[O] getting a tilde into LaTeX export

2011-11-11 Thread Eric Abrahamsen
I'm sure this has been answered many times but I can't find it…

I want to get a tilde into my LaTeX export -- not a LaTeX-escaped tilde,
but a plain tilde, that will turn into a small non-breaking space in
LaTeX. Everything I've tried in org exports as either \~ or \~{} in
LaTeX, where all I want is plain ~. Can someone help me out?

Thanks,
Eric

-- 
GNU Emacs 24.0.91.1 (i686-pc-linux-gnu, GTK+ Version 2.24.6)
 of 2011-11-07 on pellet
Org-mode version 7.7 (release_7.7.521.gf380d.dirty)




Re: [O] getting a tilde into LaTeX export

2011-11-11 Thread suvayu ali
On Fri, Nov 11, 2011 at 11:46, Eric Abrahamsen e...@ericabrahamsen.net wrote:
 I'm sure this has been answered many times but I can't find it…

 I want to get a tilde into my LaTeX export -- not a LaTeX-escaped tilde,
 but a plain tilde, that will turn into a small non-breaking space in
 LaTeX. Everything I've tried in org exports as either \~ or \~{} in
 LaTeX, where all I want is plain ~. Can someone help me out?


Try \sim.

 Thanks,
 Eric



-- 
Suvayu

Open source is the future. It sets us free.



Re: [O] getting a tilde into LaTeX export

2011-11-11 Thread Lawrence Mitchell
Eric Abrahamsen wrote:
 I'm sure this has been answered many times but I can't find it…

 I want to get a tilde into my LaTeX export -- not a LaTeX-escaped tilde,
 but a plain tilde, that will turn into a small non-breaking space in
 LaTeX. Everything I've tried in org exports as either \~ or \~{} in
 LaTeX, where all I want is plain ~. Can someone help me out?

hello \nbsp goodbye

= hello ~ goodbye

Although I can't figure out a way of having no extra whitespace
on both sides of the ~.

Lawrence

-- 
Lawrence Mitchell we...@gmx.li




Re: [O] getting a tilde into LaTeX export

2011-11-11 Thread Carsten Dominik

On Nov 11, 2011, at 11:46 AM, Eric Abrahamsen wrote:

 I'm sure this has been answered many times but I can't find it…
 
 I want to get a tilde into my LaTeX export -- not a LaTeX-escaped tilde,
 but a plain tilde, that will turn into a small non-breaking space in
 LaTeX. Everything I've tried in org exports as either \~ or \~{} in
 LaTeX, where all I want is plain ~. Can someone help me out?

Erik\nbsp{}Abrahamsen

Cheers

- Carsten


Re: [O] getting a tilde into LaTeX export

2011-11-11 Thread Eric Abrahamsen
On Fri, Nov 11 2011, Carsten Dominik wrote:

 On Nov 11, 2011, at 11:46 AM, Eric Abrahamsen wrote:

 I'm sure this has been answered many times but I can't find it…
 
 I want to get a tilde into my LaTeX export -- not a LaTeX-escaped tilde,
 but a plain tilde, that will turn into a small non-breaking space in
 LaTeX. Everything I've tried in org exports as either \~ or \~{} in
 LaTeX, where all I want is plain ~. Can someone help me out?

 Erik\nbsp{}Abrahamsen

Thanks for all the quick answers! \nbsp{} did the trick perfectly.

-- 
GNU Emacs 24.0.91.1 (i686-pc-linux-gnu, GTK+ Version 2.24.6)
 of 2011-11-07 on pellet
Org-mode version 7.7 (release_7.7.521.gf380d.dirty)




Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Matt Price
On Wed, Nov 9, 2011 at 2:39 PM, Christian Moe m...@christianmoe.com wrote:

 Hi,

 Is zotero-plain working for others?

 I test drove zotero-plain back when it was just developed. Looked
 promising, but I had uneven success with the MozRepl communication,
 possibly something to do with being on an older and slower machine.

 Trying it again today (with the most recent zotero-plain, MozRepl and
 moz.el I could find), I press `C-c z i' to insert a citation and nothing
 happens. Well, the Org buffer hangs until I press C-g, and except that the
 *MozRepl* buffer says Process MozRepl deleted.

 Similar for me -- the Org buffer hangs, and MozRepl looks like it's just
been sitting there idly.

also on the most recent MozRepl, emacs 24, fairly recent org-mode, firefox
8, ubuntu 10.10.


Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Matt Price
Responding to just a few of the excellent points raised by J 7 E

On Thu, Nov 10, 2011 at 12:48 PM, Erik Hetzner e...@e6h.org wrote:

 At Thu, 10 Nov 2011 20:47:30 +0530,
 Jambunathan K wrote:
 
 
 I should note that while the org/zotero integration in zotero-plain
 “works for me”, I would welcome changes to make it more robust and
 feature-full. But I use org for notes and todo lists, not for document
 production.

I'm trying to switch to using org for most of my writing; among other
things, I now use it for posting to wordpress and (hopefully soon) drupal,
where most of my teaching work takes place. So I htink there's a case to
make for org as a person's main workspace.


  Instead of working with JS libraries, I think the right starting point
  would be to work with the underlying zotero.sqlite database itself. It
  is not difficult to get a key of the selected item in Zotero
  pane[3]. Once this is done the underlying zotero.sqlite database could
  be queried for the item properties[4].


Wouldn't the rigt target be, not the sqlite db, but the Zoteor *service*
that runs on port 50001 when Zotero is running?  Aren't there some
higher-level tools for working through that interface -- e.g., erik, your
rst tool uses a python library, does it talk to Zotero that way?


 
  Fortunately there is already a GUI/Command line tool - Gnotero[5] -for
  accessing the sqlite database.

 This would certainly work. However, one problem would be that gnotero
 cannot generate formatted citations from a reference, that is, it
 cannot use CSL [2] style rules to generate arbitrary citation
 formats. This might be fine; some simple c

  As for exploiting the power of using zotero within libreoffice - which
  is to have the same citation presented in different citation styles -
  one need to look at how the reference marks are produced within
  OpenDocument XML.

 Not only that, but how the LibreOffice plugin communicates with
 Zotero, specifically the citeproc-js [1] part of Zotero, to generate
 in-text citations, bibliographies, etc.


so, couldn't one think of the problem as having three parts:
(1) get emacs to talk to the zotero server; and
(2) figure out how org/emacs should interact with citeproc
(3) translate the org zotero links into a syntax that LibreOffice
recognizes and can successfully manipulate

and am I further right that, as an interim measure, solving (1) and (3)
properly and throwing together a quick hack for (2)  -- in which org
supports exactly one, very simple citation style -- would make a workflow
possible in which a person could compose in Org, and translate to ODT for
the final processing of a document, and/or export to HTML using only the
one citaqtion style that is supported by the aforementioned hack?

thanks again for all the help, folks,
matt


[O] BUG: Text in single quotes not recognized by markup

2011-11-11 Thread Viktor Rosenfeld
Hi,

the text ='t'= is not recognized as code. Other markup doesn't work
either. If the quotes are in the middle (e.g. =foo'bar=) it is properly
recognized.

I'm using org-mode 7.7 pulled today from git.

Cheers,
Viktor



Re: [O] regenerating agendas automatically if any .org files change

2011-11-11 Thread Stephen J. Barr
Okay, I will give custom agenda blocks a try. Thanks for the help. I
really appreciate it.

On Fri, Nov 11, 2011 at 2:01 AM, Viktor Rosenfeld
listuse...@googlemail.com wrote:
 Hi Stephen,

 AFAIK, there can only be one agenda view (an expert correct me, if I'm
 wrong). But you can multiple blocks in the agenda. Search for Office
 block agenda in:

 http://orgmode.org/worg/org-tutorials/org-custom-agenda-commands.html

 Cheers,
 Viktor

 Stephen J. Barr wrote:

 Excellent. Thanks for the pointer. So, just to clarify, is it possible
 to have multiple simultaneous agenda views? I think it would be really
 cool to have my calendar and to-do-list and maybe another custom
 agenda view all dynamically refreshed every few minutes, just sitting
 on my second monitor. Then, as I add appointments, tasks, etc., they
 all start showing up.

 How can I make this happen? My lisp skills still introductory. I can
 modify lisp code, but I haven't really written my own from scratch
 yet.

 -stephen

 On Thu, Nov 10, 2011 at 7:09 PM, suvayu ali fatkasuvayu+li...@gmail.com 
 wrote:
  Hello Stephen,
 
  Welcome to the list. Hope you have fun using org-mode. :)
 
  On Fri, Nov 11, 2011 at 00:54, Stephen J. Barr stephenjb...@gmail.com 
  wrote:
  I would like B to simply regenerate 3 different agenda views
  whenever the .org files on Dropbox change.
 
  This is documented on our git based community wiki.
  http://orgmode.org/worg/org-hacks.html#sec-1-8-11
 
  --
  Suvayu
 
  Open source is the future. It sets us free.
 






Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Erik Hetzner
At Fri, 11 Nov 2011 10:51:22 -0500,
Matt Price wrote:
 
 Responding to just a few of the excellent points raised by J 7 E

 On Thu, Nov 10, 2011 at 12:48 PM, Erik Hetzner e...@e6h.org wrote:
 
  At Thu, 10 Nov 2011 20:47:30 +0530,
  Jambunathan K wrote:
  
  
  I should note that while the org/zotero integration in zotero-plain
  “works for me”, I would welcome changes to make it more robust and
  feature-full. But I use org for notes and todo lists, not for document
  production.

This is me you are quoting, for the record.

 I'm trying to switch to using org for most of my writing; among other
 things, I now use it for posting to wordpress and (hopefully soon) drupal,
 where most of my teaching work takes place. So I htink there's a case to
 make for org as a person's main workspace.

Definitely! Whatever works for you. I prefer the reStructuredText
syntax for longer documents, so getting real citations working in
org-mode is not a real priority for me. That’s all.

 Wouldn't the rigt target be, not the sqlite db, but the Zoteor *service*
 that runs on port 50001 when Zotero is running?  Aren't there some
 higher-level tools for working through that interface -- e.g., erik, your
 rst tool uses a python library, does it talk to Zotero that way?

the server that runs on port 50001 is undocumented, last I
checked. And there are no tools to connect to it. Frank Bennett put
together a hack of the jsbridge Firefox extension which works quite
well. [1] But that is python only, as far as I can tell.

 […]
 
 so, couldn't one think of the problem as having three parts:
 (1) get emacs to talk to the zotero server; and
 (2) figure out how org/emacs should interact with citeproc
 (3) translate the org zotero links into a syntax that LibreOffice
 recognizes and can successfully manipulate

I think that is a good summary of what needs to be done. (3) is what
zot4rst does not bother to do.

The task of weaving together the HTML output from citeproc and your
export document can be tricky.

 and am I further right that, as an interim measure, solving (1) and (3)
 properly and throwing together a quick hack for (2)  -- in which org
 supports exactly one, very simple citation style -- would make a workflow
 possible in which a person could compose in Org, and translate to ODT for
 the final processing of a document, and/or export to HTML using only the
 one citaqtion style that is supported by the aforementioned hack?

 […]

Yeah, that makes sense. I think (3) is optional as well, depending on
what your workflow looks like, and what your needs are for doing final edits.

best, Erik

1. https://github.com/mozautomation/mozmill
Sent from my free software system http://fsf.org/.


Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Erik Hetzner
At Fri, 11 Nov 2011 10:37:03 -0500,
Matt Price wrote:
 
 Similar for me -- the Org buffer hangs, and MozRepl looks like it's
 just been sitting there idly.
 
 also on the most recent MozRepl, emacs 24, fairly recent org-mode, firefox
 8, ubuntu 10.10.

I was going to suggest this sounds like a problem with Emacs 24, but I
installed Emacs 24  it works for me. I am using Firefox 7, but I
doubt that is much of an issue.

I assume that you have started MozRepl and selected an item to insert
in Zotero?

best, Erik

Sent from my free software system http://fsf.org/.


Re: [O] Property inheritance in beamer export [7.4]

2011-11-11 Thread Carsten Dominik
Hi Chris,

On 11.11.2011, at 05:34, Chris Kauffman wrote:

 
 I use org for constructing simple slide presentations quite a
 bit.  I'd like to be able to set a global property which shrinks
 all text to fit in the allotted space; this is great for source
 examples.

Have you read the beamer documentation?  After reading about
shrink, do you still mean to apply this evil thing?   :)

 After some experimentation I put
 
 #+PROPERTY: BEAMER_envargs [shrink]
 
 in the preamble and evaluated
 
 (set-variable (quote org-use-property-inheritance) t nil)
 
 According to my understanding of the documentation, this should
 make very outline entry inherit the property BEAMER_envargs,
 regardless of whether it has a properties list itself.

Yes, I agree this is what the documentation looks like.  However, the
imlementation of org-beamer.el only looks at the local properties.
TO speed up processing, Org grabs all properties at each headline
and stores them - without inheritance.

 After
 reloading the file, internally this seems to work fine: I move to
 any heading and eval the following lisp
 
 (org-entry-get (point) BEAMER_envargs 1)
 
 which gives the result [shrink].
 
 However, on exporting the org file to pdf, the shrinking does not
 seem to happen. The source code runs off the page. Is property
 inheritance not respected during export?

Could you please set in .emacs

(setq org-beamer-inherited-properties '(BEAMER_envargs))

and then try the following experimental patch

-
diff --git a/lisp/org-beamer.el b/lisp/org-beamer.el
index 118aa75..2208c60 100644
--- a/lisp/org-beamer.el
+++ b/lisp/org-beamer.el
@@ -482,4 +482,10 @@ The effect is that these values will be accessible during 
export.
(looking-at .*?:B_\\(note\\(NH\\)?\\):))
   (push (cons BEAMER_env (match-string 1)) props))
+  (when (org-bound-and-true-p org-beamer-inherited-properties)
+(mapc (lambda (p)
+(unless (assoc p props)
+  (let ((v (org-entry-get nil p 'inherit)))
+(and v (push (cons p v) props)   
+  org-beamer-inherited-properties))
   (put-text-property (point-at-bol) (point-at-eol) 'org-props props)))
   (setq org-export-latex-options-plist
-

- Carsten

 
 Cheers,
 Chris
 
 --Example .org File---
 #+TITLE: Java Lecture
 #+AUTHOR:Christopher Kauffman
 #+EMAIL: kauffma...@gmail.com
 #+LANGUAGE:  en
 #+OPTIONS:   H:3 num:t toc:nil \n:nil @:t ::t |:t ^:t -:t f:t *:t :t
 #+OPTIONS:   TeX:t LaTeX:nil skip:nil d:nil todo:t pri:nil tags:not-in-toc
 #+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 
 path:http://orgmode.org/org-info.js
 #+EXPORT_SELECT_TAGS: export
 #+EXPORT_EXCLUDE_TAGS: noexport
 #+STARTUP: beamer
 #+STARTUP: showall
 #+LaTeX_CLASS: beamer
 #+BEAMER_FRAME_LEVEL: 1
 #+PROPERTY: BEAMER_envargs [shrink]
 
 * Example
 Want this shrink
 #+BEGIN_SRC java
 public class Mouse{
   private int age = 0;  // age of mouse in days
   private double weight = 1.0;  // weight of mouse in grams
   private double percentGrowthRate; // % weight increase per day
 
   // This method assigns the mouse's percent growth rate.
   public void setPercentGrowthRate(double percentGrowthRate) {
 this.percentGrowthRate = percentGrowthRate;
   }
 
   // This method simulates one day of growth for the mouse.
   public void grow() {
 this.weight += (.01 * this.percentGrowthRate * this.weight);
 this.age++;
   }
 
   // This method prints the mouses's age and weight.
   public void display() {
 System.out.printf(
   Age = %d, weight = %.3f\n, this.age, this.weight);
   }
 } 
 #+END_SRC
 
 * Example
 :PROPERTIES:
 :BEAMER_envargs: [shrink]
 :END:
 
 Must add properties every time
 #+BEGIN_SRC java
 public class Mouse{
   private int age = 0;  // age of mouse in days
   private double weight = 1.0;  // weight of mouse in grams
   private double percentGrowthRate; // % weight increase per day
 
   // This method assigns the mouse's percent growth rate.
   public void setPercentGrowthRate(double percentGrowthRate) {
 this.percentGrowthRate = percentGrowthRate;
   }
 
   // This method simulates one day of growth for the mouse.
   public void grow() {
 this.weight += (.01 * this.percentGrowthRate * this.weight);
 this.age++;
   }
 
   // This method prints the mouses's age and weight.
   public void display() {
 System.out.printf(
   Age = %d, weight = %.3f\n, this.age, this.weight);
   }
 } 
 #+END_SRC
 
 --END EXAMPLE-
 
 current state:
 ==
 (setq org-export-latex-after-initial-vars-hook
 '(org-beamer-after-initial-vars) org-speed-command-hook
 '(org-speed-command-default-hook org-babel-speed-command-hook)
 org-agenda-files 

[O] Global Task List

2011-11-11 Thread Cameron Seader

Greetings,
Did I miss something in the Docs?

I have lots of .org files with tasks in each one, but my global task 
list does not show anything. Is there something I need to do to set this up?


Thanks,
--
Cameron



Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Matt Price
On Fri, Nov 11, 2011 at 12:51 PM, Erik Hetzner e...@e6h.org wrote:

 At Fri, 11 Nov 2011 10:37:03 -0500,
 Matt Price wrote:
 
  Similar for me -- the Org buffer hangs, and MozRepl looks like it's
  just been sitting there idly.
 
  also on the most recent MozRepl, emacs 24, fairly recent org-mode,
 firefox
  8, ubuntu 10.10.

 I was going to suggest this sounds like a problem with Emacs 24, but I
 installed Emacs 24  it works for me. I am using Firefox 7, but I
 doubt that is much of an issue.

 I assume that you have started MozRepl and selected an item to insert
 in Zotero?

 best, Erik


yes, I had done those two things (htough not hte first time round!).  If
MozRepl isn't started I get a diferent, quite helpful error message; in
this case there is just (as for Christian) a message Process MozRepl
deleted which shows up before I press C-g to end the hang.  I imagine htis
is a bug in MozRepl


Re: [O] Global Task List

2011-11-11 Thread Olivier Schwander
Le 11 Nov 2011 11:19, Cameron Seader a écrit:
 I have lots of .org files with tasks in each one, but my global task
 list does not show anything. Is there something I need to do to set
 this up?

You should have a look to the variable org-agenda-files (see 
http://orgmode.org/org.html#Agenda-files).

Olivier




Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Matt Price
On Fri, Nov 11, 2011 at 11:12 AM, Erik Hetzner e...@e6h.org wrote:

 At Fri, 11 Nov 2011 10:51:22 -0500,
 Matt Price wrote:
 
  Responding to just a few of the excellent points raised by J 7 E
 
  On Thu, Nov 10, 2011 at 12:48 PM, Erik Hetzner e...@e6h.org wrote:
 
   At Thu, 10 Nov 2011 20:47:30 +0530,
   Jambunathan K wrote:
   
   
   I should note that while the org/zotero integration in zotero-plain
   “works for me”, I would welcome changes to make it more robust and
   feature-full. But I use org for notes and todo lists, not for document
   production.

 This is me you are quoting, for the record.

 yes sorry, bad formatting on my part!


  Wouldn't the rigt target be, not the sqlite db, but the Zoteor *service*
  that runs on port 50001 when Zotero is running?  Aren't there some
  higher-level tools for working through that interface -- e.g., erik, your
  rst tool uses a python library, does it talk to Zotero that way?

 the server that runs on port 50001 is undocumented, last I
 checked. And there are no tools to connect to it. Frank Bennett put
 together a hack of the jsbridge Firefox extension which works quite
 well. [1] But that is python only, as far as I can tell.


sorry to hear about the lack of documentation.  that's a bummer actually.


  […]
 
  so, couldn't one think of the problem as having three parts:
  (1) get emacs to talk to the zotero server; and
  (2) figure out how org/emacs should interact with citeproc
  (3) translate the org zotero links into a syntax that LibreOffice
  recognizes and can successfully manipulate

 I think that is a good summary of what needs to be done. (3) is what
 zot4rst does not bother to do.

 The task of weaving together the HTML output from citeproc and your
 export document can be tricky.

if tricky for you, then likely unmanageable for me.   but I wonder if
Zotero themselves would be interested in helping a little bit with some of
this work?  Seems sort of strange to build this great tool and then limit
its usefulness to two hulking word processors, when really the goal of
portable, reformattable citations applies just as much to text and html as
to word processing documents.

best,
matt


Re: [O] Global Task List

2011-11-11 Thread Cameron Seader

I get an error when setting the variable to a folder

Here is my .emacs file

;; Org-mode settings
(require 'org-install)
(add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
(global-set-key \C-cl 'org-store-link)
(global-set-key \C-ca 'org-agenda)
(global-set-key \C-cb 'org-iswitchb)
(global-font-lock-mode 1)
(setq org-log-done t)
(setq org-agenda-custom-commands
((org-agenda-files '(~/Documents/Notes/org/))
))

(setq inhibit-splash-screen t)

I get the following error when my .emacs file is initialized.

Invalid function: (org-agenda-files (quote (~/Documents/Notes/org/)))

any ideas
TIA,

On 11/11/2011 11:36 AM, Olivier Schwander wrote:

Le 11 Nov 2011 11:19, Cameron Seader a écrit:

I have lots of .org files with tasks in each one, but my global task
list does not show anything. Is there something I need to do to set
this up?


You should have a look to the variable org-agenda-files 
(seehttp://orgmode.org/org.html#Agenda-files).

Olivier





--
Cameron



[O] Bug: Cannot include orgmode source code block [7.7]

2011-11-11 Thread Truong Nghiem
Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

 http://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org-mode mailing list.


I created a following simple org file, in which a source code block of
language org contains orgmode code:
=== BEGIN CODE 
#+TITLE: A Test

#+BEGIN_SRC org
  ,#+begin_src python
#+END_SRC

End of test.
=== END CODE ==

However, when I exported this file, either to HTML or LaTeX/PDF, it
caused an error:

ad-Orig-error: unbalanced begin/end_src blocks with #(#+BEGIN_SRC org
  ,#+begin_src python
#+END_SRC 0 15 (fontified nil font-lock-fontified t) 15 16 (fontified
  nil font-lock-fontified t) 16 37 (fontified nil font-lock-fontified t)
  37 38 (fontified nil font-lock-fontified t) 38 47 (fontified nil
  font-lock-fontified t))

I'm using the latest development version of orgmode.  Also, if I
recall correctly, I did succeed to export this kind of code in the
past (don't remember which version of orgmode though).

If I included #+end_src in the body of the org code block, it would export
the file, but the result was not what I expected: it was blank.


Emacs  : GNU Emacs 23.3.50.1 (i386-apple-darwin9.8.0, NS
apple-appkit-949.54)
 of 2011-10-25 on braeburn.aquamacs.org - Aquamacs Distribution 2.4
Package: Org-mode version 7.7

current state:
==
(setq
 org-clock-in-switch-to-state STARTED
 org-agenda-skip-scheduled-if-deadline-is-shown t
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-todo-keyword-faces '((STARTED :foreground blue :weight bold)
  (NEXT :foreground magenta :weight bold))
 org-speed-command-hook '(org-speed-command-default-hook
  org-babel-speed-command-hook)
 org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
 org-babel-load-languages '((R) (ditaa . t) (dot . t) (emacs-lisp . t)
(gnuplot . t)
(haskell) (latex . t) (matlab . t) (ocaml) (org . t)
(python . t) (ruby) (screen) (sh . t) (sql) (sqlite))
 org-agenda-exporter-settings '((ps-number-of-columns 1) (ps-landscape-mode
t)
(htmlize-output-type (quote css)))
 org-completion-use-ido t
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-agenda-skip-timestamp-if-done t
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-babel-tangle-lang-exts '((python . py) (latex . tex)
  (emacs-lisp . el))
 org-agenda-todo-ignore-scheduled t
 org-agenda-sorting-strategy '((agenda habit-down time-up priority-down
effort-up
category-keep)
   (todo priority-down effort-up category-keep)
   (tags priority-down category-keep)
   (search category-keep))
 org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
 org-agenda-restore-windows-after-quit t
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-agenda-skip-scheduled-if-done t
 org-stuck-projects '(+LEVEL=2+TODO=\PROJECT\ (TODO NEXT) nil )
 org-support-shift-select t
 org-tab-first-hook '(org-hide-block-toggle-maybe
org-src-native-tab-command-maybe
  org-babel-hide-result-toggle-maybe)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
 org-src-mode-configure-edit-buffer)
 org-confirm-shell-link-function 'yes-or-no-p
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-archive-stamp-time nil
 org-todo-keywords '((sequence TODO(t) NEXT(n) STARTED(s) |
DONE(d!/!))
 (sequence WAITING(w@/!) | CANCELLED(c@/!)
  DEFERRED(r@/!))
 (sequence PROJECT(p) | FINISHED(f!/!)))
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-default-notes-file ~/gtd/gtd.org
 org-directory ~/gtd
 org-blank-before-new-entry nil
 org-babel-pre-tangle-hook '(save-buffer)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
  org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers)
 org-mode-hook '(#[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook org-show-block-all append
local]
   5]
 #[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook org-babel-show-result-all
append local]
   5]
 org-babel-result-hide-spec org-babel-hide-all-hashes
 (lambda nil (auto-fill-mode 1)))
 org-refile-targets '((org-agenda-files :maxlevel . 3) (nil :maxlevel . 3)
  (~/gtd/someday.org :level . 0))
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-refile-use-outline-path 'file
 org-agenda-mode-hook '((lambda nil (hl-line-mode 1)))
 org-agenda-todo-ignore-with-date t
 org-export-interblocks '((lob org-babel-exp-lob-one-liners)
  (src org-babel-exp-inline-src-blocks))
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-enforce-todo-dependencies t
 

Re: [O] How to link to a fragment (aka anchor/bookmark) of a local file (e.g. a TiddlyWiki)?

2011-11-11 Thread Christoph LANGE

Hi Samuel,

2011-11-09 19:03 Samuel Wales:

If you search for ID markers in the ML archives, you will find a
proposal by me that provides mechanism for this that is non-brittle.


thanks for this pointer.  This is definitely helpful and interesting 
information for me – when working _within_ org-mode.  I am actually a 
semantic web researcher and thus highly interested in giving everything 
an ID that can be linked to – not just for my research, but, of course, 
also for my personal knowledge management.


But my question in this thread was a different one: linking to fragments 
of _external_ files, most commonly HTML files that I'd like to open 
outside of Emacs in a browser.


Cheers,

Christoph

--
Christoph Lange, http://www.facebook.com/ch.lange, Skype duke4701



Re: [O] Global Task List

2011-11-11 Thread Olivier Schwander
Le 11 Nov 2011 12:17, Cameron Seader a écrit:
 I get an error when setting the variable to a folder
 (setq org-agenda-custom-commands
 ((org-agenda-files '(~/Documents/Notes/org/))
 ))

You are not supposed to set it to a folder. I use something like:

(setq org-agenda-files (file-expand-wildcards ~/Notes/*.org))

Olivier



Re: [O] Global Task List

2011-11-11 Thread Olaf Dietsche
Cameron Seader c...@suse.com writes:

 I get an error when setting the variable to a folder

 Here is my .emacs file

 ;; Org-mode settings
 (require 'org-install)
 (add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
 (global-set-key \C-cl 'org-store-link)
 (global-set-key \C-ca 'org-agenda)
 (global-set-key \C-cb 'org-iswitchb)
 (global-font-lock-mode 1)
 (setq org-log-done t)
 (setq org-agenda-custom-commands
 ((org-agenda-files '(~/Documents/Notes/org/))
 ))

 (setq inhibit-splash-screen t)

 I get the following error when my .emacs file is initialized.

 Invalid function: (org-agenda-files (quote (~/Documents/Notes/org/)))

you mixed org-agenda-custom-commands and org-agenda-files. You can set
org-agenda-files as part of org-agenda-custom-commands, but then you
have to define at least one private command as well.

An easier way to start is just setting org-agenda-files alone.
Either with `setq':

(setq org-agenda-files ~/Documents/Notes/org/)

or with `custom-set-variables':

(custom-set-variables
 '(org-agenda-files ~/Documents/Notes/org/))

Regards, Olaf



Re: [O] Global Task List

2011-11-11 Thread Cameron Seader

Perfect.

On 11/11/2011 01:24 PM, Olaf Dietsche wrote:

Cameron Seaderc...@suse.com  writes:


I get an error when setting the variable to a folder

Here is my .emacs file

;; Org-mode settings
(require 'org-install)
(add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
(global-set-key \C-cl 'org-store-link)
(global-set-key \C-ca 'org-agenda)
(global-set-key \C-cb 'org-iswitchb)
(global-font-lock-mode 1)
(setq org-log-done t)
(setq org-agenda-custom-commands
 ((org-agenda-files '(~/Documents/Notes/org/))
 ))

(setq inhibit-splash-screen t)

I get the following error when my .emacs file is initialized.

Invalid function: (org-agenda-files (quote (~/Documents/Notes/org/)))


you mixed org-agenda-custom-commands and org-agenda-files. You can set
org-agenda-files as part of org-agenda-custom-commands, but then you
have to define at least one private command as well.

An easier way to start is just setting org-agenda-files alone.
Either with `setq':

(setq org-agenda-files ~/Documents/Notes/org/)

or with `custom-set-variables':

(custom-set-variables
  '(org-agenda-files ~/Documents/Notes/org/))

Regards, Olaf




Olivier Schwander's suggestion worked best.

I used this below:
(setq org-agenda-files (file-expand-wildcards ~/Notes/*.org))

works like a charm. Love it.
Thanks,
--
Cameron



Re: [O] How to link to a fragment (aka anchor/bookmark) of a local file (e.g. a TiddlyWiki)?

2011-11-11 Thread Samuel Wales
Hi Christoph,

Really?

Very strange.

I thought I had explained pretty clearly in the proposals that ID
markers can be put in comments in the /external/ files.

If you look up file link search, you will see that it is breakable by
corrupting the thing searched for.

Org IDs in external files -- which I propose to be in ID markers --
are as unbreakable as you can arrange in a practical way.

In any case, it is just a proposal, so if it doesn't work for you, no
need to use it.

Samuel

On 2011-11-11, Christoph LANGE ch.la...@jacobs-university.de wrote:
 Hi Samuel,

 2011-11-09 19:03 Samuel Wales:
 If you search for ID markers in the ML archives, you will find a
 proposal by me that provides mechanism for this that is non-brittle.

 thanks for this pointer.  This is definitely helpful and interesting
 information for me – when working _within_ org-mode.  I am actually a
 semantic web researcher and thus highly interested in giving everything
 an ID that can be linked to – not just for my research, but, of course,
 also for my personal knowledge management.

 But my question in this thread was a different one: linking to fragments
 of _external_ files, most commonly HTML files that I'd like to open
 outside of Emacs in a browser.

 Cheers,

 Christoph

 --
 Christoph Lange, http://www.facebook.com/ch.lange, Skype duke4701



-- 
The Kafka Pandemic: http://thekafkapandemic.blogspot.com
===
Bigotry against people with serious diseases is still bigotry.



Re: [O] Global Task List

2011-11-11 Thread Nick Dokos
Cameron Seader c...@suse.com wrote:


 (setq org-agenda-custom-commands
 ((org-agenda-files '(~/Documents/Notes/org/))
 ))
 

 I get the following error when my .emacs file is initialized.
 
 Invalid function: (org-agenda-files (quote (~/Documents/Notes/org/)))
 

Bad syntax: to set the variable, say

(setq org-agenda-files '(~/Documents/Notes/org))

This has nothing to do with org-agenda-custom-commands. If you want
to set the latter to something, do it separately.

Nick



[O] zotero-cite (A Proposal)

2011-11-11 Thread Jambunathan K

Hello Erik

Good news. 

Getting a frugal Zotero-based citations is *definitely* possible. It is
just a matter of time. Your libraries already provide the necessary
plumbing to accomplish the job. 

Long story
==

For my own understanding, I tried trimming down zot4rst to it's bare
essentials and the attached zotcite.py is the result.

What zotcite does is this: 

For two Zotero Items, it prints their Bibliogrpahic entries and their
Citation Reference, in Text format using Chicago-Author-Date style.

I believe a commandline interface could be built around this file along
the following lines. (Will you be interested in building this interface
for us?)

$ zotcite --style chicago --format text --items I1, I2 --print biblio
$ zotcite --style chicago --format text --items I1, I2 --print citeref

Once this is done, Emacs/Org can do invoke zotcite and get the required
Bibliographic definitions and references using shell-command.

The assumption is that Emacs/Org somehow has captured zotero keys
through org-protocol or org-zotero.el or someother means.

Here is a output from zotcite.py.

--8---cut here---start-8---
$ python zotcite.py
C.UTF-8
C.UTF-8
 KEYS 
I4AUIZ4S
AKJZBHRW
 ITEM_IDs 
[6, 40]
 BIBDATA 
[u'Brin, S. 1999. \u201cExtracting patterns and relations from the world wide 
web.\u201d The World Wide Web and Databases: 172\u2013183.\n', u'Jambunathan, 
K. On Choice of Connection-Polynomials for LFSR-Based Stream Ciphers. In 
Progress in Cryptology \u2014INDOCRYPT 2000, ed. Bimal Roy and Eiji Okamoto, 
1977:9-18. Berlin, Heidelberg: Springer Berlin Heidelberg. 
http://www.springerlink.com/content/n27yjr5eqhabux0g/.\n']
= CITATION REFERENCE = 
(This Brin 1999 That)
--8---cut here---end---8---

IIRC, I made two changes to the export.js in your Javascript backend.

1. I had trouble understanding the organization of citation clusters. So
   I modified getCitationBlock as below. Note the use of true as a
   second param of the appendCitationCluster. This is OK as
   registerItemIds already does updateItems().

--8---cut here---start-8---
function getCitationBlock (citation) {
var results;
var str = ;
try {
results = zotero.reStructuredCSL.appendCitationCluster(citation, true);
} catch (e) {
zotero.debug(XXX  oops: +e);
}
// var index = citation['properties']['index'];
// for (var i = 0 ; i = results.length ; i++) {
// // if (results[i][0] == index) {
// return escape(str + results[i][1]);
// // }
// }
return escape(results[0][1]);
}
--8---cut here---end---8---

2. There should be way to set the output format form python side of
   things. I had to modify instantiateCiteProc by hand to set the output
   format to text. You know what output format that LibreOffice plugin
   uses? I see text, html and rtf as output formats. But not ODT.
   See https://bitbucket.org/fbennett/citeproc-js/src/tip/src/formats.js

--8---cut here---start-8---
function instantiateCiteProc (styleid) {
// Suspenders and a belt.
try {
if (!styleid) {
styleid = chicago-author-date;
}
if (styleid.slice(0,7) !== 'http://') {
styleid = 'http://www.zotero.org/styles/' + styleid;
}
zotero.debug(XXX does this exist?:  + styleid);
var style = zotero.Styles.get(styleid);
zotero.reStructuredCSL = style.csl;
zotero.reStructuredCSL.setOutputFormat(text);
} catch (e) {
zotero.debug(XXX instantiateCiteProc oops:  + e);
}
};
--8---cut here---end---8---

Btw, I found that with my 2-day old zotero database and for printing the
above 2 keys, the whole machinery takes a perceivably a lot of time. Is
this your experience as well? I am not a netbook.


  Module

# -*- coding: utf-8 -*-
import ConfigParser
import json
import os

# Workaround for crashes seen with localename setting
print os.environ[LANG]
os.environ[LANG]=C.UTF-8
print os.environ[LANG]

import string
import sys

import jsbridge
from zot4rst.util import unquote

DEFAULT_CITATION_FORMAT = http://www.zotero.org/styles/chicago-author-date;

# placeholder for global bridge to Zotero
zotero_conn = None;

# verbose flag
verbose_flag = False

class ZoteroConn(object):
def __init__(self, format, **kwargs):
# connect  setup
self.back_channel, self.bridge = 
jsbridge.wait_and_create_network(127.0.0.1, 24242)
self.back_channel.timeout = self.bridge.timeout = 60
self.methods = jsbridge.JSObject(self.bridge, 
Components.utils.import('resource://csl/export.js'))

if zotero_conn is None:
zotero_conn = 

Re: [O] Bug: Cannot include orgmode source code block [7.7]

2011-11-11 Thread Sebastien Vauban
Hi Truong,

Truong Nghiem wrote:
 I created a following simple org file, in which a source code block of
 language org contains orgmode code:
 === BEGIN CODE 
 #+TITLE: A Test

 #+BEGIN_SRC org
   ,#+begin_src python
 #+END_SRC

 End of test.
 === END CODE ==

 However, when I exported this file, either to HTML or LaTeX/PDF, it
 caused an error:

 ad-Orig-error: unbalanced begin/end_src blocks with #(#+BEGIN_SRC org
   ,#+begin_src python
 #+END_SRC 0 15 (fontified nil font-lock-fontified t) 15 16 (fontified
   nil font-lock-fontified t) 16 37 (fontified nil font-lock-fontified t)
   37 38 (fontified nil font-lock-fontified t) 38 47 (fontified nil
   font-lock-fontified t))

 I'm using the latest development version of orgmode.  Also, if I
 recall correctly, I did succeed to export this kind of code in the
 past (don't remember which version of orgmode though).

 If I included #+end_src in the body of the org code block, it would export
 the file, but the result was not what I expected: it was blank.

I do confirm this, in a very recent Org version, and consider it as a bug too.

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] How to link to a fragment (aka anchor/bookmark) of a local file (e.g. a TiddlyWiki)?

2011-11-11 Thread Christoph LANGE

Hi Samuel,

2011-11-11 21:30 Samuel Wales:

I thought I had explained pretty clearly in the proposals that ID
markers can be put in comments in the /external/ files.


Ah, OK, sorry, I didn't notice that.  But, anyway, I'm not sure if I'd 
want to put such markers into all pages of my TiddlyWiki.  And while 
that would still be _possible_, I'm sure that there is also a use case 
for linking to fragments of local HTML files that you really don't want 
to change or can't change.  Imagine being a non-privileged user and 
linking via file:///path/to/software/manual.html#feature to some section 
of the manual of a software installed by an admin user, or to some 
downloaded e-book or archived web page.



Org IDs in external files -- which I propose to be in ID markers --
are as unbreakable as you can arrange in a practical way.


BTW that reminds me of purple numbers 
(http://en.wikipedia.org/wiki/Purple_Numbers), which I have seen in some 
wikis.  But they don't scale as well as your ID markers.


Cheers,

Christoph

--
Christoph Lange, http://www.facebook.com/ch.lange, Skype duke4701



Re: [O] Global Task List

2011-11-11 Thread Sebastien Vauban
Hi Olivier and Cameron,

Olivier Schwander wrote:
 Le 11 Nov 2011 12:17, Cameron Seader a écrit:
 I get an error when setting the variable to a folder
 (setq org-agenda-custom-commands
 ((org-agenda-files '(~/Documents/Notes/org/))
 ))

 You are not supposed to set it to a folder.

Yes, you can. See
http://www.gnu.org/software/emacs/manual/html_node/org/Agenda-files.html.

But your error comes from the way you write you agenda custom commands: no
dispatcher key, no documentation string, etc.

 I use something like:

 (setq org-agenda-files (file-expand-wildcards ~/Notes/*.org))

Cameron, use something like the above for a system-wide setting, or something
like this for a change just for some custom view:

#+begin_src emacs-lisp
(p Tasks in my personal realm
 alltodo 
 ((org-agenda-files
   '(~/Personal/TODO.org
#+end_src

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Jambunathan K

Erik

 Footnotes: 
 
 [1]  With Mozrepl 1.1 beta2 on Firefox 3.6.23, I am unable to make
 org-zotero.el work. It hangs and I have to C-g out (Christian! you are
 not alone). I am able to get as far as creating the LIBRARY_KEY for the
 selected item in the zotero pane and not further.

 […]

 Have you started MozRepl from Firefox? I re-installed mozrepl, checked
 that I am using the latest (and unmodified) versions of moz.el and
 zotero-plain. Everything seems fine. This is with Emacs 23 - perhaps
 Emacs 24 changes things?

Here is what I find:

If I put the below snippet in a javascript buffer and do a M-x
send-region, I am able to retrieve the library and key of the selected
item.


#+begin_src javascript
repl.whereAmI()

var ZoteroPane = 
Components.classes[@mozilla.org/appshell/window-mediator;1].getService(Components.interfaces.nsIWindowMediator).getMostRecentWindow(navigator:browser).ZoteroPane;
var selected_items = ZoteroPane.getSelectedItems();
new String(selected_items.length);
selected_items[0].libraryID;
selected_items[0].key;
#+end_src

Here is transaction log:

, From *MozRepl*
| 
| Welcome to MozRepl.
| 
|  - If you get stuck at the ... prompt, enter a semicolon (;) at the 
beginning of the line to force evaluation.
|  - If you get errors after every character you type, see 
http://github.com/bard/mozrepl/wikis/troubleshooting (short version: stop using 
Microsoft telnet, use netcat or putty instead)
| 
| Current working context: chrome://browser/content/browser.xul
| Current input mode: syntax
| 
| repl [object ChromeWindow] - Document title: fbennett / citeproc-js / 
source  Bitbucket - Mozilla Firefox
| 1 — {0: 1}
| 
| repl 579241
| 
| repl TPSFKWXK
| 
| repl 
`

The problem is in zotero-js-write-to-file. The problem happens even
after I increase the sleep out time to 1 sec.

See the attached backtrace with With M-x toggle-debug-on-quit RET and a
C-g

I wonder whether the issue is related to we - Matt(?), Christian(?) and
I - using Windows.


As can be seen from the transaction log, the shell interaction is
fine. I am inclined to think that it has something to do with zotero.el.

I am wondering whether there is a way to capture the selected item as
a zotero link through the jsbridge interface. Anyways with massaging of
org-protocol we can get a zotero select link by viewing the report
of the current item.

Debugger entered--Lisp error: (quit)
  sleep-for(0 10)
  (while (not (file-exists-p tmp-file)) (sleep-for 0 10))
  (let ((tmp-file (make-temp-file zotero))) (delete-file tmp-file) 
(zotero-js-write-to-file tmp-file expr) (while (not (file-exists-p tmp-file)) 
(sleep-for 0 10)) (prog1 (save-excursion (with-temp-buffer 
(insert-file-contents tmp-file) (buffer-substring-no-properties (point-min) 
(point-max (delete-file tmp-file)))
  zotero-js-get-string-value(new String(selected_items.length))
  (error %s (zotero-js-get-string-value new String(selected_items.length)))
  zotero-get-selected-item-ids()
  (let ((ids (zotero-get-selected-item-ids))) (mapc (lambda (id) (insert 
(format [[zotero://select//%s][%s]]\n id id)) 
(org-zotero-update-reference-link-at-point) (forward-line 1)) ids))
  org-zotero-insert-reference-link()
  call-interactively(org-zotero-insert-reference-link t nil)
  execute-extended-command(nil)
  call-interactively(execute-extended-command nil nil)
  recursive-edit()

  debug(error (quit))
  sleep-for(1 10)
  (while (not (file-exists-p tmp-file)) (sleep-for 1 10))
  (let ((tmp-file (make-temp-file zotero))) (delete-file tmp-file) 
(zotero-js-write-to-file tmp-file expr) (while (not (file-exists-p tmp-file)) 
(sleep-for 1 10)) (prog1 (save-excursion (with-temp-buffer 
(insert-file-contents tmp-file) (buffer-substring-no-properties (point-min) 
(point-max (delete-file tmp-file)))
  zotero-js-get-string-value(new String(selected_items.length))
  (error %s (zotero-js-get-string-value new String(selected_items.length)))
  zotero-get-selected-item-ids()
  (let ((ids (zotero-get-selected-item-ids))) (mapc (lambda (id) (insert 
(format [[zotero://select//%s][%s]]\n id id)) 
(org-zotero-update-reference-link-at-point) (forward-line 1)) ids))
  org-zotero-insert-reference-link()
  call-interactively(org-zotero-insert-reference-link t nil)
  execute-extended-command(nil)
  call-interactively(execute-extended-command nil nil)

-- 



Re: [O] Bug: Cannot include orgmode source code block [7.7]

2011-11-11 Thread Eric Schulte
Sebastien Vauban wxhgmqzgw...@spammotel.com writes:

 Hi Truong,

 Truong Nghiem wrote:
 I created a following simple org file, in which a source code block of
 language org contains orgmode code:
 === BEGIN CODE 
 #+TITLE: A Test

 #+BEGIN_SRC org
   ,#+begin_src python
 #+END_SRC

 End of test.
 === END CODE ==

 However, when I exported this file, either to HTML or LaTeX/PDF, it
 caused an error:

 ad-Orig-error: unbalanced begin/end_src blocks with #(#+BEGIN_SRC org
   ,#+begin_src python
 #+END_SRC 0 15 (fontified nil font-lock-fontified t) 15 16 (fontified
   nil font-lock-fontified t) 16 37 (fontified nil font-lock-fontified t)
   37 38 (fontified nil font-lock-fontified t) 38 47 (fontified nil
   font-lock-fontified t))

 I'm using the latest development version of orgmode.  Also, if I
 recall correctly, I did succeed to export this kind of code in the
 past (don't remember which version of orgmode though).

 If I included #+end_src in the body of the org code block, it would export
 the file, but the result was not what I expected: it was blank.

 I do confirm this, in a very recent Org version, and consider it as a bug too.


I've just pushed up a fix, thanks for the catch. -- Eric

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



[O] [bug] regression tests broken

2011-11-11 Thread Martyn Jago

Hi 

All automated regression tests broken since 7720786 commit

http://martynjago.com:

Best, Martyn




Re: [O] [bug] regression tests broken

2011-11-11 Thread Eric Schulte
Hi Martyn,

I have all tests passing in a branch in the Org-mode git repo (which I
plan to merge into master soon).  Could you try a run of this on the
standard-code-block-syntax branch?

As a side note, how automated is your crusecontrol.rb setup?  Would you
recommend this as a way to run automated tests on the Org-mode server
after every git commit?

Thanks -- Eric

Martyn Jago martyn.j...@btinternet.com writes:

 Hi 

 All automated regression tests broken since 7720786 commit

 http://martynjago.com:

 Best, Martyn



-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



[O] ORG-LIST-END-MARKER appears in HTML export of LaTeX code

2011-11-11 Thread Michael Hannon
Greetings.  I'm getting a gratuitous string:

    ORG-LIST-END-MARKER

inserted into the HTML version of some exported LaTeX code.  The PDF export
seems to be OK.

This problem was discussed in the thread starting at:

http://lists.gnu.org/archive/html/emacs-orgmode/2011-03/msg01751.html

but I can't tell what the resolution was.  If one of the discussed patches
fixed the problem, the patch doesn't seem to have survived to the version of
Org-mode that I'm using (release_7.7.328.g1a97  -- other details are
appended).

I've also appended a snippet of code that exhibits the problem.

Suggestions appreciated.

-- Mike


* My configuration

Emacs  : GNU Emacs 23.2.1 (x86_64-redhat-linux-gnu, GTK+ Version 2.24.4)
 of 2011-05-23 on x86-12.phx2.fedoraproject.org
Package: Org-mode version 7.7 (release_7.7.328.g1a97)

* Code that exhibits the problem during HTML export

#+TITLE: neural network summary
#+AUTHOR: 
#+DATE: 2011-10-30

#+LATEX_HEADER: \usepackage{amscd}
#+LATEX_HEADER: \usepackage{parskip}
#+LATEX_HEADER: \usepackage{amsmath}
#+LATEX_HEADER: \usepackage{multirow}
#+LATEX_HEADER: \usepackage[table]{xcolor}

###+STYLE:    link rel=stylesheet type=text/css 
href=./html-skeleton.css /
#+BABEL: :session *R* :cache no :results output verbatim :exports both :tangle
yes

# TOP

#+BEGIN_CENTER
All the formulas I need for logistic regression
#+END_CENTER
--


Then 
\begin{align}
  J_k\Big(\Theta\Big)  = - \frac{1}{N}
 \Big(
   \big(1 - \vec{y}_k\big)^T \log \big(1 - \vec{h}_k \big)
   + \vec{y}_k \log \vec{h}_k
 \Big)
\end{align}

Re: [O] ORG-LIST-END-MARKER appears in HTML export of LaTeX code

2011-11-11 Thread Nicolas Goaziou
Hello,

Michael Hannon jm_han...@yahoo.com writes:

    + \vec{y}_k \log \vec{h}_k

Here, you're starting a new list item within your LaTeX
environments. For now, I would suggest to avoid putting the plus sign at
the beginning of the line.

Regards,

-- 
Nicolas Goaziou



Re: [O] ORG-LIST-END-MARKER appears in HTML export of LaTeX code

2011-11-11 Thread Michael Hannon
That fixes it!  Thanks, Nicolas.

-- Mike





From: Nicolas Goaziou n.goaz...@gmail.com
To: Michael Hannon jm_han...@yahoo.com
Cc: Org-Mode List emacs-orgmode@gnu.org
Sent: Friday, November 11, 2011 2:40 PM
Subject: Re: [O] ORG-LIST-END-MARKER appears in HTML export of LaTeX code

Hello,

Michael Hannon jm_han...@yahoo.com writes:

    + \vec{y}_k \log \vec{h}_k

Here, you're starting a new list item within your LaTeX
environments. For now, I would suggest to avoid putting the plus sign at
the beginning of the line.

Regards,

-- 
Nicolas Goaziou





Re: [O] regenerating agendas automatically if any .org files change

2011-11-11 Thread Herbert Sitz
Viktor Rosenfeld listuser36 at googlemail.com writes:

 
 AFAIK, there can only be one agenda view (an expert correct me, if I'm
 wrong). But you can multiple blocks in the agenda. Search for Office
 block agenda in:
 
 http://orgmode.org/worg/org-tutorials/org-custom-agenda-commands.html 
 
 Cheers,
 Viktor

I assume an agenda view with multiple blocks would work for OP. 

But given his intended use could he not also just start up several independent
Emacs instances on his B machine, each to show a different agenda view?

-- Herb






Re: [O] BUG: org-todo-yesterday logs wrong date

2011-11-11 Thread Viktor Rosenfeld
Hi Bernt,

Bernt Hansen wrote:

 Geert Kloosterman g.j.klooster...@gmail.com writes:
 
  Hi all,
 
  On Wed, Oct 19, 2011 at 1:17 AM, Viktor Rosenfeld 
  listuse...@googlemail.com wrote:
 
 
  org-todo-yesterday and org-agenda-todo-yesterday log a note using
  the
  current timestamp and not a timestamp of 23:59 of yesterday's
  date.
 
  I'm using Org-Mode 7.7 pulled today from the git repository.
 
 
 
  I'm experiencing the same problem with the org-mode version I pulled
  from git today. 
 
  Switching back to the 7.7 tarball fixes the problem.
 
  Best regards,
  Geert Kloosterman
   
 
 Git bisect identifies the following commit as the source of this
 problem.
 
 7d2d8f884b2e22e3056553ea68858fe4fc674427 is the first bad commit
 commit 7d2d8f884b2e22e3056553ea68858fe4fc674427
 Author: John Wiegley jo...@newartisans.com
 Date:   Sat Aug 13 03:21:49 2011 -0500
 
 Add customization variable `org-use-effective-time'
 
 If non-nil, consider `org-extend-today-until' when creating timestamps.
 For example, if `org-extend-today-until' is 8, and it's 4am, then the
 effective time of any timestamps between midnight and 8am will be
 23:59 of the previous day.
 
 :04 04 a33f65040163763ed06996b9ffc18bcfc5884457 
 0782571b08e0a128fa3b072b8b8edf177c001ca3 Mlisp
 
 Regards,
 Bernt

Thanks for the info. Setting org-use-effective-time to 1 fixes the
problem, even if org-extend-today-until is zero. I'm curious though why
its type is integer and not boolean.

Thanks again,
Viktor
 



Re: [O] zotero plain, org-odt, and citations in general

2011-11-11 Thread Erik Hetzner
At Fri, 11 Nov 2011 13:45:27 -0500,
Matt Price wrote:
 
 On Fri, Nov 11, 2011 at 11:12 AM, Erik Hetzner e...@e6h.org wrote:

 […]

 if tricky for you, then likely unmanageable for me.   but I wonder if
 Zotero themselves would be interested in helping a little bit with some of
 this work?  Seems sort of strange to build this great tool and then limit
 its usefulness to two hulking word processors, when really the goal of
 portable, reformattable citations applies just as much to text and html as
 to word processing documents.

Agreed, but I think that Word, Open/LibreOffice, and LaTeX cover most
use cases. I don’t think the Zotero people have the time to do any
extra work, but they are almost helpful answering questions.

pandoc has similar support for citations and is worth taking a look
at. It requires export from Zotero, but this can be automated.

-Erik
Sent from my free software system http://fsf.org/.


Re: [O] How to reuse page keywords for LaTeX with pdfkeywords and hyperref package?

2011-11-11 Thread Mikhail Titov
Bastien bzg at altern.org writes:
 Hi Mikhail,
 
 Mikhail Titov mlt at gmx.us writes:
 
  In case someone else also wants page keywords to appear in latex export.
  Here is the link to original thread
  http://lists.gnu.org/archive/html/emacs-orgmode/2011-03/msg01429.html .
  There is a patch at the bottom that does that. It assumes that hyperred
  package is used and doesn't check that!
 
 Yes, hyperref is in ̀org-export-latex-default-packages-alist' and is
 available.
 
  I'm not sure if I'm doing it right as I don't know lisp and emacs
  much.
 
 I pushed a commit with a slightly adapted version of your patch.
 
 Please check it does the right thing for you.

Yes! It does exactly what I've wanted and even adds application name to PDF.
Sweet!

 Further improvements in this area: have a defcustom allowing the user 
 to select what hyperref options he wants in the .tex output.  Maybe you
 can improve your ELisp trying to provide a patch for this?   

I'm afraid I don't get it.
I can see org-export-latex-hyperref-format in org-latex.el .
Isn't it already in there?

Mikhail




Re: [O] Global Task List

2011-11-11 Thread Nick Dokos
Olivier Schwander olivier.schwan...@chadok.info wrote:

 Le 11 Nov 2011 12:17, Cameron Seader a écrit:
  I get an error when setting the variable to a folder
  (setq org-agenda-custom-commands
  ((org-agenda-files '(~/Documents/Notes/org/))
  ))
 
 You are not supposed to set it to a folder.

That's not true: you can set it to

   - a list of files and directories
   - a single file name 

C-h v org-agenda-files RET for the details.

 I use something like:
 (setq org-agenda-files (file-expand-wildcards ~/Notes/*.org))
 

You can do the same thing like this:

   (setq org-agenda-files '(~/Notes))

with the default value of org-agenda-file-regexp.

Nick





Re: [O] babel, beamer: Prevent apostrophe/single quote mangling, so examples can be reused from PDF

2011-11-11 Thread Eric Schulte
Mikhail Titov m...@gmx.us writes:

 Hello!

 I’ve picked up some templates from orgmode tutorials and I can
 successfully create PDF made of beamer slides with babelized R
 code. The problem is that I can’t reuse text from pdf by copy-pasting
 like SQL I used in RODBC examples.

 At some point all my single quotes are turned into something that is
 not even on my keyboard and looks like reversed back quote.

 I’m not sure if mailing list can pass all these unchanged. I’m getting
 ’ instead of ' in the output.

 What shall I look at to fix this? I really want all text to be easily 
 reusable.

 I feel like it is a LaTeX related problem since I see tex file as it
 is supposed to be. But there must be some workaround or at least
 warning for babel users of org-mode.

 P.S. I typed in message in HTML mode and converted it to plain text
 later. And it looks like even MS Outlook did this conversion in text
 :(

 P.P.S. I have the following in output tex file if it makes any difference

 \usepackage[utf8]{inputenc}
 \usepackage[T1]{fontenc}

 and I'm running MS Windows with latest org mode from git and MikTeX 2.9 .

 Mikhail


Hi Mikhail,

I have seen a similar issue in which code *executed* by R returns weird
nasty quotes.  The following works for me to remove these quotes before
the confuse TeX.

;; Replace nasty single-quotes returned by R.
(add-hook 'org-export-latex-final-hook
  (lambda () (replace-regexp ’ ')))

Hope this helps -- Eric






-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



Re: [O] babel, beamer: Prevent apostrophe/single quote mangling, so examples can be reused from PDF

2011-11-11 Thread Mikhail Titov
 -Original Message-
 From: Eric Schulte [mailto:schulte.e...@gmail.com]
 Sent: Friday, November 11, 2011 8:21 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] babel, beamer: Prevent apostrophe/single quote mangling,
 so examples can be reused from PDF
 
 I have seen a similar issue in which code *executed* by R returns weird
 nasty quotes.  The following works for me to remove these quotes before
 the confuse TeX.
 
 ;; Replace nasty single-quotes returned by R.
 (add-hook 'org-export-latex-final-hook
   (lambda () (replace-regexp ’ ')))
 
 Hope this helps -- Eric

Probably it was another issue. I've double checked in another text editor that 
I'm getting correct apostrophes in tex output. I tried with or without your 
code in dot emacs (I restarted emacs). It is something in LaTeX or some package 
that triggers it:(

I've came across this 
http://www.cs.sfu.ca/~ggbaker/reference/characters/#single . It says that for 
typewriter font LaTeX won't substitute apostrophe with closing single quote. 
However I thought that verbatim as produced by babel implies typewriter font.

Mikhail





[O] Bug: Property inheritance in beamer export [7.4]

2011-11-11 Thread Chris Kauffman
I'd like to be able to set a global property which shrinks all text
tofit in the allotted space; this is great for source examples.
Aftersome experimentation I put
#+PROPERTY: BEAMER_envargs [shrink]
in the preamble and did
(set-variable (quote org-use-property-inheritance) t nil)
According to my understanding of the documentation, this should
makeevery outline entry inherit the desired property, regardless of
whetherit has a properties list itself.  After reloading the file,
internallythis seems to work fine: I move to any heading and eval the
followinglisp
(org-entry-get (point) BEAMER_envargs 1)
which gives the result [shrink]
However, on exporting the org file to pdf through latex, the
shrinkingdoes not seem to happen. The source code runs off the page.
Is property inheritance not respected during export?
Cheers,Chris
---ORG SETUP---
Emacs  : GNU Emacs 23.2.1 (i686-pc-linux-gnu, GTK+ Version 2.24.4) of
2011-04-04 on rothera, modified by DebianPackage: Org-mode version 7.4
current state:==(setq
org-export-latex-after-initial-vars-hook
'(org-beamer-after-initial-vars) org-speed-command-hook
'(org-speed-command-default-hook org-babel-speed-command-hook)
org-agenda-files '(~/mypubs/worklog) org-agenda-window-setup
'other-window org-metaup-hook '(org-babel-load-in-session-maybe)
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
org-export-latex-format-toc-function
'org-export-latex-format-toc-default org-tab-first-hook
'(org-hide-block-toggle-maybe org-src-native-tab-command-maybe  
org-babel-hide-result-toggle-maybe) org-src-mode-hook
'(org-src-babel-configure-edit-buffer   
org-src-mode-configure-edit-buffer) org-confirm-shell-link-function
'yes-or-no-p org-export-first-hook
'(org-beamer-initialize-open-trackers) org-agenda-before-write-hook
'(org-agenda-add-entry-text) org-use-property-inheritance t
outline-mode-hook '((lambda nil       (local-set-key \356 (quote
outline-next-visible-heading))        (local-set-key \360 (quote
outline-previous-visible-heading))        (local-set-key (quote 
[f12])
(quote ck-outline-toggle)))      ) org-babel-pre-tangle-hook
'(save-buffer) org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-hide-drawers    org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers) org-mode-hook '((lambda nil
(local-set-key d (quote insert-date-heading))  (local-set-key
 (quote org-agenda))  (local-set-key \232 (quote
format-float-column)) (local-set-key e (quote org-example))  

(local-set-key v (quote org-verbatim)) (local-set-key q
(quote org-quote)) (auto-fill-mode 1) (setq org-agenda-window-setup
(quote other-window)))   #[nil \300\301\302\303\304$\207  
[org-add-hook change-major-mode-hook org-show-block-all append
local]     5]#[nil \300\301\302\303\304$\207  
   [org-add-hook
change-major-mode-hook org-babel-show-result-all append     local]  

 5]  org-babel-result-hide-spec org-babel-hide-all-hashes)
org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe) org-confirm-elisp-link-function
'yes-or-no-p org-export-interblocks '((lob
org-babel-exp-lob-one-liners) (src
org-babel-exp-inline-src-blocks)) org-occur-hook
'(org-first-headline-recenter) org-from-is-user-regexp
\\kauffman\\
org-export-preprocess-before-selecting-backend-code-hook
'(org-beamer-select-beamer-code) org-export-latex-final-hook
'(org-beamer-amend-header org-beamer-fix-toc
org-beamer-auto-fragile-frames  
org-beamer-place-default-actions-for-lists) org-metadown-hook
'(org-babel-pop-to-session-maybe) org-export-blocks '((src
org-babel-exp-src-blocks nil)    (comment
org-export-blocks-format-comment t)      (ditaa
org-export-blocks-format-ditaa nil)      (dot
org-export-blocks-format-dot nil)) )

-- 
Karypis Research Group
Dept. of Computer Science
University of Minnesota