From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Best practices for dual HTML/LaTeX export for scientific papers Date: Thu, 02 Apr 2015 11:38:24 -0400 Message-ID: References: <0D61CF76-2D92-4A9C-A90E-2F175BDDA91B@block-party.net> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41387) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YdhCT-0006e2-Hy for emacs-orgmode@gnu.org; Thu, 02 Apr 2015 11:38:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YdhCN-0005ab-Qj for emacs-orgmode@gnu.org; Thu, 02 Apr 2015 11:38:33 -0400 Received: from smtp.andrew.cmu.edu ([128.2.105.202]:37599) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YdhCN-0005aX-LP for emacs-orgmode@gnu.org; Thu, 02 Apr 2015 11:38:27 -0400 In-reply-to: <0D61CF76-2D92-4A9C-A90E-2F175BDDA91B@block-party.net> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: David Dynerman Cc: emacs-orgmode@gnu.org #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=E2=80=99m 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., =E2=80=9C= See Figure 1=E2=80=9D) > 4) LaTeX and HTML export > > This seems like a modest set of requirements, but I=E2=80=99ve had troubl= e getting it going. > > For #1, I=E2=80=99m currently using John Kitchin=E2=80=99s org-ref packag= e. This is nice - it gives me an HTML bibliography, but it has it=E2=80=99s= own link syntax for in-document links to figures that doesn=E2=80=99t expo= rt to HTML. Thus I have to use org-ref style links for citations, but regul= ar org-style links for figure cross references. > > I haven=E2=80=99t figured out how to do #2. Is this currently possible? I= s it an issue of adding some functionality to the HTML exporter? > > For #3, I=E2=80=99m currently using #+LABEL: fig:foo, followed by [[fig:f= oo]]. 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 =E2=80=9CBest practices=E2=80=9D for the above? I= =E2=80=99d be willing to collect these into a list, which I think would be = really helpful for new users. I=E2=80=99d also be willing to look into addi= ng this functionality, if someone could suggest a good way for it to fit in= to the codebase/framework. > > Thank you, > David -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu