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}