org-mode vs pandoc export

org-mode vs pandoc export

[Joseph Vidal-Rosset]

Hello,

Does someone succeeds to export scientific paper with numbering
formulas from LateX to odt or docx?

I have tried to use pandoc, but pandoc-crossref does not work...

(I hate these publishers that do not know LaTeX... )

Best wishes,

Jo.

Re: org-mode vs pandoc export

[Emmanuel Charpentier]

I suppose that you need org-mode to use Babel features (code and/or
code execution results intermixed with your paper's text).

I have had trouble with .dot exporting using the builtin .dot exporter,
but can't, for the life of me, remembering if my troubles were cross-
reference or citations-related (an academic paper usually needs
both...). I noted that the references done via John Kitchin's excellent
org-ref didn't export to .dot.

As far as I can tell, ox-pandoc does its own numbering (generating an
intermediate temporary file that I never managed to catch) and does not
use  pandoc-crossref.

ISTR that a "clever" use of org-ref allows to number equations... in
LaTeX output. I also STR that it doesn't work in .docx output. John
Kitchin (the org-ref author) thinks that the key is to generate a
correct \LaTeX file and to export that to .docx via pandoc.

At this point, writing a \LaTeX file with pandoc export in mind is
probably your best bet. There exist (limited) alternatives to the 
Babel features of org-mode:
 - knitr (supports R and Python code in "session"mode, i. e. continuity
between code chunks),
 - SageTeX (post-processing in a single Sagemath run ; can include code
for a variety of math software, including R),
 - Pythontex (postprocessor, supports Python, Sage, Octave and a couple
other, but not R ; a clever use of knitr and Pythontex is possible).

Possible alternative: Markdown + Codebraid (supports a hanful of
langiages, including R and (development branch) Sage). This should
accept pandoc-crossref numbering. But it's Markdown, with limited
formatting abilities...

So, we have an array of partial solutions, none universal. Pick your
poison...

Out of curiosity: in which domain still exist journal publishers not
accepting \LaTeX ? I suspect medicine...

HTH,

--
Emmanuel Charpentier

Re: org-mode vs pandoc export

[Joseph Vidal-Rosset]

Hello,

Many thanks Emmanuel for your help.

Indeed, I'm  using org-ref and scimax, all the  nice tools that
John offers very  generously to the community; org-ref  is so convenient
that  now I  cannot  imagine to  work  without it.  Maybe  John has  the
solution for future exports. (I did not succeed to export in odt because
of links, bibliography links.)

Finally the best result was done directly via pandoc, via a command line
like this one:

pandoc -s --filter pandoc-crossref --bibliography=reforg.bib --csl=ieee.csl -o mydocument.odt mydocument.org

But pandoc-crossref never  worked and I had also to  make png images for
tables.

The best  solution that I  found was to install  libreoffice-texmaths. I
just had  to enter "sudo  aptitude install libreoffice-texmaths"  via my
GNU/Linux Debian sid, but for other OS, the package is here

https://extensions.libreoffice.org/extensions/texmaths-1

and it works.

Of course the output is less pretty than the pdf via the tex life....

I hope that it will help other people.

Best wishes,

Jo.

PS: The publisher is in philosophy... 

Re: org-mode vs pandoc export

[CHARPENTIER Emmanuel]

1) I just checked: I was incorrect, Pythontex now has complete support
for R language. One can now use it for processing \LaTeX files
including Sage, R (and of course, Python) chunks.

2) Please, DO NOT include "images of a table" in a scientific document!
Lazy students pull this one on me in their manuscripts, and it's a
pain: you can't do a thing with such horrors, and you have to retype
manually these data if you want to work on them...

3) Did you try the route org-->LaTeX-->WhateverViaPandoc suggested by
John Kitchin ?

--
Emmanuel Charpentier

PS: I'm surprised that a philosophy journal does not accept \LaTeX
submissions: formal mathematics have been part of the philosophical
toolbox for a looooong while (since about 700 BC IIRC...).