Added figure showing project's file structure

It was a little hard to describe the file structure so instead of using a
standard listing as most papers do, I thought of showing the file and
directory structure as boxes within each other (modeled on the Gnome
disk-utility).

Some other polishing was done throughout the paper also.

4 files changed, 252 insertions, 3 deletions

diff --git a/tex/src/figure-file-architecture.tex b/tex/src/figure-file-architecture.tex
new file mode 100644
index 0000000..3a7b760
--- /dev/null
+++ b/tex/src/figure-file-architecture.tex
@@ -0,0 +1,223 @@
+\begin{tikzpicture}[
+  line width=1.5pt,
+  black!50,
+  text=black,
+]
+
+  %% Use small fonts
+  \footnotesize
+
+  %% project
+  \node [at={(0,4cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum width=15cm,
+         minimum height=7.5cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{top-project-directory/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(-6.0cm,-3cm)}] {COPYING};
+  \node [node-nonterminal-thin, at={(-3.5cm,-3cm)}] {paper.tex};
+  \node [node-nonterminal-thin, at={(-1.0cm,-3cm)}] {project};
+  \node [node-nonterminal-thin, at={(+1.5cm,-3cm)}] {README.md};
+  \node [node-nonterminal-thin, at={(+4.25cm,-3cm)},
+         text width=2.5cm, text depth=-3pt] {README-hacking.md};
+
+  %% reproduce
+  \node [at={(-1.4cm,3.5cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=6cm,
+         minimum width=11.9cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{reproduce/}}] {};
+
+  %% reproduce/software
+  \node [at={(-4.35cm,3cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=5.3cm,
+         minimum width=5.7cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{software/}}] {};
+
+  %% reproduce/analysis
+  \node [at={(1.55cm,3cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=5.3cm,
+         minimum width=5.7cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{analysis/}}] {};
+
+  %% reproduce/software/config
+  \node [at={(-5.75cm,2.5cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{config/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(-5.75cm,1.8cm)}] {LOCAL.conf.in};
+  \node [node-nonterminal-thin, at={(-5.75cm,1.3cm)}] {versions.conf};
+  \node [node-nonterminal-thin, at={(-5.75cm,0.8cm)}] {checksums.conf};
+
+
+  %% reproduce/software/make
+  \node [at={(-2.95cm,2.5cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{make/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(-2.95cm,1.8cm)}] {basic.mk};
+  \node [node-nonterminal-thin, at={(-2.95cm,1.3cm)}] {high-level.mk};
+  \node [node-nonterminal-thin, at={(-2.95cm,0.8cm)}] {python.mk};
+
+  %% reproduce/software/bash
+  \node [at={(-5.75cm,0.2cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{bash/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(-5.75cm,-0.5cm)}] {bashrc.sh};
+  \node [node-nonterminal-thin, at={(-5.75cm,-1.0cm)}] {configure.sh};
+  \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {git-pre-comit};
+
+  %% reproduce/software/bibtex
+  \node [at={(-2.95cm,0.2cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{bibtex/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(-2.95cm,-0.5cm)}] {fftw.tex};
+  \node [node-nonterminal-thin, at={(-2.95cm,-1.0cm)}] {numpy.tex};
+  \node [node-nonterminal-thin, at={(-2.95cm,-1.5cm)}] {gnuastro.tex};
+
+  %% reproduce/analysis/config
+  \node [at={(0.15cm,2.5cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{config/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(0.15cm,1.8cm)}] {INPUTS.conf};
+  \node [node-nonterminal-thin, at={(0.15cm,1.3cm)}] {param-1.conf};
+  \node [node-nonterminal-thin, at={(0.15cm,0.8cm)}] {param-2.conf};
+
+  %% reproduce/analysis/make
+  \node [at={(2.95cm,2.5cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{make/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(2.95cm,1.8cm)}] {initialize.mk};
+  \node [node-nonterminal-thin, at={(2.95cm,1.3cm)}] {download.mk};
+  \node [node-nonterminal-thin, at={(2.95cm,0.8cm)}] {analysis-1.mk};
+
+  %% reproduce/analysis/bash
+  \node [at={(0.15cm,0.2cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{bash/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(0.15cm,-0.5cm)}] {process-1.sh};
+  \node [node-nonterminal-thin, at={(0.15cm,-1.0cm)}] {process-2.sh};
+  \node [node-nonterminal-thin, at={(0.15cm,-1.5cm)}] {process-3.sh};
+
+  %% reproduce/analysis/python
+  \node [at={(2.95cm,0.2cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=2.1cm,
+         minimum width=2.6cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{python/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(2.95cm,-0.5cm)}] {operation-1.py};
+  \node [node-nonterminal-thin, at={(2.95cm,-1.0cm)}] {operation-2.py};
+  \node [node-nonterminal-thin, at={(2.95cm,-1.5cm)}] {fitting-plot.py};
+
+  %% tex
+  \node [at={(6cm,3.5cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum height=6cm,
+         minimum width=2.7cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{tex/}}] {};
+
+  %% tex/src
+  \node [at={(6cm,3cm)}, anchor=north,
+         rectangle,
+         very thick,
+         text centered,
+         font=\ttfamily,
+         minimum width=2.5cm,
+         minimum height=5.3cm,
+         draw=green!50!black!50,
+         fill=black!10!green!2!white,
+         label={[shift={(0,-5mm)}]\texttt{src/}}] {};
+  %% Its files
+  \node [node-nonterminal-thin, at={(6cm,2.2cm)}] {preamble-1.tex};
+  \node [node-nonterminal-thin, at={(6cm,1.7cm)}] {preamble-2.tex};
+  \node [node-nonterminal-thin, at={(6cm,1.2cm)}] {figure-1.tex};
+  \node [node-nonterminal-thin, at={(6cm,0.7cm)}] {figure-2.tex};
+
+\end{tikzpicture}
diff --git a/tex/src/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex
index 3f467a6..57a0128 100644
--- a/tex/src/preamble-pgfplots.tex
+++ b/tex/src/preamble-pgfplots.tex
@@ -150,6 +150,17 @@
   bottom color=green!80!black!50,
   font=\ttfamily}}
 
+\tikzset{node-nonterminal-thin/.style={
+  rectangle,
+  very thick,
+  text centered,
+  top color=white,
+  text width=2cm,
+  minimum size=4mm,
+  draw=green!50!black!50,
+  bottom color=green!80!black!50,
+  font=\ttfamily\scriptsize}}
+
 \tikzset{node-makefile/.style={
   thick,
   rectangle,
diff --git a/tex/src/preamble-style.tex b/tex/src/preamble-style.tex
index e843903..f3a96e9 100644
--- a/tex/src/preamble-style.tex
+++ b/tex/src/preamble-style.tex
@@ -22,6 +22,7 @@
 
 %% To allow a prefix to the enumeration.
 \usepackage{enumitem}
+\setlist{nolistsep}   % No space before `\begin{itemize}'
 
 %% Horizontal line with spacing
 \newcommand{\horizontalline}{\vspace{3mm}\hrule\vspace{3mm}}
diff --git a/tex/src/references.tex b/tex/src/references.tex
index 0f8171b..170ace6 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -1091,7 +1091,7 @@ Reproducible Research in Image Processing},
      author = {{Peng}, R.D.},
       title = {Reproducible Research in Computational Science},
     journal = {Science},
-       year = 2011,
+       year = {2011},
       month = dec,
      volume = 334,
       pages = {1226},
@@ -1102,6 +1102,20 @@ Reproducible Research in Image Processing},
 
 
 
+@ARTICLE{gil10,
+     author = {Yolanda Gil and Pedro A. González-Calero and Jihie Kim and Joshua Moody and Varun Ratnakar},
+      title = {A semantic framework for automatic generation of computational workflows using distributed data and component catalogues},
+    journal = {Journal of Experimental \& Theoretical Artificial Intelligence},
+       year = {2010},
+     volume = {23},
+      pages = {389},
+        doi = {10.1080/0952813X.2010.490962},
+}
+
+
+
+
+
 @ARTICLE{pence10,
        author = {{Pence}, W.~D. and {Chiappetti}, L. and {Page}, C.~G. and {Shaw}, R.~A. and
          {Stobie}, E.},
@@ -1126,8 +1140,8 @@ Reproducible Research in Image Processing},
      author = {Jeremy Goecks and Anton Nekrutenko and James Taylor},
       title = {Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
     journal = {Genome Biology},
-       year = 2010,
-     volume = 11,
+       year = {2010},
+     volume = {11},
       pages = {R86},
         doi = {10.1186/gb-2010-11-8-r86},
 }