Ben Feldman | 1 Jul 15:14 2016
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Custom source block for concept map markdown

Hi,

my goal is to create a custom source block to create concept maps. The source block contains
my custom made pseudo code. When exporting the org-file to LaTeX and PDF this pseudo code
must be translated to DOT code. This DOT code is interpreted by the dot2texi package.

The reason for the pseudo code is that it is more easy human readable. The reason for dot2texi is
that vanilla DOT does not allow for labels on edges, i.e. labels that cross the edge.

Here is an example of a concept map:

https://upload.wikimedia.org/wikipedia/commons/c/c3/Electricity_Concept_Map.gif

This is an example of my pseudo code for a single connection between two concepts
and a label for that connection:

(Electricity) {is a form of} (Energy)

As you see it looks like a sentence.

The DOT code for this would look like this:

"Electricity" -> "Energy" [label="is a form of"];

Clearly, this doesn’t look like a proper sentence. Therefore I concocted the following
function that takes a region containing my pseudo code and translates it to DOT code:

(defun concept2dot (rStart rEnd)
  (interactive "r")
  (save-restriction
(Continue reading)

John Kitchin | 1 Jul 13:57 2016
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patch for custom help-echo on links

I have attached a patch to allow org-link-display-parameters (introduced
in a previous patch for custom faces) to also provide a custom tooltip.
It can be a string or a function, and if neither the old behavior is
used.

WDYT?

--

-- 
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
 <at> johnkitchin
http://kitchingroup.cheme.cmu.edu
Attachment (custom-help-echo.patch): text/x-patch, 3105 bytes
Vladimir Alexiev | 1 Jul 12:46 2016
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Meaningful & stable anchors in HTML export

Consider e.g. http://vladimiralexiev.github.io/Multisensor/#sec-3-2-2, which
uses an anchor made from the section number.
I much prefer a readable/meaningful anchor like github does:
https://github.com/VladimirAlexiev/VladimirAlexiev.github.io/tree/master/Mul
tisensor#322-normalization-problems 
Numbered anchors are bad because they are not stable: if I move the section,
the anchor will change. 

Github makes anchors from the heading text, which in my experience are a lot
more stable.
In the above case it added the section number since I have
    #+OPTIONS: num:t
in
https://raw.githubusercontent.com/VladimirAlexiev/VladimirAlexiev.github.io/
master/Multisensor/index.org.
But I'm willing to give up section numbering in favor of stable anchors.

In the HTML exporter (ox-html.el) version org-plus-contrib-20150803, the
following are tried in succession to obtain a preferred-id:

              (list (org-element-property :CUSTOM_ID headline)
                (concat "sec-" section-number)
                (org-element-property :ID headline))))

The first is manually set CUSTOM_ID property, the second a numbered secton
(eg "sec-3-2-2") and the third an ID that's automatically inserted by
org-store-link.

The newest ox-html.el
(http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=lisp/ox-html.el;hb=HEAD
(Continue reading)

Sharon Kimble | 1 Jul 11:47 2016

more than 2 indexes in org-mode -> latex


How many indexes can you have in an org-mode document exported to latex?
My experience shows 2! So how can I have 3, or more please?

This is the relevant part, I think, of my preamble of my file -

--8<---------------cut here---------------start------------->8---
#+latex_header: \usepackage{imakeidx}
#+latex_header: \makeindex[title=Index,options=-s ./index.ist,columnseprule,intoc]
#+latex_header: \makeindex[name=ps,title=Index of Symptoms,options=-s ./index.ist,columnseprule,intoc]
# #+latex_header: \makeindex[name=se,title=Index of Side-effects,options=-s ./index.ist,columnseprule,intoc]
--8<---------------cut here---------------end--------------->8---

I can have any choice of 2, but not 3 as I would like.

In a 'straight' latex file using the above commands I can have 3 or
more, so how do I get it to allow 3 or more in org-mode please?

Thanks
Sharon.
--

-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.4, fluxbox 1.3.7, emacs 25.0.95
Mark Edgington | 30 Jun 21:06 2016
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Blank lines in LaTeX output due to org-mode comments

Assume we have the following sample org-mode document:

* Test Heading
test test test test test test test
test test test test test test test
test test test test test test test
# HERE IS A COMMENT
TEST TEST TEST TEST TEST TEST TEST
TEST TEST TEST TEST TEST TEST TEST
TEST TEST TEST TEST TEST TEST TEST

I would assume that in org-mode the comment line would be completely
ignored when exporting the document, however this seems not to be the
case -- notice the difference when exporting the following to LaTeX:

* Test Heading
test test test test test test test
test test test test test test test
test test test test test test test
TEST TEST TEST TEST TEST TEST TEST
TEST TEST TEST TEST TEST TEST TEST
TEST TEST TEST TEST TEST TEST TEST

In the first example, there is a blank line inserted at the location
of the comment, and in the second example, obviously there is not a
blank line at this location.  Let me know if there's a way to make it
so that org-mode doesn't insert the blank line.  Thanks!

John Kitchin | 30 Jun 19:56 2016
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colored-links take 2

I forgot a little piece in the last patch. This one is probably right.
It is based off of https://github.com/jkitchin/org-mode/blob/colored-link-3.

Attachment (colored-link.patch): text/x-patch, 3088 bytes

--

-- 
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
 <at> johnkitchin
http://kitchingroup.cheme.cmu.edu
Mark Edgington | 30 Jun 16:53 2016
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Need to update documentation to reflect export block syntax

I recently updated my org-mode git repository (for a long time I've
had an older git version that I was using), and I am now having
problems when doing latex exports.

I bisected with git to find that the "problem" starts with this revision:

commit 54318add34f09ff39d3fd034a4c1a89f60fd8759
Author: Nicolas Goaziou <mail <at> nicolasgoaziou.fr>
Date:   Tue Feb 3 16:16:54 2015 +0100

    Change export block syntax

It seems that #+begin_latex is no longer supported, and that when
using it, it results in escaped latex comment symbols (e.g. \% in the
tex file instead of just %), as well as \begin{latex} and \end{latex}
in the exported code.

If it is no longer supported, then it is important that the org-mode
documentation be updated (see e.g.
http://orgmode.org/manual/Quoting-LaTeX-code.html ), since those using
the latest release will have trouble exporting using the old syntax.

Sharon Kimble | 30 Jun 14:42 2016

scaling graphics in org-mode exported to latex


I'm trying to get a 'list of figures' in an org-mode export to latex,
but I'm finding difficulties in inserting graphics in org-mode. My
graphic insert code is -

--8<---------------cut here---------------start------------->8---
#+CAPTION: Percutaneous endoscopic gastrostomy tube
#+ATTR_LaTeX: scale=0.2
[[./images/percutaneous-endoscopic-gas.jpg]]
--8<---------------cut here---------------end--------------->8---

The caption works, the graphics inserts works, but how do I scale it please?

I've googled it and tried various solutions, but none are working, so
how do I do it please?

Thanks
Sharon.
--

-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.4, fluxbox 1.3.7, emacs 25.0.95
Michael Welle | 30 Jun 12:55 2016
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org-match-string-no-properties vs. match-string-[no-]properties

Hello,

org-compat.el has this line:

(define-obsolete-function-alias 'org-match-string-no-properties 'match-string-properties "Org 9.0")

Shouldn't it be match-string-no-properties?

Regards
hmw

Spencer Hill | 30 Jun 04:46 2016
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Feature request: enable toggling of \centering in Latex figure export

Hello,

First time contributor.  Emacs 24.5.1, Org mode 8.3.4.

MWE:
#+CAPTION: Figure caption.
[[file:figure01.pdf]]

Issue:
When an image is exported to LaTeX as a float, the \centering command is hard-coded into the export: see org-latex--inline-image in ox-latex.el.  This is not the case for tables, for which centering can be toggled via #+ATTR_LATEX: centering t.  I would like for this same centering option to be made available for figure floats also.

Motivation:
I am attempting to render a .tex file for an article submission to a journal, and the publisher requires the figures to be left-aligned.

It seems like a simple enough patch, but I have 0 elisp experience so wouldn't be the person for the job.  Or let me know if I'm missing something.  Thanks!

Best,
Spencer

Spencer Hill
spencerahill <at> gmail.com
(913) 515-8527

David Abernethy | 28 Jun 12:51 2016

citations not incoprporated from bib file when exporting from .org to pdflatex

I am exporting a file stroke.org using the bibliography file stroke.bib in the same directory
The citations are not being incorporated into the pdf file

An example from stroke.log: LaTeX Warning: Citation `Drummond:2014aa' on page 2 undefined on input line 71.

The header for stroke.org is:
#+LATEX_CLASS: article
#+BIBLIOGRAPHY: stroke vancouver option:-d

My emacs is from MacPorts  GNU Emacs 24.5.1 (x86_64-apple-darwin15.4.0, NS apple-appkit-1404.46)
 of 2016-05-01 on teneleven-slave.macports.org

My .emacs file contains
(setq org-latex-pdf-process '("latexmk -pdflatex='pdflatex -interaction nonstopmode' -pdf -bibtex -f %f"))

Org-mode version 8.3.4 (8.3.4-93-g0d72c3-elpaplus (I updated it as suggested here http://orgmode.org/elpa.html but it made no difference)
I’m using TexLive 2016 with fully up to date packages

Here is the preamble from stroke.tex (no mention of the .bib file)
% Created 2016-06-27 Mon 22:50
\documentclass[12pt]{article}
\usepackage[utf8]{inputenc}
..
\usepackage{wrapfig}
\author{David Abernethy}
\date{\today}
\title{}
\hypersetup{
pdfauthor={David Abernethy},
pdfcreator={Emacs 24.5.1 (Org mode 8.3.4)},..}
\begin{document}

My set up (Latex header in the .org file and .bib file with the .emacs entry) used to work for this file but I have probably updated emacs since.
Can anyone see what is wrong?  help much appreciated

David

Gmane