11 files changed, 214 insertions, 70 deletions

diff --git a/paper.tex b/paper.tex
index 45cead1..778cb19 100644
--- a/paper.tex
+++ b/paper.tex
@@ -86,7 +86,7 @@
   \vspace{2.5mm}
   \emph{Appendices} ---
   Two comprehensive appendices that review existing solutions; available
-\ifdefined\noappendix
+\ifdefined\separatesupplement
 at \href{https://arxiv.org/abs/\projectarxivid}{\texttt{arXiv:\projectarxivid}} or \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}}.
 \else
 at the end (Appendices \ref{appendix:existingtools} and \ref{appendix:existingsolutions}).
@@ -155,7 +155,7 @@ To highlight the necessity, a short review of commonly-used tools is provided be
 (3) job management (like shell scripts or Make);
 (4) notebooks (like Jupyter).
 \new{A comprehensive review of existing tools and solutions is available in the
-  \ifdefined\noappendix
+  \ifdefined\separatesupplement
   \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{appendices}.%
   \else%
   appendices (\ref{appendix:existingsolutions}).%
@@ -169,7 +169,7 @@ We will focus on Docker here because it is currently the most common.
 \new{It is hypothetically possible to precisely identify the used Docker ``images'' with their checksums (or ``digest'') to re-create an identical OS image later.
 However, that is rarely done.}
 Usually images are imported with operating system (OS) names; e.g., \cite{mesnard20}
-\ifdefined\noappendix
+\ifdefined\separatesupplement
 \new{(more examples in the \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{appendices})}%
 \else%
 \new{(more examples: see the appendices (\ref{appendix:existingtools}))}%
@@ -332,7 +332,7 @@ Acting as a link, the macro files build the core skeleton of Maneage.
 For example, during the software building phase, each software package is identified by a \LaTeX{} file, containing its official name, version and possible citation.
 These are combined at the end to generate precise software \new{acknowledgement} and citation that is shown in the
 \new{
-  \ifdefined\noappendix
+  \ifdefined\separatesupplement
   \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{appendices}.%
   \else%
   appendices (\ref{appendix:software}).%
@@ -683,21 +683,15 @@ The Pozna\'n Supercomputing and Networking Center (PSNC) computational grant 314
 
 
 
-%% Appendix (only build if 'noappendix' has not been given). So in default,
-%% the appendix is built.
-\ifdefined\noappendix
+%% Appendix (only build if 'separatesupplement' has not been given): by
+%% default, the appendices are built.
+\ifdefined\separatesupplement
 \else
 \clearpage
 \appendices
 \input{tex/src/appendix-existing-tools.tex}
 \input{tex/src/appendix-existing-solutions.tex}
-
-%% Mention all used software in an appendix.
-\section{Software acknowledgement}
-\label{appendix:software}
-\input{tex/build/macros/dependencies.tex}
-
-%% Bibliography of appendix
+\input{tex/src/appendix-used-software.tex}
 \bibliographystyleappendix{IEEEtran_openaccess}
 \bibliographyappendix{IEEEabrv,references}
 \fi
diff --git a/project b/project
index e53bcf0..33564f8 100755
--- a/project
+++ b/project
@@ -36,7 +36,6 @@ host_cc=0
 operation=
 build_dir=
 input_dir=
-noappendix=0
 check_config=
 make_targets=
 software_dir=
@@ -46,6 +45,7 @@ highlightnew=0
 all_highlevel=0
 existing_conf=0
 highlightnotes=0
+separatesupplement=0
 scriptname="./project"
 minmapsize=10000000000
 
@@ -92,6 +92,7 @@ Project 'make' special features.
   ./project make           Build the project on one thread
   ./project make -jN       Built the project in parallel on N threads.
   ./project make clean     Clean all files generated by 'make' (not software).
+  ./project make texclean  Clean all files built by (La)TeX.
   ./project make distclean Clean everything (including compiled software).
   ./project make dist      Produce a LaTeX-ready-to-build distribution tarball
                            ('tar.gz') of the project. This is ready to be
@@ -128,7 +129,7 @@ Make (analysis) options:
 Make (final PDF) options:
       --highlight-new      Highlight '\new' parts of text as green.
       --highlight-notes    Show '\tonote' regions as red text in PDF.
-      --no-appendix        Don't include the appendix in the final paper.
+      --supplement         Build the appendices as a separate supplement PDF.
 
 Mandatory or optional arguments to long options are also mandatory or optional
 for any corresponding short options.
@@ -213,8 +214,8 @@ do
   #
   # Note that Make's `debug' can take values, but when called without any
   # value, it is like giving it a value of `a'):
-  --no-appendix)          noappendix=1;                                                    shift;;
-  --no-appendix=*)        on_off_option_error --no-appendix;;
+  --supplement)           separatesupplement=1;                                            shift;;
+  --supplement=*)         on_off_option_error --supplement;;
   --highlight-new)        highlightnew=1;                                                  shift;;
   --highlight-new=*)      on_off_option_error --highlight-new;;
   --highlight-notes)      highlightnotes=1;                                                shift;;
@@ -384,7 +385,8 @@ controlled_env() {
     # Remove all existing environment variables (with `env -i') and only
     # use some pre-defined environment variables, then build the project.
     envmake=".local/bin/env -i HOME=$bdir sys_rm=$(which rm) $gopt"
-    envmake="$envmake noappendix=$noappendix highlightnew=$highlightnew"
+    envmake="$envmake separatesupplement=$separatesupplement "
+    envmake="$envmake highlightnew=$highlightnew"
     envmake="$envmake highlightnotes=$highlightnotes .local/bin/make "
     envmake="$envmake --no-builtin-rules --no-builtin-variables -f $1"
     if ! [ x"$debug" = x  ]; then envmake="$envmake --debug=$debug"; fi
@@ -507,7 +509,7 @@ case $operation in
                 numwords=$(pdftotext paper.pdf && cat paper.txt | wc -w)
                 numeff=$(echo $numwords | awk '{print $1-850+500}')
                 echo; echo "Number of words in full PDF: $numwords"
-                if [ $noappendix = 1 ]; then
+                if [ $separatesupplement = 1 ]; then
                     echo "No abstract, and captions (250 for each figure): $numeff"
                 fi
                 rm paper.txt
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 75f87ee..0cc04ee 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -77,21 +77,11 @@ endif
 # (independent parts of the paper can be added to it independently). To fix
 # this problem, when we are in a group setting, we'll use the user's ID to
 # create a separate LaTeX build directory for each user.
-#
-# The same logic applies to the final paper PDF: each user will create a
-# separte final PDF (for example `paper-user1.pdf' and `paper-user2.pdf')
-# and no `paper.pdf' will be built. This isn't a problem because
-# `initialize.tex' is a .PHONY prerequisite, so the rule to build the final
-# paper is always executed (even if it is present and nothing has
-# changed). So in terms of over-all efficiency and processing steps, this
-# doesn't change anything.
 ifeq (x$(GROUP-NAME),x)
 texbtopdir  = build
-final-paper = paper.pdf
 else
 user        = $(shell whoami)
 texbtopdir  = build-$(user)
-final-paper = paper-$(user).pdf
 endif
 texbdir     = $(texdir)/$(texbtopdir)
 tikzdir     = $(texbdir)/tikz
@@ -220,14 +210,15 @@ project-package-contents = $(texdir)/$(project-package-name)
 # we want to ensure that the file is always built in every run: it contains
 # the project version which may change between two separate runs, even when
 # no file actually differs.
-.PHONY: all clean dist dist-zip dist-lzip distclean clean-mmap \
+.PHONY: all clean dist dist-zip dist-lzip texclean distclean \
         $(project-package-contents) $(mtexdir)/initialize.tex
 
-# --------- Delete for no Gnuastro ---------
-clean-mmap:; rm -f reproduce/config/gnuastro/mmap*
-# ------------------------------------------
+texclean:
+	rm *.pdf
+	rm -rf $(BDIR)/tex/build/*
+	mkdir $(BDIR)/tex/build/tikz # 'tikz' is assumed to already exist.
 
-clean: clean-mmap
+clean:
         # Delete the top-level PDF file.
 	rm -f *.pdf
 
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index d8f18b3..1776363 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -18,6 +18,7 @@
 
 
 
+
 # LaTeX macros for paper
 # ----------------------
 #
@@ -55,8 +56,8 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 	  done
 
           # Possibly print the appendix in the final PDF.
-	  if [ x"$(noappendix)" = x1 ]; then
-	    echo "\newcommand{\noappendix}{}" >> $$projecttex
+	  if [ x"$(separatesupplement)" = x1 ]; then
+	    echo "\newcommand{\separatesupplement}{}" >> $$projecttex
 	  fi
 
           # Possibly highlight the '\new' parts of the text.
@@ -99,17 +100,18 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 # The bibliography
 # ----------------
 #
-# We need to run the `biber' program on the output of LaTeX to generate the
-# necessary bibliography before making the final paper. So we'll first have
-# one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+# We need to run the `bibtex' program on the output of LaTeX to generate
+# the necessary bibliography before making the final paper. So we'll first
+# have one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
 #
 # NOTE: `$(mtexdir)/project.tex' is an order-only-prerequisite for
 # `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl'
 # recipe and the `paper.pdf' recipe. But if `tex/src/references.bib' hasn't
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
-$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
-                      | $(mtexdir)/project.tex
+bbls = $(foreach t,$(subst .pdf,,$(top-pdfs)),$(texbdir)/$(t).bbl)
+$(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
+         $(mtexdir)/dependencies-bib.tex | $(mtexdir)/project.tex
 
         # If `$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
@@ -120,14 +122,14 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
           # building directory.
 	  p=$$(pwd)
 	  if ! [ -L $(texbdir)/references.bib ]; then
-	    ln -s $$p/tex/src/references.tex $(texbdir)/references.bib
+	    ln -sf $$p/tex/src/references.tex $(texbdir)/references.bib
 	  fi
 
           # Copy the improved IEEE bst file into the build directory.
           # The improved bst file provides ArXiv clickable URLs and
           # if available, open-access URLs based on the DOIs, with
           # closed-access URLs as a fallback, via https://oadoi.org .
-	  cp -pv $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)
+	  ln -sf $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)/
 
           # We'll run LaTeX first to generate the `.bcf' file (necessary
           # for `biber') and then run `biber' to generate the `.bbl' file.
@@ -140,19 +142,27 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
           # it. It will be built anyway once this rule is done.
 	  rm -f $@
 
+          # Put a link to the main LaTeX source that we want to build.
+	  if [ $* = paper ]; then sdir="$$p"
+	  else                    sdir="$$p"/tex/src
+	  fi
+	  ln -sf "$$sdir"/$*.tex ./
+
           # The pdflatex option '-shell-escape' is "normally disallowed for
           # security reasons" according to the `info pdflatex' manual, but
           # is enabled here in order to allow the use of PGFPlots. If you
-          # do not use PGFPlots, then you should remove the `-shell-escape'
+          # do not use PGFPlots, then you can remove the `-shell-escape'
           # option for better security. See
           # https://savannah.nongnu.org/task/?15694 for details.
-	  latex -shell-escape -halt-on-error "$$p"/paper.tex
-
-          # Since we have multiple bibliographies (one for the main body,
-          # and one for the appendix), we use 'multibib'. Multibib creates
-          # a separate '.aux' file for each bibliography.
-	  bibtex paper
-	  if [ x"$(noappendix)" != x1 ]; then
+	  latex -shell-escape -halt-on-error $*.tex
+
+          # When we are building the main paper and the appendices are to
+          # be built within the main paper's PDF, we need two
+          # bibliographies: one for the main body, and one for the
+          # appendix. For this, we use 'multibib'. Multibib creates a
+          # separate '.aux' file for each bibliography.
+	  bibtex $*
+	  if [ x"$(separatesupplement)" != x1 ]; then
 	    bibtex appendix
 	  fi
 
@@ -160,14 +170,14 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
           # TODO (better): read Part 4 of
           # http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf
           # and fix the .bst style properly.
-	  cp -pv paper.bbl paper-tmp.bbl \
-	    && sed -e "s/\'/EOLINE/g" paper-tmp.bbl \
+	  cp -pv $*.bbl $*-tmp.bbl \
+	    && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
 	    | tr -d '\n' \
 	    | sed -e 's/\([0-9]\)\( \|EOLINE\)}/\1}/g' \
 	    | sed -e 's/\([^,]\) *\( \|EOLINE\) *\\eprint/\1, \\eprint/g' \
 	    | sed -e 's/\([^,]\) *\( \|EOLINE\) *\\doi/\1, \\doi/g' \
-	    | sed -e 's/EOLINE/\n/g' > paper.bbl
-	  if [ x"$(noappendix)" != x1 ]; then
+	    | sed -e 's/EOLINE/\n/g' > $*.bbl
+	  if [ x"$(separatesupplement)" != x1 ]; then
 	    cp -pv appendix.bbl appendix-tmp.bbl \
 	      && sed -e "s/\'/EOLINE/g" appendix-tmp.bbl \
 	      | tr -d '\n' \
@@ -178,18 +188,19 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 	  fi
 
 	  # Paper-specific hacks for reducing very-long author lists.
-	  cp -pv paper.bbl paper-tmp.bbl \
-	    && sed -e "s/\'/EOLINE/g" paper-tmp.bbl \
+	  cp -pv $*.bbl $*-tmp.bbl \
+	    && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
 	    | tr -d '\n' \
 	    | sed -e 's;, D\..Chong[^{]*Forstag; et al.\\/;' \
 	    | sed -e 's;, V\..Khodiyar[^{]*Whyte; et al.\\/;' \
-	    | sed -e 's/EOLINE/\n/g' > paper.bbl
+	    | sed -e 's/EOLINE/\n/g' > $*.bbl
+
           # The pre-final run of LaTeX after 'paper.bbl' was created.
-	  latex -shell-escape -halt-on-error "$$p"/paper.tex
+	  latex -shell-escape -halt-on-error $*.tex
 	fi
 
 
-#	    | sed -e 's;Chong;HELLO MUM;' \
+
 
 
 # The final paper
@@ -200,7 +211,8 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 # to run everything cleanly from there, it is necessary to add the current
 # directory (top project directory) to the `TEXINPUTS' environment
 # variable.
-paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
+$(top-pdfs): %.pdf: $(mtexdir)/project.tex paper.tex \
+         tex/src/appendix-*.tex $(texbdir)/%.bbl
 
         # If `$(mtexdir)/project.tex' is empty, don't build the PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
@@ -213,17 +225,17 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 
           # See above for a warning and brief discussion on the the
           # pdflatex option `-shell-escape'.
-	  latex -shell-escape -halt-on-error "$$p"/paper.tex
+	  latex -shell-escape -halt-on-error $*.tex
 
           # Convert the DVI to PostScript, and the PostScript to PDF. The
           # `-dNOSAFER' option to GhostScript allows transparencies in the
           # conversion from PostScript to PDF, see
           # https://www.ghostscript.com/doc/current/Language.htm#Transparency
-	  dvips paper.dvi
-	  ps2pdf paper.ps
+	  dvips $*.dvi
+	  ps2pdf $*.ps
 
           # Come back to the top project directory and copy the built PDF
           # file here.
 	  cd "$$p"
-	  cp $(texbdir)/$@ $(final-paper)
+	  cp $(texbdir)/$*.pdf $@
 	fi
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 18d54b1..d552dc1 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -64,8 +64,13 @@ include reproduce/software/config/LOCAL.conf
 # If you are just interested in the processing and don't want to build the
 # PDF, you can skip the creation of the final PDF by giving a value of
 # `yes' to `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+ifeq ($(separatesupplement),0)
+top-pdfs = paper.pdf
+else
+top-pdfs = paper.pdf supplement.pdf
+endif
 ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
-all: paper.pdf
+all: $(top-pdfs)
 else
 all:
 	@if [ "x$(GROUP-NAME)" = x ]; then \
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}