Not able to generate the whole book using latexpdf

Describe the bug

context I’m trying to build a pdf using latex by running

jupyter-book build mybookname/ --builder pdflatex

expectation I expected a pdf of the whole book

bug But I’m getting only the first two sections of the first chapter. Here is what I get when building, it appears to have problems with cross-references? I’m not sure.

Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 6 reference(s)
Latexmk: ====List of undefined refs and citations:
  Reference `capitulos/marco-teorico/reconstruccion-jets:jets' on page 3 undefined on input line 210
  Reference `capitulos/marco-teorico/mas-alla-del-ms:bsm' on page 3 undefined on input line 210
  Reference `capitulos/marco-teorico/aprendizaje-automatico:ml' on page 3 undefined on input line 210
  Reference `capitulos/marco-teorico/reproducibilidad:rpd' on page 3 undefined on input line 210
  Reference `capitulos/marco-teorico/reconstruccion-jets:jets-desarrollo' on page 9 undefined on input line 364
  Reference `capitulos/marco-teorico/reconstruccion-jets:jets-qcd' on page 9 undefined on input line 367
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'python.log' for details
Latexmk: If appropriate, the -f option can be used to get latexmk
  to try to force complete processing.
Reverting Windows console CPs to (in,out) = (850,850)
C:\texlive\2022\bin\win32\runscript.tlu:915: command failed with exit code 12:
perl.exe c:\texlive\2022\texmf-dist\scripts\latexmk\latexmk.pl -pdf -dvi- -ps-  python.tex

I uploaded all I get in the console here problem This is a problem for people trying to get a latex pdf from their books.

Reproduce the bug

1. Clone https://github.com/marianaiv/tesis_grado_UCV/tree/marco-teorico to your computer
2. Go to the file. From the command line would be

cd path_where_cloned/tesis_grado_UCV

1. Build the pdf using

jupyter-book build tesis --builder latexpdf

List your environment

>jupyter-book --version
Jupyter Book      : 0.12.2
External ToC      : 0.2.4
MyST-Parser       : 0.15.2
MyST-NB           : 0.13.2
Sphinx Book Theme : 0.1.10
Jupyter-Cache     : 0.4.3
NbClient          : 0.5.4

• Python 3.7.4
• Windows 10
• TeX 3.141592653 (TeX Live 2022), kpathsea version 6.3.4

[michaelosthege]

@marianaiv @mmcky just swaw by accident that the issue described here is a known issue with sphinxcontrib-bibtex: https://sphinxcontrib-bibtex.readthedocs.io/en/latest/usage.html#latex-backend-fails-with-citations-in-figure-captions

Discussion in https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/276

[phockett]

Just ran into this one too, specifically for the captions in the {glue:figure} case.

The fix at https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/276#issuecomment-1102154800 worked for me (thanks @michaelosthege for pointing in that direction!), i.e. adding the following to the preamble (via my _config.yml):

sphinx:
  config:
      preamble: |+
		% Fix citations in figure captions, from https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/276#issuecomment-1102154800
        \usepackage{etoolbox}
        \AtBeginEnvironment{figure}{\pretocmd{\hyperlink}{\protect}{}{}}  

Citations in captions then seem to work without triggering latex build issues.

(I also tested the fix at https://sphinxcontrib-bibtex.readthedocs.io/en/latest/usage.html#latex-backend-fails-with-citations-in-figure-captions, but that didn’t work for me (maybe a Sphinx version thing).)

> jupyter-book --version
Jupyter Book      : 0.13.1
External ToC      : 0.2.4
MyST-Parser       : 0.15.2
MyST-NB           : 0.13.2
Sphinx Book Theme : 0.3.3
Jupyter-Cache     : 0.4.3
NbClient          : 0.5.4

Sphinx 4.5.0 Python 3.9.7