Re: [O] [BUG] worg table of contents

2013-05-17 Thread Bastien
Hi Rick,

Rick Frankel r...@rickster.com writes:

 I have pushed the update. I also pushed a minor fix to org-hacks.org
 to check if it works as expected (it does :). Republishing everything
 is a great idea.

I just republished everything.

 BTW, i noticed a bad link --- http://orgmode.org/css/lightbox.css; is
 included in the header, but the file does not exist on the server.

Fixed, thanks!

-- 
 Bastien



Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Bastien
Hi Max,

Max Mikhanosha m...@openchat.com writes:

 To try it out, you'll need /usr/bin/scrot which is available as
 scrot package on most distributions.

 Then (require 'org-screenshot) and try C-c M-s (org-screenshot-take) in an 
 Org File. Make
 sure to turn on inline image display (C-c C-x C-v) after taking the
 first screenshot.

Tested, and it works *great*!  Thanks for this neat package.

-- 
 Bastien



Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Rainer M. Krug
Bastien b...@gnu.org writes:

 Hi Max,

 Max Mikhanosha m...@openchat.com writes:

 To try it out, you'll need /usr/bin/scrot which is available as
 scrot package on most distributions.

 Then (require 'org-screenshot) and try C-c M-s (org-screenshot-take) in an 
 Org File. Make
 sure to turn on inline image display (C-c C-x C-v) after taking the
 first screenshot.

 Tested, and it works *great*!  Thanks for this neat package.
#secure method=pgpmime mode=sign

Nice and very useful. Can this be included in /contrib?

Rainer

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug



Re: [O] nested tables

2013-05-17 Thread Carsten Dominik

On 16.5.2013, at 23:40, Uwe Brauer o...@mat.ucm.es wrote:

 Hello 
 
 I am not sure whether the following is really a nested table or just one
 which contains split and merged cell. I generated it using table.el
 
 
 
 +-+-+-+
 | | | |
 +-+-+-+
 | | | |
 | +-+ |
 | | | |
 +-+-+-+
 | |   |
 +-+---+
 
 
 Are there any plans that org-table would support such a table 
 org-table-create-with-table.el does not work on this example.

Hi Uwe,

You can edit such a table in Org-mode using C-c '

Greetings

- Carsten

 
 Uwe Brauer 
 
 




[O] Exporting source code blocks as LaTeX figures

2013-05-17 Thread James Harkins
Couple of questions about exporting LaTeX figures that are neither
tables nor images -- specifically, source code blocks using the
listings package.

1. Is there any way to use #+CAPTION with a #+BEGIN_figure block, so
that the caption will be rendered underneath the text in the figure?

It seems (from reading the org manual and some experimentation on my
own) that the answer is no. That's rather inconvenient; the journal
specifies that captions should appear below their respective figures,
but as it is:

#+CAPTION: Some code
#+NAME: code1
#+BEGIN_figure
#+BEGIN_SRC {}
// blah blah

--

\begin{figure}
\caption{\label{code1}Some code}
\lstset{language={},numbers=none}
\begin{lstlisting}
// blah blah

--

Figure 1. Some code.

// blah blah
.

I can work around it by not using #+CAPTION, and writing
\caption{...}\label{...}. That shouldn't be a problem for this
project, unless for some reason I should have to re-export as, say,
ODT or HTML.

2. Is the customize variable Org Latex Default Figure Position only
used for tables and images? It would be nice if it applied to
BEGIN_figure as well (unless :options override that). #+ATTR_LaTeX:
:options [htb] is a mite inconvenient to replicate for every code
example. Certainly possible, but it would save a little effort if the
default were used here too.

hjh



Re: [O] agenda column view and/or location property visible in normal view

2013-05-17 Thread Eric S Fraga
Bastien b...@gnu.org writes:

[...]

  which works quite well except for the absence of time
  information.

 Maybe you can use %TIMESTAMP for the time?

This works.  Thanks.  It does have more information than I need
(i.e. the date) but that's okay.

Where can I find out what variables are known to column view in the
agenda?  I went through the code but couldn't figure it out.  The info
entry on Special Properties seemed to be the obvious place to look but
it has nothing relevant.

 See `org-agenda-prefix-format' -- maybe you can play with the %(exp)
 construct and try to retrieve infos with `org-entry-get' (which see.)

I'll look into this.  I missed the %(exp) possibility.  Thanks again.

-- 
: Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
: in Emacs 24.3.50.1 and Org release_8.0.2-103-gb3a88b




Re: [O] nested tables

2013-05-17 Thread Uwe Brauer

 Carsten == Carsten Dominik carsten.domi...@gmail.com writes:

On 16.5.2013, at 23:40, Uwe Brauer o...@mat.ucm.es wrote:

Hello 




Are there any plans that org-table would support such a table 
org-table-create-with-table.el does not work on this example.

Hi Uwe,

You can edit such a table in Org-mode using C-c '

Ah thanks, however orgtbl-ctrl-c-ctrl-c will not work that is 
if I write a org-mode table 


| |new |
|old | more|

Than orgtbl-ctrl-c-ctrl-c will format the table nicely (table.el has no
such a feature). 


However if I edit the table I mentioned (the one generated by table.el)
with C-c ' and insert text I have to take care myself of the boundaries.

So the next question is could org-mode try to take care of the
boundaries of the table.el table?

Uwe 




Re: [O] nested tables

2013-05-17 Thread Carsten Dominik

On 17.5.2013, at 11:55, Uwe Brauer o...@mat.ucm.es wrote:

 
 Carsten == Carsten Dominik carsten.domi...@gmail.com writes:
 
 On 16.5.2013, at 23:40, Uwe Brauer o...@mat.ucm.es wrote:
 
 Hello 
 
 
 
 
 Are there any plans that org-table would support such a table 
 org-table-create-with-table.el does not work on this example.
 
 Hi Uwe,
 
 You can edit such a table in Org-mode using C-c '
 
 Ah thanks, however orgtbl-ctrl-c-ctrl-c will not work that is 
 if I write a org-mode table 
 
 
 | |new |
 |old | more|
 
 Than orgtbl-ctrl-c-ctrl-c will format the table nicely (table.el has no
 such a feature). 

Yes it has, it automatically formats as you type.

 
 
 However if I edit the table I mentioned (the one generated by table.el)
 with C-c ' and insert text I have to take care myself of the boundaries.

As I said, this just works for me. 

- Carsten

 
 So the next question is could org-mode try to take care of the
 boundaries of the table.el table?
 
 Uwe 
 
 




Re: [O] nested tables

2013-05-17 Thread Uwe Brauer
 Carsten == Carsten Dominik carsten.domi...@gmail.com writes:

On 17.5.2013, at 11:55, Uwe Brauer o...@mat.ucm.es wrote:

Than orgtbl-ctrl-c-ctrl-c will format the table nicely (table.el has no
such a feature). 

Yes it has, it automatically formats as you type.

I started fresh from zero, generated a new file and table and you are
right!  thanks

Uwe 




Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Max Mikhanosha
At Fri, 17 May 2013 09:38:29 +0200,
Rainer M. Krug wrote:
 
 Nice and very useful. Can this be included in /contrib?

That is my intention, I have the FSF paper signed for Emacs and Org.

So what I'm looking for some minimum amount of eyes on the code, and
advice as to minimum set of things I need to adjust before committing it?

My list is.

1. Convert defvar to defcustom

2. Is (require 'dired) fine? It uses macro `dired-mark-if' defined in
   dired.el

3. The prefix C-c M-s seems awkward but Org is so big everything else
   is taken, and C-c C-x s is too close to C-c C-x C-s, which is
   archive subtree (I initially had it there and moved after archiving
   subtree by mistake)

Its its fine to go in as is, then its fine too, I'm pretty lazy :-)

Regards,
  Max



Re: [O] How to set C-o back to open-line?

2013-05-17 Thread Christopher Allan Webber
Andreas Röhler writes:

 Installing this instead should fix it:

 (defun org-open-line (n)
Insert a new row in tables, call `open-line' elsewhere.
 With \C-u NUMBER `open-line' is called the common way also in table context
(interactive *P)
(cond (n
   (open-line (prefix-numeric-value n)))
  ((org-at-table-p)
   (org-table-insert-row))
  (t (open-line (prefix-numeric-value n)

 Cheers,

 Andreas

Hm, alright.  Sadly there seems to be no way to change the key (very
un-emacs like?)  So if redefining it is the way, I replaced with the
much simpler:

  (setq org-open-line 'open-line)

Much better!  Hopefully no tooling ever makes use of org-open-line,
shooting me in the foot... :)



Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Daniel F
It looks great!
I think I'd only convert defvars to defcustom.

Personally, I don't worry about prefixes that much, because if I am not
using a command very often I just tend do run it using M-x command-name

- Dan


On Fri, May 17, 2013 at 2:41 PM, Max Mikhanosha m...@openchat.com wrote:

 At Fri, 17 May 2013 09:38:29 +0200,
 Rainer M. Krug wrote:
 
  Nice and very useful. Can this be included in /contrib?

 That is my intention, I have the FSF paper signed for Emacs and Org.

 So what I'm looking for some minimum amount of eyes on the code, and
 advice as to minimum set of things I need to adjust before committing it?

 My list is.

 1. Convert defvar to defcustom

 2. Is (require 'dired) fine? It uses macro `dired-mark-if' defined in
dired.el

 3. The prefix C-c M-s seems awkward but Org is so big everything else
is taken, and C-c C-x s is too close to C-c C-x C-s, which is
archive subtree (I initially had it there and moved after archiving
subtree by mistake)

 Its its fine to go in as is, then its fine too, I'm pretty lazy :-)

 Regards,
   Max




-- 
Sincerely yours,
-- Daniil


Re: [O] How to set C-o back to open-line?

2013-05-17 Thread Nicolas Richard
Christopher Allan Webber cweb...@dustycloud.org writes:
 Hm, alright.  Sadly there seems to be no way to change the key (very
 un-emacs like?)

That was answered by Nick Dokos ; use :
  (define-key org-mode-map [remap open-line] nil)

(btw, why does org use remap here is a mystery to me)

   (setq org-open-line 'open-line)

How could that possibly work ?

-- 
Nico.



Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Carsten Dominik

On 17.5.2013, at 09:38, Rainer M. Krug rai...@krugs.de wrote:

 Bastien b...@gnu.org writes:
 
 Hi Max,
 
 Max Mikhanosha m...@openchat.com writes:
 
 To try it out, you'll need /usr/bin/scrot which is available as
 scrot package on most distributions.
 
 Then (require 'org-screenshot) and try C-c M-s (org-screenshot-take) in an 
 Org File. Make
 sure to turn on inline image display (C-c C-x C-v) after taking the
 first screenshot.
 
 Tested, and it works *great*!  Thanks for this neat package.
 #secure method=pgpmime mode=sign
 
 Nice and very useful. Can this be included in /contrib?

Certainly!

- Carsten

 
 Rainer
 
 -- 
 Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
 UCT), Dipl. Phys. (Germany)
 
 Centre of Excellence for Invasion Biology
 Stellenbosch University
 South Africa
 
 Tel :   +33 - (0)9 53 10 27 44
 Cell:   +33 - (0)6 85 62 59 98
 Fax :   +33 - (0)9 58 10 27 44
 
 Fax (D):+49 - (0)3 21 21 25 22 44
 
 email:  rai...@krugs.de
 
 Skype:  RMkrug
 




Re: [O] M-RET and C-RET turn current line of text into a heading?

2013-05-17 Thread Carsten Dominik

On 16.5.2013, at 21:11, Jason F. McBrayer jmcb...@carcosa.net wrote:

 Bastien b...@gnu.org writes:
 
 Thanks a lot Samuel for writing this.
 
 Just a quick note to tell you that this discussion *is* important,
 and well read, as we plan to rewrite those functions.  Presenting
 features wrt contexts so clearly is great -- thanks for doing this.
 
 Another thing to take into account in the rewrite is doing the right
 thing even when electric-indent-mode or electric-layout-mode are
 enabled. The current implementation is not compatible with
 electric-indent-mode. 

Never heard about these - need to look them up.

- Carsten

 
 -- 
 +---+  
 | Jason F. McBrayerjmcb...@carcosa.net  |  
 | If someone conquers a thousand times a thousand others in |  
 | battle, and someone else conquers himself, the latter one |  
 | is the greatest of all conquerors.  --- The Dhammapada|  
 




Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Carsten Dominik

On 17.5.2013, at 09:38, Rainer M. Krug rai...@krugs.de wrote:

 Bastien b...@gnu.org writes:
 
 Hi Max,
 
 Max Mikhanosha m...@openchat.com writes:
 
 To try it out, you'll need /usr/bin/scrot which is available as
 scrot package on most distributions.
 
 Then (require 'org-screenshot) and try C-c M-s (org-screenshot-take) in an 
 Org File. Make
 sure to turn on inline image display (C-c C-x C-v) after taking the
 first screenshot.
 
 Tested, and it works *great*!  Thanks for this neat package.
 #secure method=pgpmime mode=sign
 
 Nice and very useful. Can this be included in /contrib?

Certainly!

- Carsten

 
 Rainer
 
 -- 
 Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
 UCT), Dipl. Phys. (Germany)
 
 Centre of Excellence for Invasion Biology
 Stellenbosch University
 South Africa
 
 Tel :   +33 - (0)9 53 10 27 44
 Cell:   +33 - (0)6 85 62 59 98
 Fax :   +33 - (0)9 58 10 27 44
 
 Fax (D):+49 - (0)3 21 21 25 22 44
 
 email:  rai...@krugs.de
 
 Skype:  RMkrug
 




Re: [O] How to set C-o back to open-line?

2013-05-17 Thread Carsten Dominik

On 17.5.2013, at 00:38, Christopher Allan Webber cweb...@dustycloud.org wrote:

 I really hate org-open-line... I can see why people might want it, but
 it's messed up my workflow.  I'd like to set C-o back.
 
 However, I have no idea what org-defkey is doing, but I expected this to
 work:
 
 (define-key org-mode-map (kbd C-o) 'open-line)

This one will work if you do it in org-mode-hook.

We could also introduce a variable to turn off the special behavior,
just like we do for C-a, C-e, and C-k.  This seems to me a better
option than to introduce additional context dependencies or use
prefix arguments to influence the behavior.

- Carsten

 
 it isn't working!
 
 How to get the standard-ol-open-line behavior back?
 




Re: [O] M-RET and C-RET turn current line of text into a heading?

2013-05-17 Thread Carsten Dominik
Hi everyone,

yes, thanks for making this table, Samuel.

I think the functionality is a bit overkill, in particular the implementation
with pressing M-RET twice for special functionality.  This becomes too
confusing, I think.

The elementary function of M-RET is continue in the current list/outline.
C-RET is a way to get out of list environments and to get a new heading.
Both are entirely necessary when taking notes, IMO.

So I would propose the following adapted version of Samuel's table:

|-+--++|
| command | context  | pos| action |
|-+--++|
| c-ret   | any  | any| create headline below entry|
| m-ret   | headline or item | beg| create new above header/item   |
| m-ret   | headline or item | middle | split  |
| m-ret   | headline or item | end| create new below header/item   |
| m-ret   | line | beg| turn into headline, this is|
| |  || just a special case of split   |
| m-ret   | line | middle | turn rest of line into heading |
| m-ret   | line | end| new heading after line |
| C-o M-ret   | line | beg| new heading before line|
|-+--++|

There was discussion about `C-c *'.  For me the main application
of this command it to turn an item into a headline, and to turn *several*
lines into a series of headline (by selecting the lines first) - this is
a very frequent application when I paste text that I then need to structure.
Nobody mentioned this in this thread, so maybe this feature is not known
well enough.

- Carsten





[O] Internal link with custom caption

2013-05-17 Thread Baptiste
Hi,

I would like to be able to  manage internal link that is exported with a
custom reference text. I mean define somewhere an anchor *plus the reference 
caption* and then use link mechanism to create a reference to this point with 
its given caption.

I do not find a way to do so.

Has I imagine it, it would look like

#+BEGIN_EXAMPLE
* Books
Presentation of the ref_book_1|/Important Book/.
… some text …

* What you have to read
… you should have a look at [[ref_book_1]] …

… some text …

* Where to find books
… [[ref_book_1]] is a free book from …
#+END_EXAMPLE

that would export as
#+BEGIN_EXAMPLE
* Books
Presentation of the /Important Book/.
… some text …

* What you have to read
… you should have a look at /Important Book/ …  ### (as a link to 
ref_book_1)

… some text …

* Where to find books
… /Important Book/ is a free book from …### (as a link to 
ref_book_1)
#+END_EXAMPLE

Did I miss something and there is a way to achieve this ? Or am-I the only one 
looking for such a function ?

Thank you

--

: ~^v^~ Bat



[O] conflict load of epresent - org mode 8.0.3

2013-05-17 Thread d . tchin
Hi,

This post to report a problem about epresent and new version of org mode.
I have just tried to update from releas 7.9.2 to 8.0.3 and I encountered 
several problems that are partially solved by the description of the 
changes due to the actual export and new name conventions.

From time to time, I use epresent tool that I find useful for tiny 
presentation. Tool is described here :

http://orgmode.org/worg/org-tutorials/non-beamer-presentations.html#sec-2

There are conflicts when this tool is loaded with new version of org mode.

In source files there are the following instructions :

(require 'org-exp)
(require 'org-latex)

As far I understand these modules are not available with this specific 
names. I have commented these two instruction in epresent-org.el and in 
epresent.el. 

I load ox.el and ox-latex.el in my .emacs and before loading the epresent 
tool and it seems to solve the conflicts and to work. 

Regard




Re: [O] M-RET and C-RET turn current line of text into a heading?

2013-05-17 Thread Jason F. McBrayer
Carsten Dominik carsten.domi...@gmail.com writes:

 On 16.5.2013, at 21:11, Jason F. McBrayer jmcb...@carcosa.net wrote:
 Another thing to take into account in the rewrite is doing the right
 thing even when electric-indent-mode or electric-layout-mode are
 enabled. The current implementation is not compatible with
 electric-indent-mode. 

 Never heard about these - need to look them up.

I think they were introduced in Emacs 24, to replace globally the
various hacks people were using previously. I found a workaround online
at [[http://foldl.me/2012/disabling-electric-indent-mode/][foldl]].

-- 
+---+  
| Jason F. McBrayerjmcb...@carcosa.net  |  
| If someone conquers a thousand times a thousand others in |  
| battle, and someone else conquers himself, the latter one |  
| is the greatest of all conquerors.  --- The Dhammapada|  



Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Bastien
Hi Max,

Max Mikhanosha m...@openchat.com writes:

 My list is.

 1. Convert defvar to defcustom

 2. Is (require 'dired) fine? It uses macro `dired-mark-if' defined in
dired.el

Seems fine to me.

 3. The prefix C-c M-s seems awkward but Org is so big everything else
is taken, and C-c C-x s is too close to C-c C-x C-s, which is
archive subtree (I initially had it there and moved after archiving
subtree by mistake)

I'd favor reserving C-c C-x for core packages, and use anything else
for contrib/ packages.

 Its its fine to go in as is, then its fine too, I'm pretty lazy :-)

Whatever sounds more practical to you!  You can include it now,
have more eyes watching (after) your code, then feel the pressure
to overcome the laziness in implementing the above :) 

-- 
 Bastien



Re: [O] sqlite im-/export

2013-05-17 Thread Eric Schulte
Oliver Večerník o...@vecernik.at writes:

 2. use :results drawer, and explicitly formatting the results in
Org-mode syntax w/awk

 Unfortunately this doesn't work.  The output is always printed to the
 #+RESULTS: section and not piped through awk.  But working with
 :results raw works perfect for me.  I can even produce a separator
 line in the table now with =print |-=.

 The only question left, how to import org tables on the fly to sqlite,
 to keep everthing in Org mode.  This would also be an interesting
 candidate for an ob-doc-sh.org starter I guess.

I may have missed you spelling this out in a previous email, but can you
not import Org tables directly into sqlite code blocks?

Evaluate this again after evaluating the second block.
#+BEGIN_SRC sqlite :csv :db test.sqlite
  SELECT * from t1;
#+END_SRC

#+RESULTS:
| 1 | apple pie |
| 2 | sugar |

A manually created Org-mode block.

#+name: manual
| 3 | rhubarb |
| 4 | butter  |

#+BEGIN_SRC sqlite :csv :var data=manual :db test.sqlite :results silent
  .separator ,
  .import $data t1
#+END_SRC

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


Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Max Mikhanosha
At Fri, 17 May 2013 15:05:05 +0200,
Carsten Dominik wrote:
  
  Nice and very useful. Can this be included in /contrib?
 
 Certainly!

Ok cool, I've already cleaned up the docstrings, I'll change some
defvars to defcustoms and commit it later today.

Regards,
  Max



Re: [O] using gnuplot's splot and every commands on org-mode table data

2013-05-17 Thread Eric Schulte

 I would consider this breaking the plot, in that gnuplot no longer lines
 up the two columns of data.


My fault, gnuplot does indeed still line up the data as appropriate when
missing values are simply replaced with blank space rather than .

I've just pushed up changes to gnuplot code blocks which add a :missing
header argument which may be used to specify a missing value, and which
replace missing values with blank space (rather than ) when the
missing header argument is not supplied.

The attached org-mode file demonstrates both.  Press C-c C-v v on each
code block, and then open up the data file to see the effects of the
header argument.

#+Property: :results silent

#+name: data
| 1 | 2 |
| 2 |   |
| 3 | 4 |
| 4 | 5 |

#+begin_src gnuplot :var data=data
  set key outside
  set xrange [-1:4]
  set yrange [0:6]
  plot data u 0:1, '' u 0:2
#+end_src

#+begin_src gnuplot :var data=data :missing ?
  set key outside
  set xrange [-1:4]
  set yrange [0:6]
  plot data u 0:1, '' u 0:2
#+end_src

Thanks for pushing this through
-- 
Eric Schulte
http://cs.unm.edu/~eschulte


[O] Best way to make/add tech diagrams/graphics?

2013-05-17 Thread Lawrence Bottorff
I'd like to embed images into my running org file -- for eventual
conversion to Latex or html. These would be simple diagram-style pictures
such as math or technical diagrams that cannot be done with gnuplot or
other formula-to-picture conversion software.

Examples:
http://www.library.utoronto.ca/see/SEED/Vol5-1/Queiroz_Emmeche_El-Hani_files/image003.gif
http://math.ucr.edu/home/baez/irvine/SBGN_process_description_cropped.jpg

I know emacs can draw some things, but I'd probably need better renditions.
So how does emacs/org handle such images and what sort of software (I'm on
Ubuntu) is available for making such drawings and diagrams? What about
software like Processing? Having Processing code embedded that then
produced images would be great.

Borgauf


Re: [O] Best way to make/add tech diagrams/graphics?

2013-05-17 Thread Russell Adams
Lawrence,

On Fri, May 17, 2013 at 10:13:56AM -0500, Lawrence Bottorff wrote:
 I'd like to embed images into my running org file -- for eventual
 conversion to Latex or html. These would be simple diagram-style pictures
 such as math or technical diagrams that cannot be done with gnuplot or
 other formula-to-picture conversion software.

 Examples:
 http://www.library.utoronto.ca/see/SEED/Vol5-1/Queiroz_Emmeche_El-Hani_files/image003.gif
 http://math.ucr.edu/home/baez/irvine/SBGN_process_description_cropped.jpg

 I know emacs can draw some things, but I'd probably need better renditions.
 So how does emacs/org handle such images and what sort of software (I'm on
 Ubuntu) is available for making such drawings and diagrams? What about
 software like Processing? Having Processing code embedded that then
 produced images would be great.

I routinely put diagrams in my technical documentation. I prefer to
create PDF files (ie: from Visio) and include them with Latex's
includepdf package, or inline with PNG images.

I must say however when I draw diagrams I use yEd, which is incredibly
powerful and auto-formatting. These diagrams can be exported to PDF
and put in Org easily.

Thanks.


--
Russell Adamsrlad...@adamsinfoserv.com

PGP Key ID: 0x1160DCB3   http://www.adamsinfoserv.com/

Fingerprint:1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3



Re: [O] Best way to make/add tech diagrams/graphics?

2013-05-17 Thread John Hendy
On Fri, May 17, 2013 at 10:13 AM, Lawrence Bottorff borg...@gmail.com wrote:
 I'd like to embed images into my running org file -- for eventual conversion
 to Latex or html. These would be simple diagram-style pictures such as math
 or technical diagrams that cannot be done with gnuplot or other
 formula-to-picture conversion software.

 Examples:
 http://www.library.utoronto.ca/see/SEED/Vol5-1/Queiroz_Emmeche_El-Hani_files/image003.gif
 http://math.ucr.edu/home/baez/irvine/SBGN_process_description_cropped.jpg


A few that come to mind for this sort of thing:
- ditaa: http://ditaa.sourceforge.net/
- graphviz/dot: http://www.graphviz.org/
- my personal favorite, but quite the learning curve, it PFG/TikZ:
http://www.texample.net/tikz/examples/

All are possible with babel blocks.


Good luck!
John

 I know emacs can draw some things, but I'd probably need better renditions.
 So how does emacs/org handle such images and what sort of software (I'm on
 Ubuntu) is available for making such drawings and diagrams? What about
 software like Processing? Having Processing code embedded that then
 produced images would be great.

 Borgauf



Re: [O] Best way to make/add tech diagrams/graphics?

2013-05-17 Thread Nick Dokos
Lawrence Bottorff borg...@gmail.com writes:

 I'd like to embed images into my running org file -- for eventual
 conversion to Latex or html. These would be simple diagram-style
 pictures such as math or technical diagrams that cannot be done with
 gnuplot or other formula-to-picture conversion software. 

 Examples:
 http://www.library.utoronto.ca/see/SEED/Vol5-1/Queiroz_Emmeche_El-Hani_files/image003.gif
 http://math.ucr.edu/home/baez/irvine/SBGN_process_description_cropped.jpg

 I know emacs can draw some things, but I'd probably need better
 renditions. So how does emacs/org handle such images and what sort of
 software (I'm on Ubuntu) is available for making such drawings and
 diagrams? What about software like Processing? Having Processing
 code embedded that then produced images would be great.


There is a myriad of graphics programs on Linux: graphviz/dot, ditaa,
plantuml, tikz, gimp, inkscape... There are many more. Some are general,
some are more specialized. Russell mentioned Visio but afaik that's
Windows only. Processing Processing code through a babel process should
be entirely processable too :-)

Once you produce output in some format (png, jpeg, svg, postscript -
whatever your emacs is capable of showing through the image.el
package[fn:1]), you can add a link to it in your org file. Then you can
toggle inline images on or off with C-c C-x C-v (or C-u C-c C-x C-v if
you have captions). Fundamentally, that's it - but of course, people
have been coming up with streamlined ways to do all that (e.g. Max M's
org-screenshot to take the most recent example).

Footnotes:

[fn:1] Mine can do png, jpeg, svg, xpm, but not postscript, even though
image-type-available-p says that it *is* available - there are other
formats that should also work, but that I have not tried: gif, pbm, xbm,
bmp, tiff. Not sure why postscript does not work for me.  On linux, the
various image types require that emacs be built with the various
libraries. On Windows, I think they are dynamically loaded, if present.

-- 
Nick




[O] Clocktable time Information without days (8.0) [7.9.2 (7.9.2-dist @ /usr/share/emacs/site-lisp/org/)]

2013-05-17 Thread Arne Babenhauserheide

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.


Dear Org-Hackers,

Since the update to org-mode 8.0¹ my timestamps show a day column, when
the time is longer than 24 hours. Since I use them to check a 40h
workweek, that gets in my way quite a bit. I think that I can get used
to it, but I would prefer to set it back to showing hours as highest unit.

Is there a way to tell org-mode to avoid showing days? This also
interferes with plotting via gnuplot (which does not know the day
format).

Best wishes,
Arne

PS: Sorry for abusing the report-bug function for this. It was the
fastest way to create this mail…


¹: I write this from another computer which still has org 7.

Emacs  : GNU Emacs 24.2.1 (x86_64-pc-linux-gnu, GTK+ Version 2.24.12)
 of 2013-03-20 on kaverne
Package: Org-mode version 7.9.2 (7.9.2-dist @ /usr/share/emacs/site-lisp/org/)



Re: [O] How to set C-o back to open-line?

2013-05-17 Thread Suvayu Ali
On Thu, May 16, 2013 at 09:28:35PM -0500, Christopher Allan Webber wrote:
 Suvayu Ali writes:
 
  That said, I'm curious what is so different about org-open-line?  The
  docstring says the following:
 
It is bound to C-o, insertline.

(org-open-line N)

Insert a new row in tables, call `open-line' elsewhere.
 
  So unless you are in a table, it should be the same as normal.  Is that
  broken?  Anyway, I never use open-line myself, but I was curious after I
  saw several people mention it on unrelated threads on a few lists.
 
 Right, exactly.  The way I use org-diet often involves me splitting
 apart and rejoining tables and the whole adding a new line in between
 is part of expected behavior for me.  The new system is driving me crazy!

Thanks, I see the use case.  I did have a similar need a few times.

Cheers,

-- 
Suvayu

Open source is the future. It sets us free.



[O] Bug: html quoting tags are transformed after exporting [8.0.2 (8.0.2-10-g3e1d83-elpa @ d:/SDTs/Emacs/lisp/org/)]

2013-05-17 Thread Kelvin Hu
Hi all,

First of all, I am really appreciate your good work - org mode.

Currently I meet something wrong when I am trying to export an org
buffer into html, as org manual
described(http://orgmode.org/org.html#Quoting-HTML-tags), html tags
quoted with @ should be exported as tags, but not transformed to
lt; and gt;. Now assume we have following contents:

*- @a href=somewheresome text@/a*

then I do exporting with following code(executed in that org buffer):

*(org-export-as 'html nil nil t nil)*

the output is:

*ul class=org-ul
li@lt;a href=somewheregt;some text@lt;/agt;
/li
/ul*

As you see, the quoted tag a is exported as transformed but not
original html tag.

Hope my description is not ambiguous, and it can do a little help for
you to fix this issue.

Thanks  Regards,
Kelvin


Emacs  : GNU Emacs 24.3.1 (i386-mingw-nt6.1.7601)
 of 2013-03-18 on MARVIN
Package: Org-mode version 8.0.2 (8.0.2-10-g3e1d83-elpa @
d:/SDTs/Emacs/lisp/org/)


Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Brett Viren
Hi Max, 

Max Mikhanosha m...@openchat.com writes:

 I have committed org-screenshot to master

This sounds like a great idea.  And just to prove that no good deed goes
unpunished, here is a bug report:

In an org-mode file I run M-x org-screenshot-take, scrot runs and I
can either click on a window or draw a selection box.  

However, lifting the mouse button leads to:

  error in process sentinel: Symbol's value as variable is void: return [2 
times]

An actual PNG is produced in the expected images/ subdir and also I
confirm that running /usr/bin/scrot -s /path/to/file.png by hand works
returning a 0 error code.

My org is:

  Org-mode version 8.0.3 (8.0.3-elpa @ /home/bviren/.emacs.d/elpa/org-20130514/)

Running in:

  GNU Emacs 24.1.1 (i486-pc-linux-gnu, GTK+ Version 2.24.10) of 2012-07-20 on 
murphy, modified by Debian

I copied the org-screenshot.el you just pushed from git's contrib/ to my
load path and added a (require 'org-screenshot) just after my
(require 'org).  The same behavior also occurs with the original copy
you posted to this mailing list.

A quick Google search just left me confused (I'm not great with elisp).
Is there anything I can do to debug this further?

Thanks,
-Brett.


pgpJZFNBqF1WX.pgp
Description: PGP signature


Re: [O] Internal link with custom caption

2013-05-17 Thread visayafan
Baptiste bate...@bat.fr.eu.org writes:

Hello, Baptiste


 I would like to be able to  manage internal link that is exported with a
 custom reference text. I mean define somewhere an anchor *plus the
 reference caption* and then use link mechanism to create a reference
 to this point with its given caption.


 I do not find a way to do so.


I don't think there is such a function but you can do it in this way:

#+BEGIN_EXAMPLE
* Books
Presentation of the ref_book_1 /Important Book/.
 some text 

* What you have to read
 you should have a look at /[[ref_book_1][Important Book]]/ 

 some text 

* Where to find books
 /[[ref_book_1][Important Book]]/ is a free book from 
#+END_EXAMPLE

Hope it helps.




Re: [O] RFQ - new contribution - org-screenshot.el

2013-05-17 Thread Max Mikhanosha
At Fri, 17 May 2013 13:20:16 -0400,
Brett Viren wrote:
 
 Hi Max, 
 
 Max Mikhanosha m...@openchat.com writes:
 
  I have committed org-screenshot to master
 
 This sounds like a great idea.  And just to prove that no good deed goes
 unpunished, here is a bug report:
 
 In an org-mode file I run M-x org-screenshot-take, scrot runs and I
 can either click on a window or draw a selection box.  
 
 However, lifting the mouse button leads to:
 
   error in process sentinel: Symbol's value as variable is void: return [2 
 times]

Just committed a potential fix, can you see if it works? Commit
0d68eef0372b6b57359a49cb5e35b67c651c5ee2

If it does not work, I'll need you to give me a backtrace, instructions on how
to are http://orgmode.org/manual/Feedback.html#Feedback around 1 page down
under How to create a useful backtrace

Regards,
  Max



Re: [O] M-RET and C-RET turn current line of text into a heading?

2013-05-17 Thread Rick Frankel
On Fri, May 17, 2013 at 03:26:09PM +0200, Carsten Dominik wrote:

 There was discussion about `C-c *'.  For me the main application
 of this command it to turn an item into a headline, and to turn *several*
 lines into a series of headline (by selecting the lines first) - this is
 a very frequent application when I paste text that I then need to structure.
 Nobody mentioned this in this thread, so maybe this feature is not known
 well enough.

I use `C-c *' and `C-c -' to turn lists - headlines all the time...



Re: [O] performance of exporting large tables

2013-05-17 Thread D M German

Hi Suvayu,

 Suvayu Hi Daniel,
 Suvayu On Thu, May 16, 2013 at 01:24:10PM -0700, D M German wrote:
  
  If interested, I can make the table available.

 Suvayu A working example that reproduces the issue always helps.  If you could
 Suvayu post the table (of course after removing sensitive/private information)
 Suvayu it would be great help for the developers and testers.

Here is a trivial example:

http://turingmachine.org/~dmg/temp/bigTable.org

(you can do anything with this file, including adding it to any battery
of tests in the future).

- Latex works well (export within a couple of seconds)
- ASCII, HTML, Markdown (based on html so no surpise) take more than a
  minute 

Does anybody know where the processing might be taking time? 

thanks again,

--daniel


 Suvayu Thanks,

 Suvayu -- 
 Suvayu Suvayu

 Suvayu Open source is the future. It sets us free.



--
Daniel M. German  Operating systems are like underwear,
   Bill Joy - nobody really wants to look at them.
http://turingmachine.org/
http://silvernegative.com/
dmg (at) uvic (dot) ca
replace (at) with @ and (dot) with .

 



Re: [O] using gnuplot's splot and every commands on org-mode table data

2013-05-17 Thread Paul Stansell
Hi Eric,

Thanks for your work on this.  I've tried your latest changes and I
think they're a big improvement.

I've attached another org-mode file for you to try.  It illustrates
the use of double blank lines in the first table (called block_data)
to inform gnuplot that there're two separate data sets in the single
data file.  The first code block (gnuplot_1) plots these two data sets
as red and green surfaces.  It's really nice that gnuplot can now be
used in this way from within org-mode.

One slight drawback, however, is that there still doesn't seem to be a
way to specify missing values in the org table in the way they're
frequently used by gnuplot.  An illustration of what I mean by this is
given in the table block_data_missing in the attached org file.
You'll see that I've inserted two '?' characters for missing z-values.
 If you execute the second and third code blocks (gnuplot_2 and
gnuplot_3) you'll see that neither give the desired result.

If the block_data_missing table were exported exactly as it is except
for the removal of the '|' characters and set datafile missing '?'
were specified in the gnuplot script this would enable gnuplot to plot
the red and green surfaces with the missing values.  To see this try
executing the last code block (gnuplot_4) which plots the data which
is first cleaned by the shell command you suggested in a previous
post.  This would also remove the need to have the :missing header
argument.

Kind regards,

Paul


gnuplot2.org
Description: Binary data


[O] Tbl: precision for cells

2013-05-17 Thread Manfred Lotz
I have a table like this

| Item |F1  |   F2 |   F3 |
|--++--+--|
| w| 579.12 | 110.0328 | 689.1528 |
| x|   28.8 |5.472 |   34.272 |
| y|   13.2 |2.508 |   15.708 |
| z|24. | 4.56 |28.56 |
|--++--+--|
| Sum  | 513.12 |  97.4928 | 610.6128 |

As the numeric fields are currency fields could I specify somehow for
the whole table that there are exactly 2 decimals after the dot?


So that I have this:
| Item |F1  |   F2 |   F3 |
|--++--+--|
| w| 579.12 |   110.03 |   689.15 |
| x|  28.80 | 5.47 |34.27 |
| y|  13.20 | 2.51 |15.71 |
| z|  24.00 | 4.56 |28.56 |
|--++--+--|
| Sum  | 513.12 |97.49 |   610.61 |


-- 
Thanks,
Manfred





[O] odt import

2013-05-17 Thread Uwe Brauer
Hello

I just found in wikipedia 
http://en.wikipedia.org/wiki/Org-mode

Claiming there are tools to import _from_ ODT.

Is this true? I have never seen anything like this.


Uwe Brauer 




Re: [O] Limit on length of babel block #+name: value?

2013-05-17 Thread John Hendy
I can't replicate anymore, though I did just update Org. Perhaps I
should have fiddled with it more before doing that...

If it happens again, I'll dig into it. Thanks for double
checking/attempting to replicate -- must be on my end.


John

On Thu, May 16, 2013 at 7:08 AM, Eric Schulte schulte.e...@gmail.com wrote:
 John Hendy jw.he...@gmail.com writes:

 I was just completely baffled for about 5-10 straight minutes as to
 why my block was not producing a  results section with my generated
 graphics file from an R block.

 I kept double checking my header options one by one despite having
 simply copied/pasted/modified it from a previous working block. Turns
 out it appears that #+name has a character limit!

 This (on Org-mode version 8.0.2 (release_8.0.2-65-g1e32d7)), doesn't work:

 #+name: improvement-treatment

 It appears the name can be 20 characters long (the above is 21).


 I don't think there is any name length limit.  The attached example
 works for me, and exports w/o problem to HTML.  Maybe I'm not using the
 block in the same way as you, but I'm pretty confident there is no name
 limit and your problem probably lies elsewhere.



 Best,


 Is this by design or something I accidentally uncovered? Forgive me if
 it's come up before or is documented. I did a couple searches but
 didn't see it.


 Thanks,
 John


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




Re: [O] using gnuplot's splot and every commands on org-mode table data

2013-05-17 Thread Paul Stansell
Hi Eric,

That's seems perfect now; I can't see any other issues.  Thanks!

Kind regards,

Paul



Re: [O] How to set C-o back to open-line?

2013-05-17 Thread Christopher Allan Webber
Nicolas Richard writes:

   (setq org-open-line 'open-line)

 How could that possibly work ?

It didn't... my bad :)  I had both set that and done a redefinition of
org-open-line to just call open-line like:

(defun org-open-line (n)
  (interactive *p)
  (open-line n))

Guess which one actually did anything ;)



Re: [O] How to set C-o back to open-line?

2013-05-17 Thread Christopher Allan Webber
Carsten Dominik writes:

 On 17.5.2013, at 00:38, Christopher Allan Webber cweb...@dustycloud.org 
 wrote:

 I really hate org-open-line... I can see why people might want it, but
 it's messed up my workflow.  I'd like to set C-o back.
 
 However, I have no idea what org-defkey is doing, but I expected this to
 work:
 
 (define-key org-mode-map (kbd C-o) 'open-line)

 This one will work if you do it in org-mode-hook.

Ahah... okay, great, thanks :)

 We could also introduce a variable to turn off the special behavior,
 just like we do for C-a, C-e, and C-k.  This seems to me a better
 option than to introduce additional context dependencies or use
 prefix arguments to influence the behavior.

 - Carsten

I think that would be nice.  We have options for everything else, why
not this? ;)

Thanks for the help, all!



[O] Org-mode v8 broke my workflow

2013-05-17 Thread Marcin Borkowski
Hi list,

can't resist;): http://xkcd.com/1172/

I have this at the end of my .emacs:

(setq inhibit-splash-screen t)
(org-agenda-list)
(delete-window)

The point is that I want agenda to appear as the only thing when I
start Emacs.  However, sometimes I start it e.g. when delivering a
presentation; I don't want all the people to look at my overdue todo
items;), so I used to press q while Emacs was starting (which takes
quite a while on my netbook).  This used to bury the agenda so that
*scratch* was visible.  Now, instead of *scratch*, one of my agenda
org files appears.  What do I do to restore the previous behavior?
(Really, that setup worked for me;).)

Best,

-- 
Marcin Borkowski
http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
Adam Mickiewicz University



Re: [O] odt import

2013-05-17 Thread Ethan Ligon
Uwe Brauer oub at mat.ucm.es writes:

 
 Hello
 
 I just found in wikipedia 
 http://en.wikipedia.org/wiki/Org-mode
 
 Claiming there are tools to import _from_ ODT.
 
 Is this true? I have never seen anything like this.
 
 Uwe Brauer 
 
 

Presumably a reference to

https://bitbucket.org/josemaria.alkala/odt2org/wiki/Home

I haven't used it, and it's rather old (predates org-elements, I think).  

-Ethan




Re: [O] M-RET inside the first second-level heading of the first first-level heading

2013-05-17 Thread John Hendy
On Fri, May 10, 2013 at 1:49 AM, Carsten Dominik
carsten.domi...@gmail.com wrote:

 On 7.5.2013, at 23:34, John Hendy jw.he...@gmail.com wrote:

 On Tue, May 7, 2013 at 4:54 AM, Bastien b...@gnu.org wrote:
 Hi John,

 John Hendy jw.he...@gmail.com writes:

 On Fri, Apr 26, 2013 at 1:54 AM, Bastien b...@gnu.org wrote:
 Hi Jisang,

 Jisang Yoo jisang.yoo.ac+...@gmail.com writes:

 2. Place cursor at the beginning of ** bacon and press M-RET and org 
 creates
 a first-level heading.

 This should now be fixed.  Thanks for reporting this,

 There were some same/similar/related issues as well, and I'm still not
 getting perfect results.

 Using a minimal config (below), if I create this in a new file

 * test
 ** test1
 ** test2

 and then fold on * test, I get this:

 * test...2

 I do have (setq require-final-newline t) in my config, which prevents
 this.  What happens is this: if you don't have the config above, the
 folding will get wrong and display the 2 from the end of the buffer.

 Also, after navigating to the end of * test...2 (with it folded) and
 issuing M-RET, I get a new second level heading after ** test2. I
 would have expected a new first level headline since I did M-RET on a
 first level headline. Or is that the default behavior?

 If you are before the ... ellipsis, you are on a first level
 headline and M-RET will insert a first level headline.  Otherwise you
 are on a second level headline (test2) and it will insert a second
 level headline.

 Ah, that now makes sense. But... just to be clear, take this case:

 * Headline1
 - list1
 - list2

 Now fold it:

 * Headline1cursor...

 If I do M-RET at cursor, I get:

 * Headline1
 * cursor
 - list1
 - list2

 Is that how it's supposed to work? My use case is generally to have a
 new headline after * Headline1 *and* it's contents, not putting
 contents inside the new headline.

 C-RET seems to behave more like I'd expect. In reading the manual, I
 think I was just confused on usage based on the definition of C-RET,
 however this in the description of M-RET is confusing:

 #+begin_quote
 If the command is used at the end of a folded subtree (i.e., behind
 the ellipses at the end of a headline), then a headline like the
 current one will be inserted after the end of the subtree. Calling
 this command with C-u C-u will unconditionally respect the headline's
 content and create a new item at the end of the parent subtree.
 #+end_quote

 It makes it seem like my original case in which the cursor is behind
 (after?) the ... should insert a same-level headline after the end of
 the current subtree (which I would assume means that headline and all
 contents). Am I reading that incorrectly? It doesn't really talk about
 the behavior if you're before the ellipsis.

 Yes, this is also a bit confusing.  I think it would be desirable if it
 worked as described in the manual, but this is not what is happening.
 For now, I fixed the manual.


Much appreciated, and I'll be following the other M-RET and C-RET
thread as it seems some of this behavior will change in the near
future.


Thanks!
John

 - Carsten




 Thanks for clarifying,
 John


 If so, I guess my only concern is the folding of the end of a headline
 if there's no hard return after it into the ellipsis of it's parent.

 Yes.  Maybe M-RET could/should handle this corner-case but since
 `org-insert-heading' is deserving a full rewrite, I'm not going to
 try to handle this corner-case myself... let's just keep it in mind
 when doing the rewrite.  Thanks for spotting it,

 --
 Bastien





Re: [O] Best way to make/add tech diagrams/graphics?

2013-05-17 Thread Marcin Borkowski
Dnia 2013-05-17, o godz. 11:40:17
John Hendy jw.he...@gmail.com napisał(a):

 On Fri, May 17, 2013 at 10:13 AM, Lawrence Bottorff
 borg...@gmail.com wrote:
  I'd like to embed images into my running org file -- for eventual
  conversion to Latex or html. These would be simple diagram-style
  pictures such as math or technical diagrams that cannot be done
  with gnuplot or other formula-to-picture conversion software.
 
  Examples:
  http://www.library.utoronto.ca/see/SEED/Vol5-1/Queiroz_Emmeche_El-Hani_files/image003.gif
  http://math.ucr.edu/home/baez/irvine/SBGN_process_description_cropped.jpg
 
 
 A few that come to mind for this sort of thing:
 - ditaa: http://ditaa.sourceforge.net/
 - graphviz/dot: http://www.graphviz.org/
 - my personal favorite, but quite the learning curve, it PFG/TikZ:
 http://www.texample.net/tikz/examples/

Typo: it's PGF, not PFG, just in case you wanted to google it or
something;).

I'd also mention Metapost, on which I believe TikZ was modeled (at least
to some extent).

Since you mentioned embedding in LaTeX, I'd also suggest TikZ; it has a
huge manual, but /very/ well written, with quite a few tutorials and
examples. One benefit is that it is tightly integrated into LaTeX,
but it can also export SVG (though with a few limitations compared to
the pdfLaTeX-produced output).  Also, you might want to check out the
gallery of TikZ examples here: http://www.texample.net/tikz/ .

 Good luck!
 John

Best,

-- 
Marcin Borkowski
http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
Adam Mickiewicz University



Re: [O] Best way to make/add tech diagrams/graphics?

2013-05-17 Thread John Hendy
On Fri, May 17, 2013 at 6:09 PM, Marcin Borkowski mb...@wmi.amu.edu.pl wrote:
 Dnia 2013-05-17, o godz. 11:40:17
 John Hendy jw.he...@gmail.com napisał(a):

 On Fri, May 17, 2013 at 10:13 AM, Lawrence Bottorff
 borg...@gmail.com wrote:
  I'd like to embed images into my running org file -- for eventual
  conversion to Latex or html. These would be simple diagram-style
  pictures such as math or technical diagrams that cannot be done
  with gnuplot or other formula-to-picture conversion software.
 
  Examples:
  http://www.library.utoronto.ca/see/SEED/Vol5-1/Queiroz_Emmeche_El-Hani_files/image003.gif
  http://math.ucr.edu/home/baez/irvine/SBGN_process_description_cropped.jpg
 

 A few that come to mind for this sort of thing:
 - ditaa: http://ditaa.sourceforge.net/
 - graphviz/dot: http://www.graphviz.org/
 - my personal favorite, but quite the learning curve, it PFG/TikZ:
 http://www.texample.net/tikz/examples/

 Typo: it's PGF, not PFG, just in case you wanted to google it or
 something;).


Oops -- typo on my part.

 I'd also mention Metapost, on which I believe TikZ was modeled (at least
 to some extent).

 Since you mentioned embedding in LaTeX, I'd also suggest TikZ; it has a
 huge manual, but /very/ well written, with quite a few tutorials and
 examples. One benefit is that it is tightly integrated into LaTeX,
 but it can also export SVG (though with a few limitations compared to
 the pdfLaTeX-produced output).  Also, you might want to check out the
 gallery of TikZ examples here: http://www.texample.net/tikz/ .


The examples are great. The link I provided goes right to the examples
vs. that sort of home page screen which only shows the most recent
couple that have been submitted.

I'll have to check out metapost, as I'd not heard of that one.


Thanks,
John

 Good luck!
 John

 Best,

 --
 Marcin Borkowski
 http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
 Adam Mickiewicz University




Re: [O] Bug: html quoting tags are transformed after exporting [8.0.2 (8.0.2-10-g3e1d83-elpa @ d:/SDTs/Emacs/lisp/org/)]

2013-05-17 Thread Eric Abrahamsen
Kelvin Hu ini.kel...@gmail.com writes:

 Hi all,

 First of all, I am really appreciate your good work - org mode.

 Currently I meet something wrong when I am trying to export an org
 buffer into html, as org manual
 described(http://orgmode.org/org.html#Quoting-HTML-tags), html tags
 quoted with @ should be exported as tags, but not transformed to 
 lt; and gt;. Now assume we have following contents:

 - @a href=somewheresome text@/a

The syntax for this has changed, now any backend-specific blocks can be
exported with @@backend:foo@@. So yours should be:

@@html:a href=somewheresome text/a@@

The manual's wrong, I think: if you look at the ascii or latex export
sections they mention this syntax, but it looks like html got left
behind.

Yours,
Eric

 then I do exporting with following code(executed in that org buffer):

 (org-export-as 'html nil nil t nil)

 the output is:

 ul class=org-ul
 li@lt;a href=somewheregt;some text@lt;/agt;
 /li
 /ul

 As you see, the quoted tag a is exported as transformed but not
 original html tag.

 Hope my description is not ambiguous, and it can do a little help for
 you to fix this issue.

 Thanks  Regards,
 Kelvin

 Emacs : GNU Emacs 24.3.1 (i386-mingw-nt6.1.7601)
 of 2013-03-18 on MARVIN
 Package: Org-mode version 8.0.2 (8.0.2-10-g3e1d83-elpa @
 d:/SDTs/Emacs/lisp/org/)




Re: [O] Bug: html quoting tags are transformed after exporting [8.0.2 (8.0.2-10-g3e1d83-elpa @ d:/SDTs/Emacs/lisp/org/)]

2013-05-17 Thread Eric Abrahamsen
Eric Abrahamsen e...@ericabrahamsen.net writes:

 Kelvin Hu ini.kel...@gmail.com writes:

 Hi all,

 First of all, I am really appreciate your good work - org mode.

 Currently I meet something wrong when I am trying to export an org
 buffer into html, as org manual
 described(http://orgmode.org/org.html#Quoting-HTML-tags), html tags
 quoted with @ should be exported as tags, but not transformed to 
 lt; and gt;. Now assume we have following contents:

 - @a href=somewheresome text@/a

 The syntax for this has changed, now any backend-specific blocks can be
 exported with @@backend:foo@@. So yours should be:

 @@html:a href=somewheresome text/a@@

 The manual's wrong, I think: if you look at the ascii or latex export
 sections they mention this syntax, but it looks like html got left
 behind.

 Yours,
 Eric

A documentation patch to that effect...

E

From 14d5a493375197bcdcbd0b292e1d9990f12cb83a Mon Sep 17 00:00:00 2001
From: Eric Abrahamsen e...@ericabrahamsen.net
Date: Sat, 18 May 2013 10:20:33 +0800
Subject: [PATCH] org.texi: Correct syntax for exporting HTML fragments

---
 doc/org.texi | 10 +-
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/doc/org.texi b/doc/org.texi
index 1c8b835..6f0afed 100644
--- a/doc/org.texi
+++ b/doc/org.texi
@@ -11133,11 +11133,11 @@ to @code{nil} will not insert any postamble.
 @subsection Quoting HTML tags
 
 Plain @samp{} and @samp{} are always transformed to @samp{lt;} and
-@samp{gt;} in HTML export.  If you want to include simple HTML tags
-which should be interpreted as such, mark them with @samp{@@} as in
-@samp{@@bbold text@@/b}.  Note that this really works only for
-simple tags.  For more extensive HTML that should be copied verbatim to
-the exported file use either
+@samp{gt;} in HTML export.  If you want to include simple HTML tags which
+should be interpreted as such, mark them with @samp{html:} as in
+@samp{html:bbold text/b}.  Note that this really works only for
+simple tags.  For more extensive HTML that should be copied verbatim to the
+exported file use either
 
 @cindex #+HTML
 @cindex #+BEGIN_HTML
-- 
1.8.2.3