Trying to get biber to run when generating PDF

Trying to get biber to run when generating PDF

[Lyndon Drake]

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Hi,

Last one for the day (I hope): if I generate a LaTeX file and run latexmk 
on it, I get my citations fine, but if I try to get pandoc to generate the 
PDF the citations don't come through. I.e. this works:

/usr/local/bin/pandoc -dlatex -s -o output/README.tex README.md
cd output/
latexmk -lualatex README.tex

but this doesn't - the PDF is generated with the citations unmatched:

/usr/local/bin/pandoc -dlatex -s -o output/README.pdf README.md

I'm using the following defaults file in both cases:

metadata:
  author: Lyndon Drake
  papersize: a4
  documentclass: article
  mainfont: Times New Roman
  lang: en-GB
  mainfontoptions: Ligatures=TeX, Numbers=OldStyle
  otherlangs: [grc, he]
  bibliography:
    - /Users/lyndon/repo/workflow/zot-export.bib
  biblio-style: sbl
  biblatexoptions:
    - backend=biber
    - indexing=cite
  indent: true

cite-method: biblatex

pdf-engine: lualatex

number-sections: true

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Re: Trying to get biber to run when generating PDF

[Lukas Atkinson]

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This seems about right. Either use Pandoc's built-in citation system, or
generate LaTeX and compile it yourself. Pandoc is no substitute for
latexmk. Latexmk knows how and when to run additional required programs
such as Biber or Makeindex.

I tend to write makefiles that manage the necessary Pandoc/Latexmk calls
for me, e.g.:

  %.tex : %.md
    pandoc -st latex $< -o $@

  %.pdf : %.tex
    mkdir -p build
    latexmk -pdf -outdir build -interaction=batchmode $*
    cp build/$*.pdf .

Then, a call like `make paper.pdf` will do the necessary steps, assuming
paper.md exists.

On Mon, 20 Apr 2020 at 08:36, Lyndon Drake <lyndon-S8RYeTzMgQ3QT0dZR+AlfA@public.gmane.org> wrote:

> Hi,
>
> Last one for the day (I hope): if I generate a LaTeX file and run latexmk
> on it, I get my citations fine, but if I try to get pandoc to generate the
> PDF the citations don't come through. I.e. this works:
>
> /usr/local/bin/pandoc -dlatex -s -o output/README.tex README.md
> cd output/
> latexmk -lualatex README.tex
>
> but this doesn't - the PDF is generated with the citations unmatched:
>
> /usr/local/bin/pandoc -dlatex -s -o output/README.pdf README.md
>
> I'm using the following defaults file in both cases:
>
> metadata:
>   author: Lyndon Drake
>   papersize: a4
>   documentclass: article
>   mainfont: Times New Roman
>   lang: en-GB
>   mainfontoptions: Ligatures=TeX, Numbers=OldStyle
>   otherlangs: [grc, he]
>   bibliography:
>     - /Users/lyndon/repo/workflow/zot-export.bib
>   biblio-style: sbl
>   biblatexoptions:
>     - backend=biber
>     - indexing=cite
>   indent: true
>
> cite-method: biblatex
>
> pdf-engine: lualatex
>
> number-sections: true
>
> --
> You received this message because you are subscribed to the Google Groups
> "pandoc-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/pandoc-discuss/68a5023c-3ce3-44ef-9f05-2753626caf90%40googlegroups.com
> <https://groups.google.com/d/msgid/pandoc-discuss/68a5023c-3ce3-44ef-9f05-2753626caf90%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>

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Re: Trying to get biber to run when generating PDF

[John MacFarlane]

You can use latexmk as your pdf-engine.  You'll need to pass in
--pdf-engine-opts to tell latexmk to use lualatex and biber.

Lyndon Drake <lyndon-S8RYeTzMgQ3QT0dZR+AlfA@public.gmane.org> writes:

> Hi,
>
> Last one for the day (I hope): if I generate a LaTeX file and run latexmk 
> on it, I get my citations fine, but if I try to get pandoc to generate the 
> PDF the citations don't come through. I.e. this works:
>
> /usr/local/bin/pandoc -dlatex -s -o output/README.tex README.md
> cd output/
> latexmk -lualatex README.tex
>
> but this doesn't - the PDF is generated with the citations unmatched:
>
> /usr/local/bin/pandoc -dlatex -s -o output/README.pdf README.md
>
> I'm using the following defaults file in both cases:
>
> metadata:
>   author: Lyndon Drake
>   papersize: a4
>   documentclass: article
>   mainfont: Times New Roman
>   lang: en-GB
>   mainfontoptions: Ligatures=TeX, Numbers=OldStyle
>   otherlangs: [grc, he]
>   bibliography:
>     - /Users/lyndon/repo/workflow/zot-export.bib
>   biblio-style: sbl
>   biblatexoptions:
>     - backend=biber
>     - indexing=cite
>   indent: true
>
> cite-method: biblatex
>
> pdf-engine: lualatex
>
> number-sections: true
>
> -- 
> You received this message because you are subscribed to the Google Groups "pandoc-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/68a5023c-3ce3-44ef-9f05-2753626caf90%40googlegroups.com.

Re: Trying to get biber to run when generating PDF

[John MacFarlane]

To clarify, pandoc doesn't attempt to run bibtex or biber itself.
But if you use latexmk as your pdf-engine, latexmk can do this.

John MacFarlane <jgm-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org> writes:

> You can use latexmk as your pdf-engine.  You'll need to pass in
> --pdf-engine-opts to tell latexmk to use lualatex and biber.
>

Re: Trying to get biber to run when generating PDF

[Lyndon Drake]

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Ah, OK, that makes perfect sense now that I think about it. I'll give it a 
go with latexmk as the pdf-engine.

On Tuesday, 21 April 2020 04:28:09 UTC+12, John MacFarlane wrote:
>
>
> To clarify, pandoc doesn't attempt to run bibtex or biber itself. 
> But if you use latexmk as your pdf-engine, latexmk can do this. 
>
> John MacFarlane <j...-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org <javascript:>> writes: 
>
> > You can use latexmk as your pdf-engine.  You'll need to pass in 
> > --pdf-engine-opts to tell latexmk to use lualatex and biber. 
> > 
>

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