Re-write of the paper to fit in ~6000 words and IEEE format

Following the fact that the DSJ editor decided that this paper doesn't fit
into their scope, we decided to submit it to IEEE's Computing in Science
and Engineering (CiSE). So with this commit the text was re-written to fit
into their style and word-count limitations.

5 files changed, 74 insertions, 31 deletions

diff --git a/tex/src/figure-branching.tex b/tex/src/figure-branching.tex
index 52a6303..7259f7d 100644
--- a/tex/src/figure-branching.tex
+++ b/tex/src/figure-branching.tex
@@ -120,9 +120,9 @@
   \draw [->, black!40!white, rounded corners, line width=2mm]
         (11cm,4.5cm) -- (12.5cm,5cm) -- (12.5cm,7.9cm);
   \draw [black!40!white, line width=2mm] (9.5cm,6cm) -- (12.5cm,7cm);
-  \draw [anchor=north, black!40!white] (12.7cm,4.8cm) node [scale=1.5]
-        {\bf Derivative};
-  \draw [anchor=north, black!40!white] (12.7cm,4.4cm) node [scale=1.5]
+  \draw [anchor=north, black!40!white] (12.6cm,4.8cm) node [scale=1.5]
+        {\bf Derived};
+  \draw [anchor=north, black!40!white] (12.6cm,4.4cm) node [scale=1.5]
         {\bf project};
 
   %% Maneage commits.
diff --git a/tex/src/figure-data-lineage.tex b/tex/src/figure-data-lineage.tex
index 146a833..fcc52d9 100644
--- a/tex/src/figure-data-lineage.tex
+++ b/tex/src/figure-data-lineage.tex
@@ -46,9 +46,9 @@
          text centered,
          font=\ttfamily,
          text width=2.8cm,
+         minimum width=15cm,
          minimum height=7.8cm,
          draw=green!50!black!50,
-         minimum width=\linewidth,
          fill=black!10!green!2!white,
          label={[shift={(0,-5mm)}]\texttt{top-make.mk}}] {};
 
@@ -62,7 +62,7 @@
   \node (analysis2mk)  [node-makefile, at={(2.67cm,-1.3cm)},
     label={[shift={(0,-5mm)}]\texttt{demo-plot.mk}}] {};
   \node [opacity=0.6] (analysis3mk)  [node-makefile, at={(5.47cm,-1.3cm)},
-    label={[shift={(0,-5mm)}, opacity=0.6]\texttt{another-step.mk}}] {};
+    label={[shift={(0,-5mm)}, opacity=0.6]\texttt{next-step.mk}}] {};
 
   %% verify.mk
   \node [at={(-5.3cm,-2.8cm)},
@@ -137,14 +137,16 @@
   %% input-2.dat
   \ifdefined\inputtwo
   \node (input2) [node-terminal, at={(-2.93cm,1.9cm)}] {menke20.xlsx};
-  \draw [->] (input2) -- (downloadtex);
   \fi
 
   %% INPUTS.conf
   \ifdefined\inputsconf
   \node (INPUTS) [node-nonterminal, at={(-2.93cm,4.6cm)}] {INPUTS.conf};
   \node (input2-west) [node-point, at={(-4.33cm,1.9cm)}] {};
+  \node (downloadtex-west) [node-point, at={(-4.33cm,-0.8cm)}] {};
   \draw [->,rounded corners] (INPUTS.west) -| (input2-west) |- (input2);
+  \draw [->,rounded corners] (INPUTS.west) -| (downloadtex-west)
+                                           |- (downloadtex);
   \fi
 
   %% analysis1.tex
@@ -155,7 +157,7 @@
 
   %% out1b.dat
   \ifdefined\outoneb
-  \node (out1b) [node-terminal, at={(-0.13cm,1.1cm)}] {menke20-table-3.txt};
+  \node (out1b) [node-terminal, at={(-0.13cm,1.1cm)}] {table-3.txt};
   \draw [->] (out1b) -- (a1tex);
   \fi
 
@@ -173,9 +175,9 @@
 
   %% out-2b.dat
   \ifdefined\outtwob
-  \node (menkedemoyear) [node-nonterminal, at={(2.67cm,4.6cm)}] {menke-demo-year.conf};
+  \node (menkedemoyear) [node-nonterminal, at={(2.67cm,4.6cm)}] {demo-year.conf};
   \node (a2tex-west) [node-point, at={(1.27cm,-0.8cm)}] {};
-  \node (out2b) [node-terminal, at={(2.67cm,0.3cm)}] {tools-per-year.txt};
+  \node (out2b) [node-terminal, at={(2.67cm,0.3cm)}] {columns.txt};
   \draw [->] (out2b) -- (a2tex);
   \draw [->,rounded corners] (menkedemoyear.west) -| (a2tex-west) |- (a2tex);
   \fi
@@ -187,7 +189,7 @@
 
   %% analysis3.tex
   \ifdefined\analysisthreetex
-  \node [opacity=0.6] (a3tex) [node-terminal, at={(5.47cm,-0.8cm)}] {another-step.tex};
+  \node [opacity=0.6] (a3tex) [node-terminal, at={(5.47cm,-0.8cm)}] {next-step.tex};
   \draw [opacity=0.6, rounded corners, -, dashed] (a3tex) |- (initialize-south);
   \fi
 
@@ -216,7 +218,7 @@
   \ifdefined\outthreeadep
   \node [opacity=0.6] (out3a-west) [node-point, at={(4.07cm,2.7cm)}] {};
   \draw [opacity=0.6, ->,rounded corners, dashed] (input2) |- (out3a);
-  \node [opacity=0.6] (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}]  {param-3.conf};
+  \node [opacity=0.6] (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}]  {param.conf};
   \draw [opacity=0.6, rounded corners, dashed] (a3conf1.west) -| (out3a-west) |- (out3a);
   \fi
 \end{tikzpicture}
diff --git a/tex/src/figure-tools-per-year.tex b/tex/src/figure-tools-per-year.tex
index 75557ac..f82402f 100644
--- a/tex/src/figure-tools-per-year.tex
+++ b/tex/src/figure-tools-per-year.tex
@@ -1,4 +1,4 @@
-\begin{tikzpicture}
+\begin{tikzpicture}[scale=0.9]
   \begin{axis}[
       ymin=0,
       ymax=100,
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
index c4d7feb..9b956cf 100644
--- a/tex/src/preamble-project.tex
+++ b/tex/src/preamble-project.tex
@@ -8,11 +8,9 @@
 %% For the `\url' command.
 \usepackage{url}
 
-% correct bad hyphenation here
-\hyphenation{op-tical net-works semi-conduc-tor}
-
-%% To use colors.
-\usepackage{xcolor}
+%% No need to load xcolor, its included by others below (it conflicts with
+%% the listings package.
+%\usepackage{xcolor}
 
 %% To have links.
 \usepackage[
@@ -25,3 +23,32 @@
 
 %% To have typewriter font
 \usepackage{courier}
+
+%% To have bold monospace
+%\usepackage[scaled=0.85]{beramono}
+\usepackage{inconsolata}
+
+%% To display codes.
+\usepackage{listings}
+\usepackage{etoolbox}
+\input{listings-bash.prf}
+\lstset{
+  frame=lines,
+  numbers=none,
+  language=bash,
+  commentstyle=\color{gray},
+  abovecaptionskip=0mm,
+  belowcaptionskip=0mm,
+  keywordstyle=\mdseries,
+  basicstyle=\small\ttfamily\color{blue!35!black},
+}
+\makeatletter
+\preto\lstlisting{\def\@captype{table}}
+\pretocmd\lst@makecaption{\noindent{\rule{\linewidth}{1pt}}}{}{}
+\makeatother
+
+
+
+
+%% Custom macros
+\newcommand{\inlinecode}[1]{\textcolor{blue!35!black}{\texttt{#1}}}
diff --git a/tex/src/references.bib b/tex/src/references.tex
index e19ec16..f355bba 100644
--- a/tex/src/references.bib
+++ b/tex/src/references.tex
@@ -1,10 +1,11 @@
-@ARTICLE{clement19,
-     author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois},
-      title = {Encouraging a wider usage of software derived from research},
-       year = {2019},
-    journal = {Archives ouvertes HAL},
-     volume = {},
-      pages = {\href{https://hal.archives-ouvertes.fr/hal-02545142}{hal-02545142}},
+@ARTICLE{mesnard20,
+     author = {Olivier Mesnard and Lorena A. Barba},
+      title = {Reproducible Workflow on a Public Cloud for Computational Fluid Dynamics},
+       year = {2020},
+    journal = {Computing in Science \& Engineering},
+     volume = {22},
+      pages = {102-116},
+        doi = {10.1109/MCSE.2019.2941702},
 }
 
 
@@ -73,7 +74,7 @@ archivePrefix = {arXiv},
         month = "Feb",
        volume = {491},
        number = {4},
-        pages = {5317},
+        pages = {5317-5329},
           doi = {10.1093/mnras/stz3111},
 archivePrefix = {arXiv},
        eprint = {1911.01430},
@@ -100,13 +101,26 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{clement19,
+     author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois},
+      title = {Encouraging a wider usage of software derived from research},
+       year = {2019},
+    journal = {Archives ouvertes HAL},
+     volume = {},
+      pages = {\href{https://hal.archives-ouvertes.fr/hal-02545142}{hal-02545142}},
+}
+
+
+
+
+
 @ARTICLE{pimentel19,
      author = {{Jo\~ao Felipe} Pimentel and Leonardo Murta and Vanessa Braganholo and Juliana Freire},
       title = {A large-scale study about quality and reproducibility of jupyter notebooks},
        year = {2019},
     journal = {Proceedings of the 16th International Conference on Mining Software Repositories},
      volume = {1},
-      pages = {507},
+      pages = {507-517},
         doi = {10.1109/MSR.2019.00077},
 }
 
@@ -234,7 +248,7 @@ archivePrefix = {arXiv},
       title = {Reproducibility and Replicability in Science},
     journal = {The National Academies Press},
        year = 2019,
-      pages = {1},
+      pages = {1-256},
         doi = {10.17226/25303},
 }
 
@@ -316,7 +330,7 @@ author = "Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and
      keywords = {Computer Science - Digital Libraries, Computer Science - Software Engineering},
          year = "2019",
         month = "May",
-        pages = {39},
+        pages = {39-52},
 archivePrefix = {arXiv},
        eprint = {1905.11123},
  primaryClass = {cs.DL},
@@ -742,7 +756,7 @@ archivePrefix = {arXiv},
       journal = {International Journal on Digital Libraries},
        volume = {18},
          year = {2017},
-        pages = {77},
+        pages = {77-92},
           doi = {10.1007/s00799-016-0178-2},
 }
 
@@ -982,7 +996,7 @@ archivePrefix = {arXiv},
       month = sep,
      volume = 220,
         eid = {1},
-      pages = {1},
+      pages = {1-33},
         doi = {10.1088/0067-0049/220/1/1},
      adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A},
     adsnote = {Provided by the SAO/NASA Astrophysics Data System}
@@ -1647,7 +1661,7 @@ Reproducible Research in Image Processing},
     journal = {SEG Technical Program Expanded Abstracts},
        year = {1992},
      volume = {1},
-      pages = {601},
+      pages = {601-604},
         doi = {10.1190/1.1822162},
 }