Re: Best practices for dual HTML/LaTeX export for scientific papers

[John Kitchin <jkitchin@andrew.cmu.edu>]

#1 org-ref does an ok job with this. It isn't as good at html output as
 for latex output (because latex has a dedicated citation processor via
 bib(la)tex, and org-ref has a hackery for generating mostly ok entries
 from the bibtex file, for the common types I have used.). For example,
 you often need to escape things like % and & in bibtex, and there is
 limited support for removing those in org-ref. Also, org-ref currently
 does not support latex in the bibtex entries for html output. There is
 potential for this by replacing fragments with images, but I probably
 won't look into that until the summer. The output style is
 user-customizable, but currently somewhat limited. I may look into
 improving this over the summer to make it more flexible.

Cannot comment on #2. I solve this by manually by putting both figures
in a single image file, and using a single caption with a) and b) in the
caption text.

#3 I just pushed a small enhancement to org-ref that makes the ref links
point to a #id in the html document. this works for figures at least. It
will take some post processing to change the link from the label to a
number, and maybe a custom exporter to do that. A temporary solution is to
label your figures with numbers, e.g. #+LABEL: fig:1. It isn't pretty,
but it would be functional.

David Dynerman writes:

> Hi all,
>
> I’m currently trying to use org mode to write a scientific paper. Here is my wishlist:
>
> 1) Citations to an external bibliography
> 2) Figures containing multiple side-by-side figures with subcaptions (e.g. in LaTeX I would use minipage + subcaption)
> 3) In-document links (i.e., cross references) to figures (e.g., “See Figure 1”)
> 4) LaTeX and HTML export
>
> This seems like a modest set of requirements, but I’ve had trouble getting it going.
>
> For #1, I’m currently using John Kitchin’s org-ref package. This is nice - it gives me an HTML bibliography, but it has it’s own link syntax for in-document links to figures that doesn’t export to HTML. Thus I have to use org-ref style links for citations, but regular org-style links for figure cross references.
>
> I haven’t figured out how to do #2. Is this currently possible? Is it an issue of adding some functionality to the HTML exporter?
>
> For #3, I’m currently using #+LABEL: fig:foo, followed by [[fig:foo]]. Is this the suggested way of doing it?
>
> The hard part seems #4: org-ref gives a workable HTML bibliography, but I run into some other issues listed above.
>
> Can anyone suggest some “Best practices” for the above? I’d be willing to collect these into a list, which I think would be really helpful for new users. I’d also be willing to look into adding this functionality, if someone could suggest a good way for it to fit into the codebase/framework.
>
> Thank you,
> David

--
Professor John Kitchin
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