initial commit

.gitignore

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+/*.pdf
+
+.DS_Store
+
+.vscode*
+
+*.ist
+
+# ---> TeX
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# comment
+*.cut
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+# fixme
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.lzo
+*.lzs
+
+# uncomment this for glossaries-extra (will ignore makeindex's style files!)
+# *.ist
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
+# *.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# luatexja-ruby
+*.ltjruby
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# tcolorbox
+*.listing
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# todonotes
+*.tdo
+
+# vhistory
+*.hst
+*.ver
+
+# easy-todo
+*.lod
+
+# xcolor
+*.xcp
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices and outlines
+*.xyc
+*.xyd
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# gummi
+.*.swp
+
+# KBibTeX
+*~[0-9]*
+
+# TeXnicCenter
+*.tps
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+# Makeindex log files
+*.lpz
+
+# xwatermark package
+*.xwm
+
+# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
+# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
+# Uncomment the next line to have this generated file ignored.
+#*Notes.bib
+

.latexmkrc

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+# overleaf template
+
+# Settings
+$xdvipdfmx = "xdvipdfmx -z 6 -o %D %O %S";
+
+###############################
+# Post processing of pdf file #
+###############################
+
+# assume the jobname is 'output' for sharelatex
+my $ORIG_PDF_AGE = -M "output.pdf"; # get age of existing pdf if present
+
+END {
+    my $NEW_PDF_AGE = -M "output.pdf";
+    return if !defined($NEW_PDF_AGE); # bail out if no pdf file
+    return if defined($ORIG_PDF_AGE) && $NEW_PDF_AGE == $ORIG_PDF_AGE; # bail out if pdf was not updated
+    $qpdf //= "/usr/local/bin/qpdf";
+    $qpdf = $ENV{QPDF} if defined($ENV{QPDF}) && -x $ENV{QPDF};
+    return if ! -x $qpdf; # check that qpdf exists
+    $qpdf_opts //= "--linearize --newline-before-endstream";
+    $qpdf_opts = $ENV{QPDF_OPTS} if defined($ENV{QPDF_OPTS});
+    my $status = system($qpdf, split(' ', $qpdf_opts), "output.pdf", "output.pdf.opt");
+    my $exitcode = ($status >> 8);
+    print "qpdf exit code=$exitcode\n";
+    # qpdf returns 0 for success, 3 for warnings (output pdf still created)
+    return if !($exitcode == 0 || $exitcode == 3);
+    print "Renaming optimised file to output.pdf\n";
+    rename("output.pdf.opt", "output.pdf");
+}
+
+##############
+# Glossaries #
+##############
+add_cus_dep( 'glo', 'gls', 0, 'glo2gls' );
+add_cus_dep( 'acn', 'acr', 0, 'glo2gls');  # from Overleaf v1
+sub glo2gls {
+    system("makeglossaries $_[0]");
+}
+
+#############
+# makeindex #
+#############
+@ist = glob("*.ist");
+if (scalar(@ist) > 0) {
+    $makeindex = "makeindex -s $ist[0] %O -o %D %S";
+}
+
+################
+# nomenclature #
+################
+add_cus_dep("nlo", "nls", 0, "nlo2nls");
+sub nlo2nls {
+        system("makeindex $_[0].nlo -s nomencl.ist -o $_[0].nls -t $_[0].nlg");
+}
+
+#########
+# Knitr #
+#########
+my $root_file = $ARGV[-1];
+
+add_cus_dep( 'Rtex', 'tex', 0, 'rtex_to_tex');
+sub rtex_to_tex {
+    do_knitr("$_[0].Rtex");
+}
+
+sub do_knitr {
+    my $dirname = dirname $_[0];
+    my $basename = basename $_[0];
+    system("Rscript -e \"library('knitr'); setwd('$dirname'); knit('$basename')\"");
+}
+
+my $rtex_file = $root_file =~ s/\.tex$/.Rtex/r;
+unless (-e $root_file) {
+    if (-e $rtex_file) {
+        do_knitr($rtex_file);
+    }
+}
+
+##########
+# feynmf #
+##########
+push(@file_not_found, '^feynmf: Files .* and (.*) not found:$');
+add_cus_dep("mf", "tfm", 0, "mf_to_tfm");
+sub mf_to_tfm { system("mf '\\mode:=laserjet; input $_[0]'"); }
+
+push(@file_not_found, '^feynmf: Label file (.*) not found:$');
+add_cus_dep("mf", "t1", 0, "mf_to_label1");
+sub mf_to_label1 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t1"); }
+add_cus_dep("mf", "t2", 0, "mf_to_label2");
+sub mf_to_label2 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t2"); }
+add_cus_dep("mf", "t3", 0, "mf_to_label3");
+sub mf_to_label3 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t3"); }
+add_cus_dep("mf", "t4", 0, "mf_to_label4");
+sub mf_to_label4 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t4"); }
+add_cus_dep("mf", "t5", 0, "mf_to_label5");
+sub mf_to_label5 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t5"); }
+add_cus_dep("mf", "t6", 0, "mf_to_label6");
+sub mf_to_label6 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t6"); }
+add_cus_dep("mf", "t7", 0, "mf_to_label7");
+sub mf_to_label7 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t7"); }
+add_cus_dep("mf", "t8", 0, "mf_to_label8");
+sub mf_to_label8 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t8"); }
+add_cus_dep("mf", "t9", 0, "mf_to_label9");
+sub mf_to_label9 { system("mf '\\mode:=laserjet; input $_[0]' && touch $_[0].t9"); }
+
+##########
+# feynmp #
+##########
+push(@file_not_found, '^dvipdf: Could not find figure file (.*); continuing.$');
+add_cus_dep("mp", "1", 0, "mp_to_eps");
+sub mp_to_eps {
+    system("mpost $_[0]");
+    return 0;
+}
+
+#############
+# asymptote #
+#############
+sub asy {return system("asy --offscreen '$_[0]'");}
+add_cus_dep("asy","eps",0,"asy");
+add_cus_dep("asy","pdf",0,"asy");
+add_cus_dep("asy","tex",0,"asy");
+
+#############
+# metapost  #  # from Overleaf v1
+#############
+#add_cus_dep('mp', '1', 0, 'mpost')
+#sub mpost {
+#    my $file = $_[0];
+#    my ($name, $path) = fileparse($file);
+#    pushd($path);
+#    my $return = system "mpost $name";
+#    popd();
+#    return $return;
+#}
+
+##########
+# chktex #
+##########
+unlink 'output.chktex' if -f 'output.chktex';
+if (defined $ENV{'CHKTEX_OPTIONS'}) {
+    use File::Basename;
+    use Cwd;
+
+    # identify the main file
+    my $target = $ARGV[-1];
+    my $file = basename($target);
+
+    if ($file =~ /\.tex$/) {
+        # change directory for a limited scope
+        my $orig_dir = cwd();
+        my $subdir = dirname($target);
+        chdir($subdir);
+        # run chktex on main file
+        $status = system("/usr/bin/run-chktex.sh", $orig_dir, $file);
+        # go back to original directory
+        chdir($orig_dir);
+
+        # in VALIDATE mode we always exit after running chktex
+        # otherwise we exit if EXIT_ON_ERROR is set
+
+        if ($ENV{'CHKTEX_EXIT_ON_ERROR'} || $ENV{'CHKTEX_VALIDATE'}) {
+            # chktex doesn't let us access the error info via exit status
+            # so look through the output
+            open(my $fh, "<", "output.chktex");
+            my $errors = 0;
+            {
+                local $/ = "\n";
+                while(<$fh>) {
+                    if (/^\S+:\d+:\d+: Error:/) {
+                        $errors++;
+                        print;
+                    }
+                }
+            }
+            close($fh);
+            exit(1) if $errors > 0;
+            exit(0) if $ENV{'CHKTEX_VALIDATE'};
+        }
+    }
+};

Makefile

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+.PHONY: main.pdf clean redo test_git versioned
+
+main.pdf: main.tex main.bib
+	latexmk -pdf main.tex
+
+clean:
+	x=`biber --cache` && if [ -d "$x" ]; then $(RM) $x; fi
+	$(RM) *.out *.aux *.log *.bbl *.blg *~ \#*\# *.toc *.idx *.eps dummy *.fls *.fdb_latexmk
+	$(RM) $(patsubst %.tex, %.ps, $(wildcard *.tex))
+	$(RM) $(patsubst %.tex, %.dvi, $(wildcard *.tex))
+	$(RM) $(patsubst %.tex, %.pdf, $(wildcard *.tex))
+
+redo: clean main.pdf
+
+test_git:
+	if [ -z "$(git status --untracked-files=no --porcelain)" ]; then exit 0; else echo -e "\nERROR: working directory not clean. commit changes before running versioned build"; exit 1; fi
+# TODO check if we are also synced to at least one remote
+
+versioned: test_git clean main.pdf
+	GITVER=$(shell git rev-parse --short HEAD) && mv main.pdf "main-${GITVER}.pdf"
+

sections/abstract.tex

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+\begin{abstract}
+
+% Your abstract text goes here. Just a few facts. Whet our appetites. Not more than 200 words, if possible, and preferably closer to 150.
+% see for reference: https://www.nature.com/documents/nature-summary-paragraph.pdf
+
+One or two sentences providing a basic introduction to the field,  comprehensible to a scientist in any discipline. 
+Two to three sentences of more detailed background, comprehensible  to scientists in related disciplines.
+One sentence clearly stating the general problem being addressed by  this particular study. 
+One sentence summarizing the main result (with the words “here we  show” or their equivalent). 
+Two or three sentences explaining what the main result reveals in direct comparison to what was thought to be the case previously, or how the  main result adds to previous knowledge. One or two sentences to put the results into a more general context. 
+Two or three sentences to provide a broader perspective, readily comprehensible to a scientist in any discipline, may be included in the first paragraph if the editor considers that the accessibility of the paper  is significantly enhanced by their inclusion. Under these circumstances,  the length of the paragraph can be up to 300 words. (This example is  190 words without the final section, and 250 words with it).
+\end{abstract}

sections/approach.tex

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+\section{Approach}
+\label{sec:approach}
+
+This section will be the most adjusted per aper as it presents the scientific approach, data, experiments, and evaluations.

sections/background.tex

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+\section{Background}
+\label{sec:background}
+
+Lotsa folks did lotsa things.

sections/conclusion.tex

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+\section{Conclusion}
+\label{sec:conclusion}
+
+A summary, write last with abstract.

sections/discussion.tex

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+\section{Discussion}
+\label{sec:discussion}
+
+As opposed to the evaluations, the authors will present their opinions and interpretations here.

sections/evaluation.tex

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+\section{Evaluation}
+\label{section:evaluation}
+
+The evaluation results will be presented here .. by zombies!

sections/future_work.tex

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+\section{Future Work}
+\label{sec:future-work}
+
+Always more to do.

sections/introduction.tex

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+\section{Introduction}
+\label{sec:introduction}
+
+The introduction provides context and some motivation for the research.

sections/related_work.tex

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+\section{Related Work}
+\label{sec:related-work}
+
+On the shoulders of giants is a joke on the height of