Poster figures and Dartmouth style update

publishing/Makefile

@@ -63,6 +63,9 @@ figs/diff_pages.pdf: data/paperdiff.csv
 figs/topology.pdf: data/topology.dot
 	cd data; dot -Tpdf topology.dot -o ../figs/topology.pdf 2>| topology.log
 
+figs/workflow.pdf: data/workflow.dot
+	cd data; dot -Tpdf workflow.dot -o ../figs/workflow.pdf 2>| workflow.log
+
 
 #
 # Article build rules

publishing/metadata.yaml

@@ -5,7 +5,7 @@
 #  - For a successful replication, it shoudl be prefixed with "[Re]"
 #  - For a failed replication, it should be prefixed with "[¬Re]"
 #  - For other article types, no instruction (but please, not too long)
-title: "Full Reexecution of Article Analyzing effective functional VTA connectivity"
+title: "Neuroimaging Article Reexecution and Reproduction Assesment System"
 
 # List of authors with name, orcid number, email and affiliation
 # Affiliation "*" means contact author

publishing/poster.tex

@@ -1,9 +1,17 @@
 \input{poster/header.tex}
 
-\title{\href{https://github.com/TheChymera/RepSeP}{\Large github.com/TheChymera/RepSeP}\\\vspace{.15em}Reproducible Publishing --- Reference Poster Implementation}
-% \title{Longitudinal opto-pharmaco-fMRI of Selective\\ Serotonin Reuptake Inhibition}
-\author{Horea-Ioan Ioanas$^{1}$, Markus Rudin$^{1}$}
-\institute[ETH]{$^{1}$Institute for Biomedical Engineering, ETH and University of Zurich}
+\title{
+	\href{https://github.com/con/opfvta-reexecution}{
+		\Large github.com/con/opfvta-reexecution
+	}\\\vspace{.15em}
+	Neuroimaging Article Reexecution and Reproduction Assesment System
+}
+\author{
+	Horea-Ioan Ioanas$^{1}$,
+	Austin Macdonald$^{1}$,
+	Yaroslav O. Halchenko$^{1}$
+}
+\institute[CON]{$^{1}$Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College}
 \date{\today}
 
 \newlength{\columnheight}
@@ -11,26 +19,6 @@
 
 \begin{document}
 
-\begin{myverbbox}[\small]{\tabcode}
-\begin{table}[]
-      \py{
-	    pytex_tab(
-		  script='scripts/stim_table.py', label='sp',
-		  caption='BIDS \cite{bids} event file table, from \cite{irsabi}',
-		  options_pre='\\centering \\resizebox{0.9\\textwidth}{!}{',
-		  data='data/JogB.tsv', options_post='}',
-		  )
-	  }
-\end{table}
-\end{myverbbox}
-\begin{myverbbox}[\small]{\spcode}
-\py{pytex_fig(
-	'scripts/3dplot.py',
-	conf='poster/3dplot.conf', label='3dplot',
-	caption='A 3D plot. Plot script from matplotlib exampes \cite{matplotlib}.',
-	)}
-\end{myverbbox}
-
 \begin{frame}
 \begin{columns}
 	\begin{column}{.42\textwidth}
@@ -41,29 +29,41 @@
 						\input{common/abstract.tex}
 					\end{myblock}\vfill
 					\vspace{-0.3em}
-					\begin{myblock}{Lala}
+					\begin{myblock}{Workflow}
+						\vspace{0.5em}
+						\begin{figure}
+							\includegraphics[width=0.99\textwidth]{figs/workflow.pdf}
+							\caption{
+								Schematic representation of the workflow, encompassing both the reexecutable article system and the meta-article generation, which takes a collection of article reexecutions as an input for its reproduction assessment showcase.
+							}
+						\end{figure}
+					\end{myblock}\vfill
+					\vspace{-0.3em}
+					\begin{myblock}{Topoplogy}
+						\vspace{0.5em}
 						\begin{figure}
 							\captionsetup{width=.9\linewidth}
-							\includegraphics[width=0.9\textwidth]{figs/topology.pdf}
-							\vspace{-1.8em}
+							\includegraphics[width=0.99\textwidth]{figs/topology.pdf}
 							\caption{
 								Mycaption lalalalal
 							}
-							\vspace{1em}
 						\end{figure}
-
 					\end{myblock}\vfill
-					\vspace{-0.3em}
-					\begin{myblock}{Technologies}
-						\vspace{0.75em}
-						\begin{minipage}{.28\textwidth}
-							\begin{figure}
-								\includegraphics[width=0.9\textwidth]{figs/diff_fig.pdf}
-							\end{figure}
-							\begin{figure}
-								\includegraphics[width=0.9\textwidth]{figs/diff_date.pdf}
-							\end{figure}
-						\end{minipage}
+					\begin{myblock}{Best Practice Guidelines}
+						\vspace{0.5em}
+						\Large
+						\begin{itemize}
+							\item Errors should be fatal more often than not
+							\item Avoid assuming or hard-coding absolute paths to resources
+							\item Avoid assuming a directory context for execution
+							\item Workflow granularity greatly benefits efficienc
+							\item Container image size should be kept small
+							\item Resources should be bundled into a DataLad superdataset
+							\item Containers should fit the scope of the underlying workflow steps
+							\item Do not write debug-relevant data inside the container
+							\item Parameterize scratch directories
+							\item Dependency versions inside container environments should be frozen as soon as feasible
+						\end{itemize}
 					\end{myblock}\vfill
 		}\end{minipage}\end{beamercolorbox}
 	\end{column}
@@ -71,25 +71,51 @@
 		\begin{beamercolorbox}[center]{postercolumn}
 			\begin{minipage}{.98\textwidth} % tweaks the width, makes a new \textwidth
 				\parbox[t][\columnheight]{\textwidth}{ % must be some better way to set the the height, width and textwidth simultaneously
-					\begin{myblock}{Technologies}
+					\begin{myblock}{Reproduction Assessment Showcase}
 						\vspace{0.75em}
-						\begin{minipage}{.28\textwidth}
-							\begin{figure}
-								\includegraphics[width=0.9\textwidth]{figs/diff_fig.pdf}
-							\end{figure}
+						\begin{minipage}{.58\textwidth}
+						\begin{figure}
+							\includegraphics[width=0.95\textwidth]{figs/diff_pages.pdf}
+							\vspace{0.2em}
+							\caption{
+								Mycaption lalalalal
+							}
+						\end{figure}
+						\begin{figure}
+							\fbox{\includegraphics[width=0.9\textwidth]{figs/diff_fig.pdf}}
+							\vspace{0.2em}
+							\caption{
+								Mycaption lalalalal
+							}
+						\end{figure}
 						\end{minipage}~
-						\begin{minipage}{.68\textwidth}
+						\begin{minipage}{.38\textwidth}
+						\begin{figure}
+							\fbox{\includegraphics[width=0.9\textwidth]{figs/diff_text.pdf}}
+							\vspace{0.2em}
+							\caption{
+								Mycaption lalalalal
+							}
+						\end{figure}
+						\begin{figure}
+							\fbox{\includegraphics[width=0.9\textwidth]{figs/diff_date.pdf}}
+							\vspace{0.2em}
+							\caption{
+								Mycaption lalalalal
+							}
+						\end{figure}
+						Evaluating the coherence of reexecution results across the manuscript ... text commentary, basically the same thing we'll be telling people if they ask for an audio version.
 						\end{minipage}
 					\end{myblock}\vfill
-					\begin{myblock}{Technologies}
+					\begin{myblock}{Full Document comparison}
 						\vspace{0.75em}
-						\begin{minipage}{.28\textwidth}
-							\begin{figure}
-								\includegraphics[width=0.9\textwidth]{figs/diff_fig.pdf}
-							\end{figure}
-						\end{minipage}~
-						\begin{minipage}{.68\textwidth}
-						\end{minipage}
+							%\includepdf[pages=-,frame,scale=.1,pagecommand={}]{data/paperdiff_singularity_20230908122618.pdf}
+						\fbox{\includegraphics[page=4,scale=1.04]{data/paperdiff_singularity_20230908122618.pdf}}
+						\fbox{\includegraphics[page=5,scale=1.04]{data/paperdiff_singularity_20230908122618.pdf}}
+						\\
+						\vspace{.3em}
+						\fbox{\includegraphics[page=13,scale=1.04]{data/paperdiff_singularity_20230908122618.pdf}}
+						\fbox{\includegraphics[page=14,scale=1.04]{data/paperdiff_singularity_20230908122618.pdf}}
 					\end{myblock}\vfill
 		}\end{minipage}\end{beamercolorbox}
 	\end{column}

publishing/scripts/diff_text.sh

@@ -17,7 +17,7 @@ gs \
   -o ../figs/diff_text.pdf \
   -dFirstPage=4 -dLastPage=4 \
   -sDEVICE=pdfwrite \
-  -c "[/CropBox [290 540 560 860]" \
+  -c "[/CropBox [290 540 560 820]" \
   -c " /PAGES pdfmark" \
   -f ../${SHOWCASE_PDF}
 

publishing/sty/beamerthemeDartmouth.sty

@@ -12,8 +12,13 @@
 
 \mode<presentation>
 
-\definecolor{DartmouthBG}{RGB}{0,105,62}
-\definecolor{Dartmouth1}{RGB}{18,49,43}
+\definecolor{DartmouthPineGreen}{RGB}{0,105,62}
+\definecolor{DartmouthForestGreen}{RGB}{18,49,43}
+\definecolor{DartmouthRiverBlue}{RGB}{155,200,235}
+\definecolor{DartmouthRiverNavy}{RGB}{0,60,115}
+\definecolor{DartmouthSpringGreen}{RGB}{165,215,95}
+\definecolor{DartmouthSummerYellow}{RGB}{245,220,105}
+\definecolor{DartmouthBonfireOrange}{RGB}{255,160,15}
 
 \definecolor{ETH1}{RGB}{31,64,122}
 \definecolor{ETH3}{RGB}{0,105,180}
@@ -27,7 +32,7 @@
 %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=DartmouthBG}
+\setbeamercolor{headline}{fg=red,bg=DartmouthPineGreen}
 \setbeamercolor{footline}{fg=red, bg=red}
 \setbeamerfont{footline}{size=\large,series=\bf}
 \setbeamercolor{separation line}{bg=ETH3}
@@ -36,12 +41,12 @@
 \setbeamercolor{institute in headline}{fg=white}
 
 \setbeamercolor{framesubtitle}{fg=red, bg=ta2gray}
-\setbeamercolor{author in head/foot}{fg=white, bg=DartmouthBG}
+\setbeamercolor{author in head/foot}{fg=white, bg=DartmouthPineGreen}
 \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}
+\setbeamercolor*{block title}{fg=black,bg=DartmouthSpringGreen}
 \setbeamerfont{block title}{size=\large,series=\bf}
 \setbeamercolor{upper separation line head}{fg=red}
 
@@ -71,7 +76,7 @@
 	\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%
+	\end{beamercolorbox}\vskip-3pt%
 	{\ifbeamercolorempty[bg]{block body}{}{\nointerlineskip\vskip-0.5ex}}%
 	\usebeamerfont{block body}%
 	\begin{beamercolorbox}[rounded=false,shadow=false,center,wd=\textwidth,]{block body}%
@@ -91,24 +96,24 @@
 		\vspace{3.ex}\\
 		\vspace{1em}
 		\begin{columns}[c]
-			\begin{column}{.06\paperwidth}
+			\begin{column}{.04\paperwidth}
 			\end{column}
-			\begin{column}{.82\paperwidth}
+			\begin{column}{.85\paperwidth}
 				\raggedleft
 				\usebeamercolor{title in headline}{\color{fg}\textbf{\Huge{\inserttitle}}\\[1ex]}
 				\usebeamercolor{author in headline}{\color{fg}\Large{\insertauthor}\\[1ex]}
 				\vspace{-.5em}
 				\usebeamercolor{institute in headline}{\color{fg}\normalsize{\insertinstitute}\\[1ex]}
 			\end{column}
-			\begin{column}{.01\paperwidth}
+			\begin{column}{.001\paperwidth}
 			\end{column}
 			\begin{column}{.10\paperwidth}
-				\vspace{-1em}
+				\vspace{-.1em}
                                 \begin{center}
                                         \includegraphics[width=.9\textwidth, height=.77\textwidth, keepaspectratio]{img/dartmouth_shield_inverted_nomargins}
                                 \end{center}
                         \end{column}
-			\begin{column}{.015\paperwidth}
+			\begin{column}{.012\paperwidth}
 			\end{column}
 		\end{columns}
 		\vspace{3.ex}\\