Supplement (containing appendices) optionally built separately

Until now, the build strategy of the paper was to have a single output PDF
that either contains (1) the full paper with appendices in the same paper
(2) only the main body of the paper with no appencies.

But the editor in chief of CiSE recently recommended publishing the
appendices as supplements that is a separate PDF (on its webpage). So with
this commit, the project can make either (1) a single PDF (containing both
the main body and the appendices) that will be published on arXiv and will
be the default output (this is the same as before). (2) two PDFs: one that
is only the main body of the paper and another that is only the appendices.

Since the appendices will be printed as a PDF in any case now, the old
'--no-appendix' option has been replaced by '--supplement'. Also, the
internal shell/TeX variable 'noappendix' has been renamed to
'separatesupplement'.

6 files changed, 143 insertions, 3 deletions

diff --git a/tex/src/appendix-existing-solutions.tex b/tex/src/appendix-existing-solutions.tex
index d80c0b4..919f4e5 100644
--- a/tex/src/appendix-existing-solutions.tex
+++ b/tex/src/appendix-existing-solutions.tex
@@ -1,3 +1,18 @@
+%% Appendix on reviewing existing reproducible workflow solutions. This
+%% file is loaded by the project's 'paper.tex' or 'tex/src/supplement.tex',
+%% it should not be run independently.
+%
+%% Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%
+%% This file is free software: you can redistribute it and/or modify it
+%% under the terms of the GNU General Public License as published by the
+%% Free Software Foundation, either version 3 of the License, or (at your
+%% option) any later version.
+%
+%% This file is distributed in the hope that it will be useful, but WITHOUT
+%% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+%% FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+%% for more details. See <http://www.gnu.org/licenses/>.
 \section{Survey of common existing reproducible workflows}
 \label{appendix:existingsolutions}
 
diff --git a/tex/src/appendix-existing-tools.tex b/tex/src/appendix-existing-tools.tex
index 8ad1cc3..794a3fe 100644
--- a/tex/src/appendix-existing-tools.tex
+++ b/tex/src/appendix-existing-tools.tex
@@ -1,3 +1,19 @@
+%% Appendix on reviewing existing low-level tools that are used in
+%% high-level reproducible workflow solutions. This file is loaded by the
+%% project's 'paper.tex' or 'tex/src/supplement.tex', it should not be run
+%% independently.
+%
+%% Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%
+%% This file is free software: you can redistribute it and/or modify it
+%% under the terms of the GNU General Public License as published by the
+%% Free Software Foundation, either version 3 of the License, or (at your
+%% option) any later version.
+%
+%% This file is distributed in the hope that it will be useful, but WITHOUT
+%% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+%% FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+%% for more details. See <http://www.gnu.org/licenses/>.
 \section{Survey of existing tools for various phases}
 \label{appendix:existingtools}
 
diff --git a/tex/src/appendix-necessity.tex b/tex/src/appendix-necessity.tex
index 6578e5f..325fb69 100644
--- a/tex/src/appendix-necessity.tex
+++ b/tex/src/appendix-necessity.tex
@@ -1,5 +1,18 @@
-
-
+%% Appendix on reviewing the necessity for reproducible research
+%% papers. This file is loaded by the project's 'paper.tex' or
+%% 'tex/src/supplement.tex', it should not be run independently.
+%
+%% Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%
+%% This file is free software: you can redistribute it and/or modify it
+%% under the terms of the GNU General Public License as published by the
+%% Free Software Foundation, either version 3 of the License, or (at your
+%% option) any later version.
+%
+%% This file is distributed in the hope that it will be useful, but WITHOUT
+%% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+%% FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+%% for more details. See <http://www.gnu.org/licenses/>.
 \section{Necessity for reproducible research}
 \label{appendix:necessity}
 
diff --git a/tex/src/appendix-used-software.tex b/tex/src/appendix-used-software.tex
new file mode 100644
index 0000000..aa06d45
--- /dev/null
+++ b/tex/src/appendix-used-software.tex
@@ -0,0 +1,4 @@
+%% Mention all used software in an appendix.
+\section{Software acknowledgement}
+\label{appendix:software}
+\input{tex/build/macros/dependencies.tex}
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
index 11bf9c3..f360ce9 100644
--- a/tex/src/preamble-project.tex
+++ b/tex/src/preamble-project.tex
@@ -49,9 +49,16 @@
 
 %% To have multiple bibliographies (one for the main paper, one for the
 %% appendix). With 'multibib' we need to specify a name for each
-%% bibliography.
+%% bibliography. But this is only necessary when the appendices are to be
+%% included in the final paper. When the supplement should be separate, it
+%% will be treated as a completely independent build, so '\citeappendix'
+%% should just be mapped to '\cite'.
+\ifdefined\separatesupplement
+\newcommand{\citeappendix}{\cite}
+\else
 \usepackage{multibib}
 \newcites{appendix}{Bibliography}
+\fi
 
 %% To have typewriter font
 \usepackage{courier}
diff --git a/tex/src/supplement.tex b/tex/src/supplement.tex
new file mode 100644
index 0000000..e1db463
--- /dev/null
+++ b/tex/src/supplement.tex
@@ -0,0 +1,85 @@
+%% The top-level file to build the separate supplement that contains the
+%% appendices (to be published as a separate PDF file).
+%
+%% Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%
+%% This file is free software: you can redistribute it and/or modify it
+%% under the terms of the GNU General Public License as published by the
+%% Free Software Foundation, either version 3 of the License, or (at your
+%% option) any later version.
+%
+%% This file is distributed in the hope that it will be useful, but WITHOUT
+%% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+%% FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+%% for more details. See <http://www.gnu.org/licenses/>.
+\documentclass[journal]{IEEEtran}
+
+%% This is a convenience variable if you are using PGFPlots to build plots
+%% within LaTeX. If you want to import PDF files for figures directly, you
+%% can use the standard `\includegraphics' command. See the definition of
+%% `\includetikz' in `tex/preamble-pgfplots.tex' for where the files are
+%% assumed to be if you use `\includetikz' when `\makepdf' is not defined.
+\newcommand{\makepdf}{}
+
+%% VALUES FROM ANALYSIS (NUMBERS AND STRINGS): this file is automatically
+%% generated at the end of the processing and includes LaTeX macros
+%% (defined with '\newcommand') for various processing outputs to be used
+%% within the paper.
+\input{tex/build/macros/project.tex}
+\input{tex/src/preamble-maneage.tex}
+
+%% Import the other necessary TeX files for this particular project.
+\input{tex/src/preamble-project.tex}
+
+%% Title and author names.
+\title{Supplement to\\ \projecttitle}
+\author{
+  Mohammad Akhlaghi,
+  Ra\'ul Infante-Sainz,
+  Boudewijn F. Roukema,
+  Mohammadreza Khellat,\\
+  David Valls-Gabaud,
+  Roberto Baena-Gall\'e
+  \thanks{Manuscript received MM DD, YYYY; revised MM DD, YYYY.}
+}
+
+%% The paper headers
+\markboth{Computing in Science and Engineering, Vol. X, No. X, MM YYYY}%
+{Akhlaghi \MakeLowercase{\textit{et al.}}: \projecttitle}
+
+
+
+
+
+
+
+
+
+
+%% Start the paper.
+\begin{document}
+
+% make the title area
+\maketitle
+
+% For peer review papers, you can put extra information on the cover
+% page as needed:
+% \ifCLASSOPTIONpeerreview
+% \begin{center} \bfseries EDICS Category: 3-BBND \end{center}
+% \fi
+%
+% For peerreview papers, this IEEEtran command inserts a page break and
+% creates the second title. It will be ignored for other modes.
+\IEEEpeerreviewmaketitle
+
+%% Import the appendices.
+\input{tex/src/appendix-existing-tools.tex}
+\input{tex/src/appendix-existing-solutions.tex}
+\input{tex/src/appendix-used-software.tex}
+
+%% Bibliography.
+\bibliographystyle{IEEEtran_openaccess}
+\bibliography{IEEEabrv,references}
+
+%% End the paper.
+\end{document}