make biblatex cite all papers despite includeonly

Question

I use \includeonly to do the page layout for single chapters. I worked an our one a lengthy chapter only to find out that it does not work with the whole document. After some search I found the reason. A single letter caused a cascade of different page layouts. When I did the layout with only one chapter included there was just one paper by Müller from 2004 in this chapter and the following was the result:

In the full book, I had four papers and I got a reference to Müller (2004d) instead of Müller (2004). This single letter caused the paragraph to take an extra line, which caused two lines floating to the next page, which ruined everything I did so far.

So, question: Can I make biblatex to include everthing it finds cited in aux files?

Edit 1:

I adapted https://tex.stackexchange.com/a/418639/18561 to biblatex, but it does not work. It only cites one reference. bibtex works out of the box without any additional mechanisms.

\documentclass{report}
\usepackage{filecontents}
\usepackage{pgffor}
\usepackage{lipsum}

\usepackage[backend=biber]{biblatex}

%\bibliographystyle{apalike}
\bibliography{bibliography}

\def\mincludeonly#1{\foreach \file in {#1} {\xdef\temp{#1}\global\expandafter\let\csname fileincluded\file\endcsname\temp}}
\newsavebox{\mybox}
\def\savecitations#1{\savebox\mybox{\vbox{\noindent\begin{minipage}[inner sep=0]{\textwidth}\include{#1}\end{minipage}}}}
\def\minclude#1{\ifcsname fileincluded#1\endcsname\include{#1}\else\savecitations{#1}%More needed commands
\addtocounter{chapter}{-1}%
\fi}

\mincludeonly{chap1}

\begin{filecontents}{bibliography.bib}
@article{item1,
  title = {Title Item 1},
  year  = {1998},
  author = {Author},
}
@article{item2,
  title = {Title Item 1},
  year  = {1998},
  author = {Author},
}
\end{filecontents}

\begin{filecontents}{chap1.tex}
  \chapter{test 1}
  This is a citation:\cite{item1}
\end{filecontents}
\begin{filecontents}{chap2.tex}
  \chapter{test 2}
  This is a citation:\cite{item2}

  \lipsum[1-20]
\end{filecontents}


\begin{document}
\tableofcontents

\minclude{chap1}
%\minclude{chap2}

\printbibliography 
\end{document}

Edit 2:

MWE based on the code above:

\documentclass{report}
\usepackage{filecontents}
\usepackage{lipsum}

\usepackage[backend=biber]{biblatex}

\bibliography{bibliography}

\includeonly{chap1}

\begin{filecontents}{bibliography.bib}
@article{item1,
  title = {Title Item 1},
  year  = {1998},
  author = {Author},
}
@article{item2,
  title = {Title Item 1},
  year  = {1998},
  author = {Author},
}
\end{filecontents}

\begin{filecontents}{chap1.tex}
  \chapter{test 1}
  This is a citation:\cite{item1}
\end{filecontents}
\begin{filecontents}{chap2.tex}
  \chapter{test 2}
  This is a citation:\cite{item2}

  \lipsum[1-20]
\end{filecontents}


\begin{document}
\tableofcontents

\include{chap1}
%\include{chap2}

\printbibliography 
\end{document}

Answer 1

biblatex always writes to the main .aux file, so the .aux files for the chapters do not contain enough information. But even if that were changed, the issue is still biblatex does not only manage its citations with the .aux file, it also writes them to the .bcf.

biblatex only writes to the .bcf if the citation is actually processed by TeX. If the citation lives in a file not included in the current run, the citations are not processed.

The following is a copy of the original \include and \includeonly (see ltfiles.dtx or source2e) that also secretly \inputs the chapter in a box that is never printed to let LaTeX process it for citations.

\documentclass{report}
\usepackage{filecontents}
\usepackage{lipsum}
\usepackage[backend=biber, style=authoryear]{biblatex}
\addbibresource{biblatex-examples.bib}

\begin{filecontents}{chap1.tex}
  \chapter{Chapter One}
  \cite{sigfridsson,knuth:ct:a,knuth:ct:b}
  \lipsum[1-5]
\end{filecontents}
\begin{filecontents}{chap2.tex}
  \chapter{Chapter Two}
  \cite{worman,knuth:ct:a,knuth:ct:c}
  \lipsum[1-5]
\end{filecontents}

\makeatletter
\newif\if@blx@partsw \@blx@partswfalse

\def\blxincludeonly#1{%
  \@blx@partswtrue
  \edef\@blx@partlist{\zap@space#1 \@empty}}
\@onlypreamble\blxincludeonly

\def\blxinclude#1{\relax
  \ifnum\@auxout=\@partaux
    \@latex@error{\string\include\space cannot be nested}\@eha
  \else \@blx@include#1 \fi}

\def\@blx@include#1 {%
  \clearpage
  \if@filesw
    \immediate\write\@mainaux{\string\@input{#1.aux}}%
  \fi
  \@tempswatrue
  \if@blx@partsw
    \@tempswafalse
    \edef\reserved@b{#1}%
    \@for\reserved@a:=\@blx@partlist\do
      {\ifx\reserved@a\reserved@b\@tempswatrue\fi}%
  \fi
  \if@tempswa
    \let\@auxout\@partaux
    \if@filesw
      \immediate\openout\@partaux #1.aux
      \immediate\write\@partaux{\relax}%
    \fi
    \@input@{#1.tex}%
    \clearpage
    \@writeckpt{#1}%
    \if@filesw
      \immediate\closeout\@partaux
    \fi
  \else
    \setbox0=\vbox{\begingroup\@input@{#1.tex}\endgroup}%
    \deadcycles\z@
    \@nameuse{cp@#1}%
  \fi
  \let\@auxout\@mainaux}
\makeatletter

\blxincludeonly{chap2}

\begin{document}
\tableofcontents

\blxinclude{chap1}
\blxinclude{chap2}

\printbibliography 
\end{document}

Answer 2

This is what I do now: I copy my main file that includes the chapters to a file (check-gt.tex) and change the bibliography that is loaded (check-gt.bib). Instead of using my bibliography that contains 6000 items I use the bib that cites all items in the book (just 1471). I include a \nocite{*} in this file so that all items that are cited in the full book (grammatical-theory.tex) are also cited in the file that does not include all chapters (check-gt.tex). The following line produces the list of references that I include

 biber --output_format=bibtex --output_resolve grammatical-theory.bcf -O check-gt.bib

This has to be done once and I do not have to compile all the files that are not included. The book is over 800 pages long and I guess this solution is the most efficient one.

Answer 3

Here is a way with my versions of\include and \includeonly commands:

\documentclass{report}
\usepackage{filecontents}
\usepackage{pgffor}
\usepackage{lipsum}

%CHANGE TO 1 FOR BIBLATEX(BIBER)
\xdef\testonbiblatex{0}

%THE PART OF CODE NEEDED
\xdef\inclonl{0}
\def\mincludeonly#1{\xdef\inclonl{1}\foreach \file in {#1} {\xdef\temp{#1}\global\expandafter\let\csname fileincluded\file\endcsname\temp}}
\newsavebox{\mybox}
\def\savecitations#1{\savebox\mybox{\vbox{\noindent\begin{minipage}[inner sep=0]{\textwidth}\include{#1}\end{minipage}}}}
\def\minclude#1{\ifnum\inclonl=1\ifcsname fileincluded#1\endcsname\include{#1}\else\savecitations{#1}%More needed commands
  %This indented part fix the isue of @moewe's commant about pages numbers  
  \pgfmathsetmacro\pagestobeadded{int(round((\ht\mybox+\dp\mybox)/\textheight))}%
  \pgfmathsetmacro\morepagestobeadded{round((\ht\mybox+\dp\mybox)/\textheight)-(\ht\mybox+\dp\mybox)/\textheight))}%
  \ifdim\morepagestobeadded pt>0pt %
  \pgfmathsetmacro\finalpagestobeadded{int(\pagestobeadded)}%
  \else%
  \pgfmathsetmacro\finalpagestobeadded{int(\pagestobeadded+1)}%
  \fi%
  \addtocounter{page}{\finalpagestobeadded}%
\addtocounter{chapter}{-1}%
\fi\else\include{#1}\fi}

%ADDED FOR EASY TEST
\ifnum\testonbiblatex=1
\usepackage[style=authoryear,backend=biber]{biblatex}
\addbibresource{bibliography.bib}
\fi

\mincludeonly{chap1}

\begin{filecontents}{bibliography.bib}
  \@article{item1,
    title = {Title Item 1},
    year  = {1998},
    author = {Author}}
    \@article{item2,
    title = {Title Item 2},
    year  = {1998},
    author = {Author}}
\end{filecontents}

\begin{filecontents}{chap1.tex}
  \chapter{test 1}
  This is a citation:\cite{item1}
\end{filecontents}
\begin{filecontents}{chap2.tex}
  \chapter{test 2}
  This is a citation:\cite{item2}

  \lipsum[1-20]
\end{filecontents}


\begin{document}

\tableofcontents


\minclude{chap1}
\minclude{chap2}%My problem on your question Edit 1 was a % here

%ADDED just to make easy check of chapter numbers and possible side effects
\chapter{test}
\lipsum[1-2]

%ADDED FOR EASY TEST
\ifnum\testonbiblatex=1
\printbibliography
\else
\bibliographystyle{apalike}
\bibliography{bibliography}
\fi


\end{document}

Of course it will be much slower because it will read all the chapters included or not... But the idea can be used in other ways too.

(I haven't use or check enough how the original \includeonly command is supposed to work and I am not sure what would be the way to not use the other chapters... but this can be fixed in your needs I suppose)

Edit: all the parts with comment %ADDED FOR EASY TEST , are needed only to test between biblatex(biber) [variable \testonbiblatex value =1] and bibtex. The only needed change I made was to remove the "%" between second \minclude command. Also changed second article title but not really needed to work.

Output (bibtex):

Output (biblatex):