New publishing material directory name

.gitignore

@@ -15,9 +15,9 @@ __pycache__
 # but we don't want to commit the freshly produced one in that location
 article/article.pdf
 
-.nfs*
-article.bbl
-article.blg
-article.run.xml
+*.nfs*
+*.bbl
+*.blg
+*.run.xml
 
-article/metadata.tex
+publishing/metadata.tex

Makefile

@@ -103,19 +103,19 @@ analysis-oci-interactive:
 #
 .PHONY: container-article
 container-article:
-	$(MAKE) container-article -C article/
+	$(MAKE) container-article -C publishing/
 
 .PHONY: article
 article:
-	$(MAKE) -C article/
+	$(MAKE) -C publishing/
 
 .PHONY: article-clean
 article-clean:
-	$(MAKE) clean -C article/
+	$(MAKE) clean -C publishing/
 
 .PHONY: article-upload
 article-upload:
-	$(MAKE) upload -C article/
+	$(MAKE) upload -C publishing/
 
 
 #

publishing/sty/beamerposter.sty

@@ -0,0 +1,301 @@
+% Copyright 2007 by 
+% Philippe Dreuw <dreuw@cs.rwth-aachen.de> and 
+% Thomas Deselaers <deselaers@cs.rwth-aachen.de>
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+%
+% ChangeLog:
+%
+% 1.10 - imrpoved PackageWarning and PackageInfo outputs
+% 1.09 - bugfixed the list indention problem, can be overwritten by user with the \setdefaultleftmargin command.
+%      - added 'printer' option for external printer definition files
+% 1.08 - supports external printer definition files
+%      - added grid mode option
+%      - renamed beamer specific variables
+%      - added font size normalization, so that scale=1.0 is the default font size for all DIN-A(n) sizes
+% 1.07 - bugfixed custom size handling, portrait or landscape settings are ignored now
+% 1.06 - added the type1cm package for scalable math fonts
+% 1.05 - added version check for xkeyval package
+% 1.04 - added custom size handling
+% 1.03 - improved predefined size handling
+% 1.02 - minor bugfixes
+% 1.01 - bugfixed size handling
+% 1.00 - first beamerposter release
+%
+\def\beamerposter@name{beamerposter}
+\def\beamerposter@version{1.10}
+\def\beamerposter@date{2009/09/02}
+\def\beamerposter@msg{latex-beamer poster extension}
+\def\beamerposter@releaseinfo{\beamerposter@date \space v.\beamerposter@version \space \beamerposter@msg}
+\def\beamerposter@Error#1#2{\PackageError{\beamerposter@name}{#1}{#2}}
+\def\beamerposter@Warning#1{\PackageWarning{\beamerposter@name}{#1}}
+\def\beamerposter@Info#1{\PackageInfo{\beamerposter@name}{#1}}
+
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{\beamerposter@name}[\beamerposter@releaseinfo]
+\RequirePackage{xkeyval}[2006/11/18]
+\RequirePackage{type1cm} %% get it from ftp://cam.ctan.org/tex-archive/macros/latex/contrib/type1cm.zip
+\RequirePackage{fp}
+\RequirePackage{paralist}
+
+\newif\if@beamerposter@portrait
+\newif\if@beamerposter@customsize
+\newif\if@beamerposter@extern
+\newif\if@beamerposter@debug
+
+
+\DeclareOptionX{size}[a0]{
+  \beamerposter@Info{checking size input, please wait.}
+  \XKV@cc*+[\val\nr]{#1}{a0b,a0,a1,a2,a3,a4,custom}{%
+    \beamerposter@Info{the input \val\ \nr\ was correct, we proceed.}
+    \ifcase\nr\relax
+    %a0b
+    \edef\paperwidthValue{119}
+    \edef\paperheightValue{88}
+    \edef\textwidthValue{116}
+    \edef\textheightValue{88}
+    \edef\fontscale{1.0}
+    \or
+    %a0
+    \edef\paperwidthValue{118.82}
+    \edef\paperheightValue{83.96}
+    \edef\textwidthValue{117.82}
+    \edef\textheightValue{82.96}
+    \edef\fontscale{1.0}
+    \or
+    %a1
+    \edef\paperwidthValue{83.96}
+    \edef\paperheightValue{59.4}
+    \edef\textwidthValue{82.96}
+    \edef\textheightValue{58.4}
+    \edef\fontscale{0.70710678}    % fontscale=(1/sqrt(2))^1
+    \or
+    %a2
+    \edef\paperwidthValue{59.4}
+    \edef\paperheightValue{41.98}
+    \edef\textwidthValue{58.4}
+    \edef\textheightValue{40.98}
+    \edef\fontscale{0.5}           % fontscale=(1/sqrt(2))^2
+    \or
+    %a3
+    \edef\paperwidthValue{41.98}
+    \edef\paperheightValue{29.7}
+    \edef\textwidthValue{40.98}
+    \edef\textheightValue{28.7}
+    \edef\fontscale{0.35355339}    % fontscale=(1/sqrt(2))^3
+    \or
+    %a4
+    \edef\paperwidthValue{29.7}
+    \edef\paperheightValue{21.0}
+    \edef\textwidthValue{28.7}
+    \edef\textheightValue{20.0}
+    \edef\fontscale{0.25}          % fontscale=(1/sqrt(2))^4
+    \or
+    \@beamerposter@customsizetrue
+    \fi    
+  }{%
+    \beamerposter@Warning{the input \val\ was incorrect and was ignored.}
+  }%
+  \beamerposter@Info{finished size input check.}
+}
+\DeclareOptionX{orientation}[portrait]{
+  \beamerposter@Info{checking orientation input, please wait.}
+  \XKV@cc*+[\val\nr]{#1}{portrait,landscape}{%
+    \beamerposter@Info{the input \val\ \nr\ was correct, we proceed.}
+    \ifcase\nr\relax
+    \@beamerposter@portraittrue
+    \or
+    \@beamerposter@portraitfalse
+    \fi    
+  }{%
+    \beamerposter@Warning{the input \val\ was incorrect and was ignored.}
+  }%
+  \beamerposter@Info{finished orientation check.}
+}
+\DeclareOptionX{scale}[1.0]{\edef\myfontscale{#1}\beamerposter@Info{myfontscale=\myfontscale}}
+\DeclareOptionX{width}{\edef\customwidth{#1}\beamerposter@Info{custom poster width=\customwidth}}
+\DeclareOptionX{height}{\edef\customheight{#1}\beamerposter@Info{custom poster height=\customheight}}
+\DeclareOptionX{debug}{\beamerposter@Info{enabled debug mode}\@beamerposter@debugtrue}
+\DeclareOptionX{grid}{\beamerposter@Info{enabling grid}\beamertemplategridbackground[1cm]}% Display a grid to help align images
+\DeclareOptionX{printer}{\edef\printerToUse{#1}\@beamerposter@externtrue}
+\DeclareOptionX*{\beamerposter@Warning{Unknown option ignored: \CurrentOption}}
+%\DeclareOptionX*{\PassOptionsToClass{\CurrentOption}{beamer}}
+\ExecuteOptionsX{size=a0,scale=1.0}
+\ProcessOptionsX\relax
+
+%% enable debug mode for fp package (mainly for upn functions)
+\if@beamerposter@debug
+  \FPdebugtrue  
+\fi
+
+%% normalize scale depending on poster size
+\FPupn{\myfontscale}{myfontscale fontscale * 2 round}
+
+%% swap sizes for portrait orientation
+\if@beamerposter@portrait
+  \newdimen\tmp
+  \setlength{\tmp}{\paperwidthValue cm}
+  \setlength{\paperwidth}{\paperheightValue cm}
+  \setlength{\paperheight}{\tmp}
+  \setlength{\tmp}{\textwidthValue cm}
+  \setlength{\textwidth}{\textheightValue cm}
+  \setlength{\textheight}{\tmp}
+\else
+  \setlength{\paperwidth}{\paperwidthValue cm}
+  \setlength{\paperheight}{\paperheightValue cm}
+  \setlength{\textwidth}{\textwidthValue cm}
+  \setlength{\textheight}{\textheightValue cm}
+\fi
+
+%% overwrite dimensions if custom size
+\if@beamerposter@customsize
+  \setlength{\paperwidth}{\customwidth cm}
+  \setlength{\paperheight}{\customheight cm}
+  \FPupn{\resulttextwidth}{1 customwidth  -}
+  \FPupn{\resulttextheight}{1 customheight -}
+  \setlength{\textwidth}{\resulttextwidth cm}
+  \setlength{\textheight}{\resulttextheight cm}
+\fi
+
+%% Setting proper dimensions for a DIN A0 printer
+\setlength{\headheight}{0 cm}
+\setlength{\headsep}{0 cm}
+\setlength{\topmargin}{-12.7 mm}     % -1in +1.47cm
+\setlength{\oddsidemargin}{-25.4 mm} % -1in +0.4cm
+
+%% For the page layout
+\beamerposter@Info{paperwidth=\the\paperwidth, paperheight=\the\paperheight}
+\beamerposter@Info{textwidth=\the\textwidth, textwidth=\the\textheight}
+\beamerposter@Info{fontscale=\fontscale, myfontscale=\myfontscale}
+\geometry{
+  paperwidth=\the\paperwidth,
+  paperheight=\the\paperheight,
+  hmargin=1cm,%
+  vmargin=0cm,%
+  head=0.5cm, % 
+  headsep=0pt,%
+  foot=0.5cm  % 
+}
+
+%%
+%% printer definition file example 'rwth-glossy-uv.df':
+%% ----
+%% \typeout{beamerposter: RWTH RZ printer, glossy paper, UV resistant, maximum settings}
+%% \edef\printermaxwidthValue{108} %unit should be cm
+%% \newlength{\printermaxwidth}
+%% \setlength{\printermaxwidth}{\printermaxwidthValue cm}
+%% ----
+%%
+%% now load printer definitions from file (e.g. \usepackage[printer=rwth-glossy-uv.df]{beamerposter}")
+\if@beamerposter@extern
+  \InputIfFileExists{\printerToUse}{\typeout{load \printerToUse}}{\beamerposter@Error{\printerToUse\space not found!}{Please use another printer definition file}}
+  \ifx\printermaxwidthValue\@empty%
+    \relax%
+  \else%
+    %%  @todo: calc poster ratios, scale to maximum printer size, and check if they still fit
+    %%  this here is still very basic ...
+    \FPsub{\resultmaxwidth}{\printermaxwidthValue}{\paperwidthValue}
+    \FPifneg{\resultmaxwidth}
+    \beamerposter@Error{%
+      resultmaxwidth=\resultmaxwidth \MessageBreak
+      printermaxwidthValue=\printermaxwidthValue \MessageBreak
+      paperwidthValue=\paperwidthValue \MessageBreak 
+      The specified poster dimensions might not be printable using
+      '\printerToUse'.
+    }{%
+      Try to reduce your poster dimension and have a look at the aspect ratio.
+    }
+    \else
+      \relax
+    \fi
+  \fi
+%\fi
+
+%% scalable vector fonts
+\edef\fontSizeX{12}\edef\fontSizeY{14}
+\FPupn{\resulttinyX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resulttinyY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\tiny}{\fontsize{\resulttinyX}{\resulttinyY}\selectfont}
+
+\edef\fontSizeX{14.4}\edef\fontSizeY{18}   
+\FPupn{\resultscriptsizeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultscriptsizeY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\scriptsize}{\fontsize{\resultscriptsizeX}{\resultscriptsizeY}\selectfont}
+
+\edef\fontSizeX{17.28}\edef\fontSizeY{22}
+\FPupn{\resultfootnotesizeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultfootnotesizeY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\footnotesize}{\fontsize{\resultfootnotesizeX}{\resultfootnotesizeY}\selectfont}
+
+\edef\fontSizeX{20.74}\edef\fontSizeY{25}
+\FPupn{\resultsmallX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultsmallY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\small}{\fontsize{\resultsmallX}{\resultsmallY}\selectfont}
+
+\edef\fontSizeX{24.88}\edef\fontSizeY{30}
+\FPupn{\resultnormalsizeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultnormalsizeY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\normalsize}{\fontsize{\resultnormalsizeX}{\resultnormalsizeY}\selectfont}
+
+\edef\fontSizeX{29.86}\edef\fontSizeY{37}
+\FPupn{\resultlargeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultlargeY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\large}{\fontsize{\resultlargeX}{\resultlargeY}\selectfont}
+
+\edef\fontSizeX{35.83}\edef\fontSizeY{45}
+\FPupn{\resultLargeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultLargeY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\Large}{\fontsize{\resultLargeX}{\resultLargeY}\selectfont}
+
+\edef\fontSizeX{43}\edef\fontSizeY{54}
+\FPupn{\resultLARGEX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultLARGEY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\LARGE}{\fontsize{\resultLARGEX}{\resultLARGEY}\selectfont}
+
+\edef\fontSizeX{51.6}\edef\fontSizeY{64}
+\FPupn{\resulthugeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resulthugeY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\huge}{\fontsize{\resulthugeX}{\resulthugeY}\selectfont}
+
+\edef\fontSizeX{61.92}\edef\fontSizeY{77}
+\FPupn{\resultHugeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultHugeY}{myfontscale fontSizeY * 2 round}
+\renewcommand*{\Huge}{\fontsize{\resultHugeX}{\resultHugeY}\selectfont}
+
+\edef\fontSizeX{74.3}\edef\fontSizeY{93}
+\FPupn{\resultveryHugeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultveryHugeY}{myfontscale fontSizeY * 2 round}
+\newcommand*{\veryHuge}{\fontsize{\resultveryHugeX}{\resultveryHugeY}\selectfont}
+
+\edef\fontSizeX{89.16}\edef\fontSizeY{112}
+\FPupn{\resultVeryHugeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultVeryHugeY}{myfontscale fontSizeY * 2 round}
+\newcommand*{\VeryHuge}{\fontsize{\resultVeryHugeX}{\resultVeryHugeY}\selectfont}
+
+\edef\fontSizeX{107}\edef\fontSizeY{134}
+\FPupn{\resultVERYHugeX}{myfontscale fontSizeX * 2 round}
+\FPupn{\resultVERYHugeY}{myfontscale fontSizeY * 2 round}
+\newcommand*{\VERYHuge}{\fontsize{\resultVERYHugeX}{\resultVERYHugeY}\selectfont}
+
+% set the normalfont (default)
+\renewcommand*{\normalfont}{\normalsize}
+
+% adapt list indention (e.g. itemize/enumeration/... see paralist docu)
+\edef\indentionLevelValuei{4}       % 4em indention for first level for an A0 poster
+\edef\indentionLevelValueii{2.2}    % etc. ...
+\edef\indentionLevelValueiii{1.87}
+\edef\indentionLevelValueiiii{1.7}
+\edef\indentionLevelValueiiiii{1}
+\edef\indentionLevelValueiiiiii{1}
+\FPupn{\indentionLevelValuei}{indentionLevelValuei fontscale * 2 round}
+\FPupn{\indentionLevelValueii}{indentionLevelValueii fontscale * 2 round}
+\FPupn{\indentionLevelValueiii}{indentionLevelValueiii fontscale * 2 round}
+\FPupn{\indentionLevelValueiiii}{indentionLevelValueiiii fontscale * 2 round}
+\FPupn{\indentionLevelValueiiiii}{indentionLevelValueiiiii fontscale * 2 round}
+\FPupn{\indentionLevelValueiiiiii}{indentionLevelValueiiiiii fontscale * 2 round}
+\setdefaultleftmargin{\indentionLevelValuei em}{\indentionLevelValueii em}{\indentionLevelValueiii em}{\indentionLevelValueiiii em}{\indentionLevelValueiiiii em}{\indentionLevelValueiiiiii em}
+\setbeamersize{description width=\indentionLevelValuei em} % the description environment needs special treatment

publishing/sty/beamerthemeZH.sty

@@ -0,0 +1,144 @@
+% this style was created by Horea Christian and is basted on the ETH Zürich corporate design color palette https://www.ethz.ch/services/en/service/communication/corporate-design/colour.html
+\ProvidesPackage{beamerthemeZH}
+
+\newcommand{\vcenteredinclude}[1]{\begingroup
+\setbox0=\hbox{\includegraphics[width=.8\textwidth, height=.06\paperheight, keepaspectratio]{#1}}%
+\parbox{\wd0}{\box0}\endgroup}
+
+
+\usepackage{calc}
+\newlength{\mylength}
+
+\mode<presentation>
+
+\definecolor{ETH1}{RGB}{31,64,122}
+\definecolor{ETH3}{RGB}{0,105,180}
+\definecolor{ETH6}{RGB}{111,111,110}
+\definecolor{ETH8}{RGB}{0,122,146}
+\definecolor{ETH10}{RGB}{130,190,30}
+\definecolor{tlg}{RGB}{230,230,230}
+\definecolor{elg}{RGB}{240,240,240}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%It seems many of the following entries do not control any visible Behaviour. All such entries are
+%set to red, so that they are easy to spot if they ever become visible
+
+\setbeamercolor{headline}{fg=red,bg=ETH3} % This is the recommended color for Specialist community usage: change to ETH1 for general communication
+\setbeamercolor{footline}{fg=red, bg=red}
+\setbeamerfont{footline}{size=\large,series=\bf}
+\setbeamercolor{separation line}{bg=ETH3}
+\setbeamercolor{title in headline}{fg=white}
+\setbeamercolor{author in headline}{fg=white}
+\setbeamercolor{institute in headline}{fg=white}
+
+\setbeamercolor{framesubtitle}{fg=red, bg=ta2gray}
+\setbeamercolor{author in head/foot}{fg=white, bg=ETH3}
+\setbeamercolor{title in head/foot}{fg=red, bg=red}
+
+\setbeamercolor*{normal text}{fg=ETH6, bg=tlg}
+\setbeamercolor*{block body}{fg=black, bg=white}
+\setbeamercolor*{block title}{fg=black,bg=ETH10}
+\setbeamerfont{block title}{size=\large,series=\bf}
+\setbeamercolor{upper separation line head}{fg=red}
+
+\setbeamercolor*{example body}{fg=red,bg=red}
+\setbeamercolor*{example text}{fg=red,bg=red}
+\setbeamercolor*{example title}{bg=red,fg=red}
+
+\setbeamercolor{alerted text}{fg=red}
+\setbeamercolor{structure}{fg=ETH1}
+
+\setbeamertemplate{itemize items}{\color{ETH10}$\blacktriangleright$}
+\setbeamertemplate{navigation symbols}{}  % no navigation on a poster
+
+\newenvironment<>{myblock}[1]{%
+	\begin{actionenv}#2%
+	\def\insertblocktitle{\centering#1}%
+	\par%
+	\usebeamertemplate{block begin}\leftskip=14pt\rightskip=14pt\vspace{10pt}}
+	{\par\vspace{1em}\usebeamertemplate{block end}
+	\end{actionenv}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% !!! This environment can't both have nice margins AND display the contained text as justified:
+% We preferentially use the above but keep this one just-in-case
+\setbeamertemplate{block begin}{
+	\setlength{\mylength}{\textwidth+2ex}%
+	\vskip2ex
+	\begin{beamercolorbox}[ht=2.8ex,dp=2ex, wd=\mylength, center,rounded=false,shadow=false,leftskip=1cm,colsep*=0ex]{block title}%
+		\usebeamerfont*{block title}\centering \insertblocktitle
+	\end{beamercolorbox}\vskip-9pt%
+	{\ifbeamercolorempty[bg]{block body}{}{\nointerlineskip\vskip-0.5ex}}%
+	\usebeamerfont{block body}%
+	\begin{beamercolorbox}[rounded=false,shadow=false,center,wd=\textwidth,]{block body}%
+		\ifbeamercolorempty[bg]{block body}\vbox{}%
+		\begin{minipage}{0.96\textwidth}\vbox{}%
+		\justify
+		}
+\setbeamertemplate{block end}{
+	\end{minipage}
+	\end{beamercolorbox}
+	}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\setbeamertemplate{headline}{
+	\leavevmode
+	\begin{beamercolorbox}[wd=\paperwidth]{headline}
+		\vspace{3.ex}\\
+		\begin{columns}[c]
+			\begin{column}{.06\paperwidth}
+			\end{column}
+			\begin{column}{.75\paperwidth}
+				\raggedleft
+				\usebeamercolor{title in headline}{\color{fg}\textbf{\Huge{\inserttitle}}\\[1ex]}
+				\usebeamercolor{author in headline}{\color{fg}\Large{\insertauthor}\\[1ex]}
+				\usebeamercolor{institute in headline}{\color{fg}\normalsize{\insertinstitute}\\[1ex]}
+			\end{column}
+			\begin{column}{.01\paperwidth}
+			\end{column}
+			\begin{column}{.16\paperwidth}
+                                \begin{center}
+                                        \includegraphics[width=.9\textwidth, height=.52\textwidth, keepaspectratio]{img/zh_logo}
+                                \end{center}
+                        \end{column}
+			\begin{column}{.02\paperwidth}
+			\end{column}
+		\end{columns}
+		\vspace{3.ex}\\
+	\end{beamercolorbox}
+
+ 	\begin{beamercolorbox}[wd=\paperwidth]{lower separation line head}
+		\rule{0pt}{2pt}
+	\end{beamercolorbox}
+	\vskip-17.ex
+	}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\setbeamertemplate{footline}{
+	\begin{beamercolorbox}[wd=\paperwidth]{upper separation line foot}
+		\rule{0pt}{2pt}
+	\end{beamercolorbox}
+	\leavevmode%
+	\begin{beamercolorbox}[ht=4ex,leftskip=1cm,rightskip=1cm]{author in head/foot}%
+		\href{http://doi.org/10.5281/zenodo.3477675}{DOI: 10.5281/zenodo.3477675}
+		\hfill
+		Open Innovation in Life Sciences --- 2019-10-10
+		\hfill
+		\href{mailto:my_address@wikibooks.org}{ioanas@biomed.ee.ethz.ch}
+		\vskip1ex
+	\end{beamercolorbox}
+	\vskip0pt%
+	\begin{beamercolorbox}[wd=\paperwidth]{lower separation line foot}
+		\rule{0pt}{2pt}
+	\end{beamercolorbox}
+	}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Display a grid to help align images ... and it looks nice with this color scheme
+% \beamertemplategridbackground[1cm]
+
+%Some beamer customizations:
+\setbeamertemplate{bibliography item}[text]
+\setbeamertemplate{caption}[numbered]{}% Number float-like environments
+
+\mode<all>

publishing/sty/graphviz.sty

@@ -0,0 +1,77 @@
+% graphviz.sty
+% by Mark Aufflick
+% 2006-03-25
+% mark@aufflick.com
+% http://mark.aufflick.com/
+%
+% based on graphviz.tex by Derek Rayside 2003
+
+% Modified by Mike Prentice (mjp44@buffalo.edu)
+% 2011-02-21
+% To use PDF output directly from dot
+% dot -Tpdf
+
+% Modified by Remi Dubot (remi.dubot@irit.fr)
+% 2012-12-3
+% To distinguish errors from tex and from dot. 
+% Report dot errors
+% Indications for non english writers
+
+% add the following lines to your preamble:
+
+% \usepackage[pdftex]{graphicx}
+% \usepackage{graphviz}
+
+% parameters to \digraph:
+% 1 - parameters for \includegraphics (optional; default value is "scale=1")
+% 2 - name of the digraph
+% 3 - body of the digraph
+
+% parameters to \includedot
+% 1 - parameters for \includegraphics (optional; default value is "scale=1")
+% 2 - name of the dot file (w/out file extension, which must be `.dot')
+
+% ASSUMES pdflatex 
+% If you are not using pdflatex, go back on an older version of this style. 
+
+% If you are not writing english, pay attention to your charset. 
+% If is not UTF-8, you may have to indicate your charset to dot with "-Gccharset=XXXX".  
+
+\ProvidesPackage{graphviz}
+
+\newcommand{\includedot}[2][scale=1]{%
+  \ifnum\pdfshellescape=1
+  % Yes, enabled
+    \immediate\write18{bash -c "dot -Tpdf #2.dot -o #2.pdf 2> #2.log"}%
+    \IfFileExists{#2.pdf}
+    % the pdf exists: include it
+    {\includegraphics[#1]{#2}}
+    % the pdf was not created - show a hint
+    { \fbox{ \begin{tabular}{l}
+          The file \texttt{#2.pdf} hasn't been created from
+          \texttt{#2.dot} yet. \\
+          We attempted to create it with:\\
+          `\texttt{dot -Tpdf #2.dot -o #2.pdf}' \\
+          but that seems not to have worked.\\
+          \texttt{dot} said : \\
+          "\texttt{\input{#2.log}}"
+        \end{tabular}}
+    }
+  \else
+    \fbox{ \begin{tabular}{l}
+            You need to execute `\texttt{pdflatex}' with the `\texttt{-shell-escape}' option.\\
+            This allows the graphviz package to execute the program dot. 
+          \end{tabular}}
+  \fi
+}
+
+\newcommand{\digraph}[3][scale=1]{ 
+  \newwrite\dotfile 
+  \immediate\openout\dotfile=#2.dot 
+  \immediate\write\dotfile{digraph #2 {\string#3}} 
+  \immediate\closeout\dotfile
+  \includedot[#1]{#2}
+}
+
+
+