 1;
+  for (int i = 2; i < max; i++)
+	if (!(number % i))
+	  return false;
+  return true;
+}
+
+int
+main(int argc, char** argv) {
+  int number;
+  scanf("%d", &number);
+  if (is_prime(number))
+	printf("%d: prime\n", number);
+  else 
+	printf("%d: not prime\n", number);
+  return 0;
+}

archive/HS19-debugging-on-linux/code/strace/file.c

+#include<stdio.h>
+
+int
+main(int argc, char **argv) {
+  FILE *f = fopen("/tmp/test", "w+");
+  fprintf(f, "Hello\n");
+  fclose(f);
+  printf("Done!\n");
+  return 0;
+}

archive/HS19-debugging-on-linux/code/strace/simple.c

+#include<stdio.h>
+
+int
+main(int argc, char **argv) {
+  printf("Hello World!");
+  return 0;
+}

archive/HS19-debugging-on-linux/template.tex

+\documentclass[aspectratio=169,12pt]{beamer}
+\usepackage{lmodern}
+\usepackage[T1]{fontenc} %pipes don't display properly without this
+\usepackage[utf8]{inputenc}
+\usepackage{listings}
+\usepackage{color}
+\usepackage{datapie}
+\usepackage{multicol}
+\usepackage{siunitx} %pretty measurement unit rendering
+\usepackage{hyperref} %enable hyperlink for urls
+\usepackage{caption} % needed to tweak caption size
+\usepackage{booktabs}
+\usepackage{longtable}
+\usepackage{graphicx}
+
+\newcommand{\passthrough}[1]{#1}
+
+\usefonttheme[onlymath]{serif}
+\setcounter{MaxMatrixCols}{20}
+
+\DeclareSIUnit\pixel{px}
+
+\usecolortheme[RGB={37,68,113}]{structure}
+\usetheme{Dresden}
+
+\newenvironment{figurehere}
+{\def\@captype{figure}}
+{}
+\makeatother
+
+%commands to exclude sections from miniframes
+\makeatletter
+\let\beamer@writeslidentry@miniframeson=\beamer@writeslidentry
+\def\beamer@writeslidentry@miniframesoff{%
+   	\expandafter\beamer@ifempty\expandafter{\beamer@framestartpage}{}% does not happen normally
+   	{%else
+   		% removed \addtocontents commands
+   		\clearpage\beamer@notesactions%
+   	}
+}
+\newcommand*{\miniframeson}{\let\beamer@writeslidentry=\beamer@writeslidentry@miniframeson}
+\newcommand*{\miniframesoff}{\let\beamer@writeslidentry=\beamer@writeslidentry@miniframesoff}
+\beamer@compresstrue
+\makeatother
+
+
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+
+%various gray colors
+\definecolor{slg}{gray}{0.25}
+\definecolor{lg}{gray}{0.55}
+\definecolor{vlg}{gray}{0.73}
+\definecolor{tlg}{gray}{0.9}
+
+%TheAlt colors
+\definecolor{ldorange}{HTML}{F18A20}
+\colorlet{ldbright}{ldorange!70!white} % tinted version of orange, used in miniframes
+\definecolor{ldblue}{HTML}{254471}
+
+%%Theme colors
+%\definecolor{thgreen}{HTML}{A1A92C}
+%\definecolor{thmauve}{HTML}{97284D}
+
+%Theme colors
+\definecolor{thgreen}{HTML}{539727}
+\definecolor{thmauve}{HTML}{572272}
+
+%reduce caption font size:
+\captionsetup{font={scriptsize,color=lg}}
+
+%do not prepend numbering/lettering to figures/subfigures
+\captionsetup{labelformat=empty} %do not prepend letters to figure captions
+
+%Apply TheAlt colors to theme
+ % section titles in top navigation bar
+\setbeamercolor{section in head/foot}{parent=palette tertiary,fg=ldorange}
+\setbeamertemplate{section in head/foot shaded}{\color{ldbright}\usebeamertemplate{section in head/foot}}
+ % miniframes (little navigation circles)
+\setbeamercolor*{mini frame}{fg=ldorange,bg=ldbright}
+\setbeamertemplate{mini frame in other section}[default][0]
+\setbeamertemplate{mini frame in other subsection}[default][0]
+ % others
+\setbeamercolor{author in head/foot}{fg=white}
+\setbeamercolor{subsection in head/foot}{fg=white}
+\setbeamercolor{caption name}{fg=vlg}
+\setbeamercolor{caption}{fg=vlg}
+\setbeamercolor{frametitle}{fg=ldblue}
+
+\setbeamertemplate{caption}{\raggedright\insertcaption\par}
+\setbeamertemplate{navigation symbols}{}
+\setbeamertemplate{bibliography item}[text]
+
+\definecolor{mygreen}{rgb}{0,0.6,0}
+\definecolor{mygray}{rgb}{0.5,0.5,0.5}
+\definecolor{mymauve}{rgb}{0.58,0,0.82}
+
+\lstdefinestyle{custombash}{
+	belowcaptionskip=1\baselineskip,
+	captionpos=,
+	breaklines=true,
+	frame=L,
+	xleftmargin=\parindent,
+	language=bash,
+    morestring=[b]',
+    morekeywords=[2]{sudo,zypper,notify-send,feh,youtube-dl,sort,tee,head,tail,shuf,mpv,find,convert,xrandr,curl,wget,grep,xdotool,rm,cp,mv,touch,bash,chmod,mkdir,rsync,mplayer,mpv,xdotool,jshon},
+	showstringspaces=false,
+	basicstyle=\scriptsize\ttfamily,
+	rulecolor=\color{tlg},
+	backgroundcolor=\color{tlg},
+	fillcolor=\color{tlg},
+	rulesepcolor=\color{tlg},
+	commentstyle=\itshape\color{thmauve!60!black},
+    keywordstyle=\bfseries\color{thgreen},
+    identifierstyle=\color{ldblue},
+    stringstyle=\color{thmauve}
+}
+
+\lstset{
+    style=custombash,
+    caption={Descriptive Caption Text},
+    label=DescriptiveLabel
+}
+
+$if(title)$
+\title{$title$}
+$endif$
+$if(subtitle)$
+\subtitle{$subtitle$}
+$endif$
+$if(author)$
+\author{$for(author)$$author$$sep$ \and $endfor$}
+$endif$
+
+\institute{\includegraphics[width=0.35\textwidth]{img/logo_blue.pdf}}
+\date{$date$}
+
+\renewcommand{\emph}[1]{\textcolor{ldorange}{#1}}
+\let\oldtextbf\textbf
+\renewcommand{\textbf}[1]{\textcolor{ldorange}{\oldtextbf{#1}}}
+\newcommand{\soft}[1]{\textcolor{lg}{#1}}
+\newcommand{\textt}[1]{\textcolor{blue}{\texttt{#1}}}
+\newcommand{\bigtext}[1]{\centering\Huge \textbf{\textcolor{ldorange}{#1}}\normalsize}
+
+%shortcut to insert small logo in footline
+\def\logo{%
+	\resizebox{!}{3ex}{\includegraphics{img/logo_white.pdf}}
+}
+
+% Define a custom footline that includes our logo
+\setbeamertemplate{footline}
+{%
+	\begin{beamercolorbox}[wd=\paperwidth,ht=2.5ex,dp=1.125ex,%
+		leftskip=.3cm,rightskip=.3cm plus1fil]{title in head/foot}
+		\usebeamerfont{title in head/foot}%
+		\insertshorttitle\hfill\insertframenumber
+	\end{beamercolorbox}
+	\begin{beamercolorbox}[wd=\paperwidth,ht=3.5ex,dp=1.625ex,%
+		leftskip=.3cm,rightskip=.3cm plus1fil]{author in head/foot}
+		\usebeamerfont{author in head/foot}
+		\raisebox{0.5ex}{\insertshortauthor}\hfill\raisebox{-0.5ex}{\logo}
+	\end{beamercolorbox}
+}
+
+\begin{document}
+
+$if(title)$
+\frame{\titlepage}
+$endif$
+
+$for(include-before)$
+$include-before$
+
+$endfor$
+
+$if(toc)$
+\begin{frame}
+\tableofcontents[hideallsubsections]
+\end{frame}
+
+$endif$
+
+$body$
+
+$for(include-after)$
+$include-after$
+
+$endfor$
+
+\end{document}

archive/HS19-scientific_software_management/bib.bib

+@conference{repsep,
+	author = {Horea-Ioan Ioanas and Markus Rudin},
+	title = {Reproducible Self-Publishing for {P}ython-Based Research},
+	year = 2018,
+	month = aug,
+	publisher = {EuroSciPy},
+	url = {https://figshare.com/articles/Reproducible_Self-Publishing_for_Python-Based_Research/7247339},
+	doi = {10.6084/m9.figshare.7247339.v1},
+}
+@article{Ioanas2017,
+	author = {Horea-Ioan Ioanas and Bechara Saab and Markus Rudin},
+	title = {Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software},
+	volume = {3},
+	number = {},
+	year = {2017},
+	doi = {10.3897/rio.3.e12095},
+	publisher = {Pensoft Publishers},
+	abstract = {},
+	issn = {},
+	pages = {e12095},
+	URL = {https://doi.org/10.3897/rio.3.e12095},
+	eprint = {https://doi.org/10.3897/rio.3.e12095},
+	journal = {Research Ideas and Outcomes}
+}

archive/HS19-scientific_software_management/compile.sh

+#!/usr/bin/env bash
+
+pdflatex -shell-escape slides.tex
+bibtex slides
+pdflatex -shell-escape slides.tex
+pdflatex -shell-escape slides.tex

archive/HS19-scientific_software_management/get_samri_data.sh

+#!/usr/bin/env bash
+
+wget https://raw.githubusercontent.com/IBT-FMI/SAMRI/master/setup.py -O samri/setup.py

archive/HS19-scientific_software_management/reset_system.sh

+# reset the system
+rm -rf /var/db/repos/chymeric/
+emerge -C samri
+eix-sync
+
+# reset the overlay repo
+cd overlay/location/with/Chymera/account
+git reset --hard commitwhichwasbeforethepull
+git push -f origin master

archive/HS19-scientific_software_management/samri/metadata.xml

+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>chr@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		SAMRI (Small Animal Magnetic Resonance Imaging) — pronounced "Sam-rye" — provides
+		fMRI preprocessing, metadata parsing, and data analysis functions and workflows.
+		SAMRI integrates functionalities from a number of other packages to create
+		higher-level tools. The resulting interfaces aim to maximize reproducibility,
+		simplify batch processing, and minimize the number of function calls required to
+		generate figures and statistical summaries from the raw data.
+	</longdescription>
+	<upstream>
+		<remote-id type="github">IBT-FMI/SAMRI</remote-id>
+	</upstream>
+</pkgmetadata>

archive/HS19-scientific_software_management/samri/samri-0.4.ebuild

+# Copyright 1999-2019 Gentoo Authors