Finalize LaTeX projects for submission

finalize-latex-for-submission.md

latex-finalize.sh

A script to prepare LaTeX source files for submission

What it does

• Copies all source files into single destination directory
• Flattens LaTeX files that were included inline into main.tex
• Flattens BibTeX bibliography into main.tex
• Compiles LaTeX to PDF in destination folder
• Archives and compresses all TeX sources into ZIP file

Requirements

• rekka/latex-flatten

Directory map

project_foobar/
├─ tex/ # working directory
│  ├─ main.tex
│  ├─ mybibfile.bib
│  ├─ nature.bst
│  ├─ chapters/
│  │  ├─ 00-abstract.tex
│  │  ├─ 01-introduction.tex
│  │  ├─ 02-methods.tex
│  ├─ figure/
│  │  ├─ figure-1.pdf
│  │  ├─ figure-2.pdf
│  ├─ scripts/
│  │  ├─ latex-flatten.py
│  │  ├─ latex-finalize.sh
├─ manuscript-for-submission/
│  ├─ 2022-07-03T17-54-56/ # Destination directory
│  │  ├─ tex-sources/
│  │  │  ├─ main.tex # All TeX files and BibTeX are flattened
│  │  │  ├─ figure-1.pdf
│  │  │  ├─ figure-2.pdf
│  │  ├─ manuscript.pdf # Compiled PDF
│  │  ├─ tex-sources.zip

latex-finalize.sh

#!/bin/zsh
set -euo pipefail

rootDir='/Users/john/Dropbox/Research/projecct_foobar'

currenttime=$(date +"%Y-%m-%dT%H-%M-%S")
originalTeXDir=$rootDir"/tex" # LaTeX working directory
submissionDir=$rootDir"/manuscript-for-submission/"$currenttime # Target directory
submissionTeXDir=$submissionDir"/tex-sources" # Target directory

# Create directory to store submission
mkdir -p $submissionTeXDir

# Copy source files
cp $originalTeXDir/main.tex $submissionTeXDir
cp $originalTeXDir/*.bst $submissionTeXDir
cp $originalTeXDir/*.bib $submissionTeXDir
cp $originalTeXDir/figure/*.pdf $submissionTeXDir
cp -r $originalTeXDir/chapters/ $submissionTeXDir/chapters/

# Flatten chapters into main.tex
$originalTeXDir/scripts/latex-flatten.py $submissionTeXDir/main.tex $submissionTeXDir/main-flattened.tex

# Remove original TeX file before flattening
rm -rf $submissionTeXDir/chapters/
rm $submissionTeXDir/main.tex

# Rename flattend file as main.tex
mv $submissionTeXDir/main-flattened.tex $submissionTeXDir/main.tex

# Change figure path
# We have moved figures just under the tex-source directory
sed -i '' -e "s%{figure/%{%g" $submissionTeXDir/main.tex

cd $submissionTeXDir

# Prepare for bibtex
pdflatex main.tex

# Generate bibliography (bbl)
bibtex main.aux

# Flatten bibliography
# Remove \bibliography{mybibfile.bib} and include bbl contents in main.tex
sed -i '' -e "s%bibliography{mybibfile}%input{main.bbl}%g" $submissionTeXDir/main.tex
$originalTeXDir/scripts/latex-flatten.py $submissionTeXDir/main.tex $submissionTeXDir/main-flattened.tex
mv $submissionTeXDir/main-flattened.tex $submissionTeXDir/main.tex

# Compile the final PDF
latexmk -pdf main.tex

# Move comipled PDF to parent directory
mv $submissionTeXDir/main.pdf $submissionDir/manuscript.pdf

# Remove .bib from tex-source directory
rm $submissionTeXDir/*.bib

# Remove auxilary files from tex-source directory
rm $submissionTeXDir/*.aux
rm $submissionTeXDir/*.log
rm $submissionTeXDir/*.blg
rm $submissionTeXDir/*.bbl

# Archive and compress tex-source directory
zip -r $submissionDir/tex-sources.zip .