From mboxrd@z Thu Jan 1 00:00:00 1970 From: Emmanuel Charpentier Subject: Re: org-mode vs pandoc export Date: Fri, 27 Sep 2019 07:13:27 +0200 Message-ID: <966cb1982dd484f5b1cf813ff3bc82e22a51627c.camel@free.fr> Mime-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:41312) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iDiZV-0006tF-Bh for emacs-orgmode@gnu.org; Fri, 27 Sep 2019 01:13:38 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iDiZT-0004Me-6K for emacs-orgmode@gnu.org; Fri, 27 Sep 2019 01:13:37 -0400 Received: from smtp1-g21.free.fr ([212.27.42.1]:1128) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1iDiZS-0004Jp-Uj for emacs-orgmode@gnu.org; Fri, 27 Sep 2019 01:13:35 -0400 In-Reply-To: CAD-VTcHvr6thPe+9FSCfC94s-8j8F7rSXyvxiZbo9cyaarZCLg@mail.gmail.com 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" To: joseph.vidal.rosset@gmail.com, emacs-orgmode 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