#### Writing a LaTeX book with multiple subfiles and a single bibliography file

June 20, 2019

I was recently editing the second edition of my book on 3D digitisation using LaTeX and stumbled on an unexpected obstacle. The book consists of a number of chapters thus it is more convenient to edit them separately. In addition, I wanted to have bibliography at the end of each chapter, so that each chapter can be circulated independently. But still, I wanted all the bibliography references to be in the same bib file. Apparently, I needed to be able to compile the chapters separately and the book as a whole. Although this might seem trivial, it is not! And as it turned out after posting the problem on tex.stackexchange there was no answer…So I had to work it through and eventually found a solution, although not so elegant as it should be. The complete thread on tex.stackexchange can be found here.

In order to make it happen, I created the following file structure:

• the root folder: with book.tex, bibliography.bib
• a /figures folder with all figures
• a /chapterX folder: for each chapterX.tex

In the main (master) TeX file (book.tex) I have something like the following minimal code (for a typical double-sided B5 paper size, 11 points characters):

[matlab]
% define the basic document properties
\documentclass[11pt,b5paper,twoside,openright]{book}

\usepackage[semicolon,round,sort&compress,sectionbib]{natbib}

\usepackage[sectionbib]{chapterbib} % load the chapterbib library
\usepackage{apalike} % load the APA style for the bibliography
\usepackage[toc,page,titletoc]{appendix} % settings for Appendices
\bibliographystyle{apalike} % set the bibliography style to APA
\usepackage{subfiles} % load the subfiles library

\usepackage{bibunits} % load the bibunits library
\defaultbibliography{bibliography} % This is the one and only bibliography file for all chapters
\defaultbibliographystyle{apalike} % This is the style to be used throughout the book

\begin{document}
\subfile{chapter0/chapter0}
\subfile{chapter1/chapter1}
\subfile{chapter2/chapter2}
\subfile{chapter3/chapter3}
% ……… more chapters
\begin{appendices}
\subfile{appendixI/appendixI}
\subfile{appendixII/appendixII}
% ……… more appendices
\end{appendices}
\end{document}
[/matlab]

Then each of the chapters has the following minimal form:

[matlab]
\makeatletter
\def\input@path{{../}}
\makeatother
\documentclass[../book.tex]{subfiles}
\begin{document}
\begin{bibunit}

%…….text with \cite{…} commands

\putbib % this is the command that renders the chapter bibliography here!
\end{bibunit}
\end{document}
[/matlab]

When the main file is compiled, then a series of [shell]bu*.aux[/shell] files are created that correspond to the auxiliary files for the subfiles (chapters). Then those auxiliary files need to be used as input to [shell]bibtex[/shell] but this might not be so easy, since we are talking about multiple files and in many cases, like when using [shell]TeXShop[/shell] on MacOS, there is no option to run multiple arbitrarily-named auxiliary files. To tackle this I had to create a very simple “engine” with the following code (which practically runs [shell]bibtex[/shell] for every [shell]bu*.aux[/shell] file):

[shell]
#!/bin/sh
for auxfile in bu*.aux
do
echo —Running bibtex $auxfile bibtex “$auxfile”
done
[/shell]

I saved this code as [shell]BIBunits.engine[/shell] and moved it in the [shell]Engines[/shell] folder in the [shell]Library[/shell] of TeXShop ([shell]~\Library\TeXShop\Engines[/shell]) so that the “engine” becomes available within the [shell]TeXShop[/shell] GUI.

After all those steps the scenario runs smoothly and I get a complete book with the bibliography of each chapter where it should be. If everything is done the way presented above here is the overall compilation pipeline:

1. create and edit the files
2. compile the main file
3. run the BIBunits.engine (bibtex all bu*aux files)
4. compile the main file twice