Setting up additional topics

doc/src/How2ReadData/How2ReadData.do.txt

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+TITLE: Data Analysis and Machine Learning: Representing data
+AUTHOR: Morten Hjorth-Jensen {copyright, 1999-present|CC BY-NC} at Department of Physics, University of Oslo & Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University
+DATE: today
+
+
+!split
+===== Representing data, overarching aims  =====
+!bblock
+
+!eblock
+

doc/src/How2ReadData/beamerthemered_plain.sty

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+\mode<presentation>
+\usecolortheme[rgb={0.8, 0.2, 0}]{structure}
+\usefonttheme[onlysmall]{structurebold}
+
+\setbeamertemplate{navigation symbols}{}
+%\setbeamertemplate{footline}[frame number]
+
+\usepackage{tikz}
+\usetikzlibrary{arrows,shapes,backgrounds,decorations,mindmap}
+
+\mode
+<all>

doc/src/How2ReadData/beamerthemered_shadow.sty

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+\mode<presentation>
+
+\useoutertheme{smoothbars}
+\useinnertheme[shadow=true]{rounded}
+\usecolortheme{orchid}
+\usecolortheme{whale}
+\usecolortheme[rgb={0.7, 0.2, 0}]{structure}  % (darker red)
+\useoutertheme{shadow}
+\usefonttheme[onlysmall]{structurebold}
+
+\setbeamercolor{title}{use=structure,fg=white,bg=structure.fg}
+\setbeamerfont{block title}{size={}}
+
+\mode
+<all>

doc/src/How2ReadData/clean.sh

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+#!/bin/sh
+doconce clean
+rm -rf *.pdf *.tex ipynb*.tar.gz *.html ._*.html *~ reveal.js Trash README.txt

doc/src/How2ReadData/make.sh

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+#!/bin/sh
+set -x
+
+function system {
+  "$@"
+  if [ $? -ne 0 ]; then
+    echo "make.sh: unsuccessful command $@"
+    echo "abort!"
+    exit 1
+  fi
+}
+
+if [ $# -eq 0 ]; then
+echo 'bash make.sh slides1|slides2'
+exit 1
+fi
+
+name=$1
+rm -f *.tar.gz
+
+opt="--encoding=utf-8"
+# Note: Makefile examples contain constructions like ${PROG} which
+# looks like Mako constructions, but they are not. Use --no_mako
+# to turn off Mako processing.
+opt="--no_mako"
+
+rm -f *.aux
+
+
+html=${name}-reveal
+system doconce format html $name --pygments_html_style=perldoc --keep_pygments_html_bg --html_links_in_new_window --html_output=$html $opt
+system doconce slides_html $html reveal --html_slide_theme=beige
+
+# Plain HTML documents
+
+html=${name}-solarized
+system doconce format html $name --pygments_html_style=perldoc --html_style=solarized3 --html_links_in_new_window --html_output=$html $opt
+system doconce split_html $html.html --method=space10
+
+html=${name}
+system doconce format html $name --pygments_html_style=default --html_style=bloodish --html_links_in_new_window --html_output=$html $opt
+system doconce split_html $html.html --method=space10
+
+# Bootstrap style
+html=${name}-bs
+system doconce format html $name --html_style=bootstrap --pygments_html_style=default --html_admon=bootstrap_panel --html_output=$html $opt
+system doconce split_html $html.html --method=split --pagination --nav_button=bottom
+
+# IPython notebook
+#system doconce format ipynb $name $opt
+
+# LaTeX Beamer slides
+beamertheme=red_plain
+system doconce format pdflatex $name --latex_title_layout=beamer --latex_table_format=footnotesize $opt
+system doconce ptex2tex $name envir=minted
+# Add special packages
+doconce subst "% Add user's preamble" "\g<1>\n\\usepackage{simplewick}" $name.tex
+system doconce slides_beamer $name --beamer_slide_theme=$beamertheme
+system pdflatex -shell-escape ${name}
+system pdflatex -shell-escape ${name}
+cp $name.pdf ${name}-beamer.pdf
+cp $name.tex ${name}-beamer.tex
+
+# Handouts
+system doconce format pdflatex $name --latex_title_layout=beamer --latex_table_format=footnotesize $opt
+system doconce ptex2tex $name envir=minted
+# Add special packages
+doconce subst "% Add user's preamble" "\g<1>\n\\usepackage{simplewick}" $name.tex
+system doconce slides_beamer $name --beamer_slide_theme=red_shadow --handout
+system pdflatex -shell-escape $name
+pdflatex -shell-escape $name
+pdflatex -shell-escape $name
+pdfnup --nup 2x3 --frame true --delta "1cm 1cm" --scale 0.9 --outfile ${name}-beamer-handouts2x3.pdf ${name}.pdf
+rm -f ${name}.pdf
+
+# Ordinary plain LaTeX document
+rm -f *.aux  # important after beamer
+system doconce format pdflatex $name --minted_latex_style=trac --latex_admon=paragraph $opt
+system doconce ptex2tex $name envir=minted
+# Add special packages
+doconce subst "% Add user's preamble" "\g<1>\n\\usepackage{simplewick}" $name.tex
+doconce replace 'section{' 'section*{' $name.tex
+pdflatex -shell-escape $name
+pdflatex -shell-escape $name
+mv -f $name.pdf ${name}-minted.pdf
+cp $name.tex ${name}-plain-minted.tex
+
+
+
+# Publish
+dest=../../pub
+if [ ! -d $dest/$name ]; then
+mkdir $dest/$name
+mkdir $dest/$name/pdf
+mkdir $dest/$name/html
+mkdir $dest/$name/ipynb
+fi
+cp ${name}*.pdf $dest/$name/pdf
+cp -r ${name}*.html ._${name}*.html reveal.js $dest/$name/html
+
+# Figures: cannot just copy link, need to physically copy the files
+if [ -d fig-${name} ]; then
+if [ ! -d $dest/$name/html/fig-$name ]; then
+mkdir $dest/$name/html/fig-$name
+fi
+cp -r fig-${name}/* $dest/$name/html/fig-$name
+fi
+
+cp ${name}.ipynb $dest/$name/ipynb
+ipynb_tarfile=ipynb-${name}-src.tar.gz
+if [ ! -f ${ipynb_tarfile} ]; then
+cat > README.txt <<EOF
+This IPython notebook ${name}.ipynb does not require any additional
+programs.
+EOF
+tar czf ${ipynb_tarfile} README.txt
+fi
+cp ${ipynb_tarfile} $dest/$name/ipynb