Example shell script to prepare lyx file to upload to arxiv or to journal with zip

_COPY_FOR_SUBMIT_.sh

#!/bin/sh
# Tested on MacOS
# @license: APACHE 2.0
# @author:  Zlatko K. Minev (2020) 


###############################################################
### User define!  

alias lyx="/Applications/LyX.app/Contents/MacOS/lyx" # # https://wiki.lyx.org/LyX/ManPage
DEST="_SUBMIT_"
MAIN="epr-main" # "$MAIN.lyx"

###############################################################
### General initialization 

# Colors 
red=$'\e[1;31m'
grn=$'\e[1;32m'
yel=$'\e[1;33m'
blu=$'\e[1;34m'
mag=$'\e[1;35m'
cyn=$'\e[1;36m'
end=$'\e[0m'

# horizontal rule; http://wiki.bash-hackers.org/snipplets/print_horizontal_line
hr() {
  local start=$'\e(0' end=$'\e(B' line='qqqqqqqqqqqqqqqq'
  local cols=${COLUMNS:-$(tput cols)}
  while ((${#line} < cols)); do line+="$line"; done
  echo ""
  printf '%s%s%s\n' "$start" "${line:0:cols}" "$end"
  echo ""
}

 
BASEDIR=$(dirname "$0") # directory of file 
cd "${BASEDIR}"
#cd ".."


###############################################################
### Main

clear
printf "\n\n$grn Lyx to latex.$end\n\n"
echo "pwd: $grn$(pwd)$end"

# FOLDERS: delete dir & make
rm -rf "$DEST" 
mkdir "$DEST"
mkdir "$DEST/img-main" # USER-SPECIFY
mkdir "$DEST/img-app"

###############################################################
### Export lyx 
echo "$grn\nExport LyX -> TeX: $end"
lyx --force-overwrite --export pdflatex "$MAIN.lyx"
mv -f "$MAIN.tex"          "$DEST/$MAIN.tex"
mv -f "epr-macros.tex"     "$DEST/epr-macros.tex"   # EXTRA FILES created by conversion, since included as include files
cp -f "epr-preamble.tex"   "$DEST/epr-preamble.tex" # This is a tex file include din the lyx, so dont move, copy only, we need it 
python __copy_python_utils__.py -d "$DEST" -f "$MAIN"

# Encoding: of file 								# https://stackoverflow.com/questions/805418/how-to-find-encoding-of-a-file-via-script-on-linux
echo "$yel File encodings: $end"
file -I "$DEST/$MAIN.tex" 
file -I "$DEST/epr-macros.tex"
file -I "$DEST/epr-preamble.tex"

# Encoding: Check for invalind encoding in file - remove these manuallly. Use https://tex.stackexchange.com/tags/accents/info
echo "$yel\n Invalid encoding (non UTF-8):$end\n  (Assumming locale is UTF-8)\n" # https://stackoverflow.com/questions/29465612/how-to-detect-invalid-utf8-unicode-binary-in-a-text-file
grep -axv '.*' "$DEST/$MAIN.tex"
grep -axv '.*' "$DEST/epr-macros.tex"
grep -axv '.*' "$DEST/epr-preamble.tex"

# Library file
echo "$yel\n Change library.$end"
sed -i'.backup' 's|../../library|library|g' "$DEST/$MAIN.tex"
cp "../../library.bib" "$DEST/library.bib"
rm -f "$DEST/$MAIN.tex.backup"

echo "$yel File encoding (after 'sed'): $end"
file -I "$DEST/$MAIN.tex" 


###############################################################
# Copy all pdf files for figures 
echo "$grn\nCopy figures: $end" 
cp img-main/**.pdf "$DEST/img-main"
cp img-app/**.pdf "$DEST/img-app"


###############################################################
echo "\n\n\n$grn"; hr
echo "          C O M P I L E          "
echo "$end"; hr

echo $(type -a pdflatex) # should be something like pdflatex is /Library/TeX/texbin/pdflatex
echo $(type -a bibtex)
printf "\n\n\n\n"; hr

cd "$DEST"

pdflatex "$MAIN.tex"; hr 
bibtex   "$MAIN"; hr
pdflatex "$MAIN.tex"; hr
pdflatex -synctex=1 -interaction=nonstopmode "$MAIN.tex"; hr  # SyncTeX is a utility written by Jérôme Laurens which enables synchronization between your source document and the PDF output. If your editor/viewer supports it, then you can click in your source and jump to the equivalent place in the PDF or click in the PDF and it will jump to the appropriate place in your source document.

### Check for errors
echo "\n\n"
echo "$grn\CHECK FOR ERRORS:"
echo "$end$grn\nCheck for errors: Latex $end $yel"
grep -i "error" "$MAIN.log"
echo "$end$grn\nCheck for errors: BibTex $end $yel"
grep -i "error" "$MAIN.blg" # Bibtex
echo "$end\n"; hr

echo "$grn\CHECK FOR WARNINGS:"
echo "$end$grn\nCheck for warnings: Latex $end $yel"
grep -i "warning" "$MAIN.log"
echo "$end$grn\nCheck for warnings: BibTex $end $yel"
grep -i "warning" "$MAIN.blg" # Bibtex
echo "$end"; hr;

if true
then # final run for Arxiv, make zip
	# worry about hyperindex,breaklinks
	echo "$grnClear, format, and zip for arxiv.org:$end"

	cd .. 
	rm -f "$DEST.zip"
	sed -i'.backup' 's|\\usepackage{pdfsync}||' "$DEST/$MAIN.tex" # arxiv doesn't need synctex
	sed -i'.backup' 's|\\synctex=-1||' "$DEST/$MAIN.tex"
	rm -f "$DEST/$MAIN.tex.backup"

	rm -f "$DEST/$MAIN.aux"
	rm -f "$DEST/$MAIN.blg"
	rm -f "$DEST/$MAIN.log"
	rm -f "$DEST/$MAIN.out"
	rm -f "$DEST/$MAIN.synctex"
	rm -f "$DEST/$MAIN.pdfsync"
	rm -f "$DEST/$MAIN.synctex.gz"
	
	#rm -f "$DEST/$MAIN.pdf"
	rm -f "$DEST/library.bib"

	# remove SI figures
	rm -f "$DEST/img-app/FE_JJsurf.pdf"
	rm -f "$DEST/img-app/FE-junc.pdf"
	rm -f "$DEST/img-app/frustrated-circuit-ex-simplify.pdf"
	rm -f "$DEST/img-app/frustrated-circuit-ex.pdf"
	rm -f "$DEST/img-app/mechanical-analogy.pdf"
	rm -f "$DEST/img-app/pumped-process.pdf"
	rm -f "$DEST/img-app/signs-matter-example.pdf"
	rm -f "$DEST/img-app/transmon-cavity-spectrum.pdf"

	zip -r "$DEST.zip" "$DEST"
fi