Re: [O] [dev] New version of org-index.el --- A personal index for org and beyond

2013-09-23 Thread Alan Schmitt

m...@ihm.name writes:

 Here are a few notes I'm taking as I'm playing with it.

 First, the table seems to be different from the one on worg. Here are
 the columns I have:

   | |  |  | |   | comment   |
   | ref | link | created  | count;s | last-accessed | ;c|
   | | 4  |  | |   |   |

 I guess comment includes Type, description, and Keywords? Or can I
 extend this table as I see fit?


 Yes, just add any further columns you need. As long as the do not have a
 semicolon, they are ignored. You can also reorder columns according to
 your needs.

Ah, good to know, thanks.

 Also, I noticed it's impossible to create a link to a file. If a file
 does not have any org entry, then org-index link will fail with Before
 first headline at position 35591 in buffer  I can go around this by
 creating an headline, but then I cannot use saveplace or something like
 that to put me in the same place in the file (typically at the very end
 of a long data table, to input more data).

 Currently org-index uses the function org-id-get-create to create the
 link. This function needs an org-mode nodes and whence org-index has the
 same limitation. However, it might be possible to create more general
 links here, that would be able to point to non-org files. I will check
 this for the next version.

This would be great. Maybe a support for usual org links could be a way
to do this?

 Finally, what is the workflow to create a new reference? The way I do it
 is link from the place to link, then call +fill in the table. Is
 there a simpler way (that would do both in one stroke)?

 Definitely: With the initial prompt just choose ref; this will only
 create a new reference, but not a link. If you want both, then you
 currently have to use the workflow you described. However, having a
 feature, that allows both, would be easy to implement, if needed.

Could you give examples of when one would want a link without a ref, or
a ref without a link?

Thanks again,

Alan



Re: [O] [Babel] Padlines

2013-09-23 Thread Sebastien Vauban
Hi Eric,

Eric Schulte wrote:
 Sebastien Vauban sva-n...@mygooglest.com writes:
 Eric Schulte wrote:
 aditya siram aditya.si...@gmail.com writes:
 What's the rationale for having padlines by default in tangled source? It
 generates wrong programs for languages where whitespace is significant
 (Haskell) and, for me, doesn't noticeably improve the look of the tangled
 file in cases where it isn't.

 It is possible to change the value of default header arguments on a
 per-language basis because e.g., while (:padlines yes) may make sense
 for sh, it probably doesn't for Haskell.

 Could it be possible that :padline yes does not insert a blank line in 
 front
 of the very first block, only *between* all blocks?

 I just pushed up a commit which implements this behavior.  See the
 attached file for an example.

 #+Title: Examples with the new padline behavior

 #+headers: :tangle pad-yes-with-shebang.sed
 #+headers: :shebang #!/bin/sed -f 
 #+headers: :padline yes
 #+begin_src sed
   1 {N;s/\n//1}
 #+end_src

 #+headers: :tangle pad-no-with-shebang.sed
 #+headers: :shebang #!/bin/sed -f
 #+headers: :padline no
 #+begin_src sed
   1 {N;s/\n//1}
 #+end_src

 #+headers: :tangle pad-yes-without-shebang.sed
 #+headers: :padline yes
 #+begin_src sed
   1 {N;s/\n//1}
 #+end_src
 #+headers: :tangle pad-no-without-shebang.sed
 #+headers: :padline no
 #+begin_src sed
   1 {N;s/\n//1}
 #+end_src

 1. Tangle the above four blocks with =C-c C-v t=.
 2. Execute the following code block to view the contents of the
resulting sed files.

 #+begin_src sh :results scalar
   head pad*sed
 #+end_src

 #+RESULTS:
 : == padline-example.sed ==
 : #!/bin/sed -f
 : 
 : 1 {N;s/\n//1}
 : 
 : == pad-no-without-shebang.sed ==
 : 1 {N;s/\n//1}
 : 
 : == pad-no-with-shebang.sed ==
 : #!/bin/sed -f
 : 1 {N;s/\n//1}
 : 
 : == pad-yes-without-shebang.sed ==
 : 1 {N;s/\n//1}
 : 
 : == pad-yes-with-shebang.sed ==
 : #!/bin/sed -f
 : 
 : 1 {N;s/\n//1}

That seems perfect, and solves corner-cases I wouldn't have thought of (with
shebang). Thanks a lot!

Best regards,
  Seb

-- 
Sebastien Vauban




[O] [BUG] in Release 8.2 - editing code in indirect buffer

2013-09-23 Thread Rainer M Krug
I just resend this bug report which has been confirmed by Ista Zahn.

Updated via git ust now:

Org-mode version 8.2 (release_8.2-14-ge5f16b @
/Users/rainerkrug/.emacs.d/org-mode/lisp/)


When starting to edit a code block via C-c ' everything works as expected
and the code block is highlighted and an indirect buffer is opened.

When I click into the highlighted block, I an send to the indirect
buffer. This behavior changes, after saving with C-s, even when nothing
has been edited: the area in the original org file looses its magic, and
looks normal again and can also be edited! 

The indirect buffer stays functional and, upon close via C-c ' saves the
changes into the original buffer and *overwrites* changes done in this
block in the org document.

Rainer

-- 
Rainer M. Krug

email: RMKrugatgmaildotcom


pgpJdi4wn5Nmu.pgp
Description: PGP signature


Re: [O] Strange Behaviour while rescheduling date

2013-09-23 Thread Sebastien Vauban
Hello,

G. Martin Butz wrote:
 In case I try to reschedule a date from the weekly agenda view I get the
 following backtrace; I am under the impression, that this seems not to be the
 bug, which I have tried to describe in the last message, but at least it
 shows, that something is wrong (with my setup/emacs/org?)

 Debugger entered--Lisp error: (error Before first headline at position 1 in
 buffer date.org)

FYI, I also experience that (annoying) message now and then, but I never
understood which conditions did make it appear -- and, no, it's not an advised
split-window in my case ;-(.

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] Strange Behaviour while rescheduling date

2013-09-23 Thread Carsten Dominik

On 23.9.2013, at 09:46, Sebastien Vauban sva-n...@mygooglest.com wrote:

 Hello,
 
 G. Martin Butz wrote:
 In case I try to reschedule a date from the weekly agenda view I get the
 following backtrace; I am under the impression, that this seems not to be the
 bug, which I have tried to describe in the last message, but at least it
 shows, that something is wrong (with my setup/emacs/org?)
 
 Debugger entered--Lisp error: (error Before first headline at position 1 in
 buffer date.org)
 
 FYI, I also experience that (annoying) message now and then, but I never
 understood which conditions did make it appear -- and, no, it's not an advised
 split-window in my case ;-(.


This message happens when Org tries to go back to a heading and the cursor is 
before the first headline.  Most of the time this should not cause an error - 
please make a backtrace when it happens.

- Carsten
 
 Best regards,
  Seb
 
 -- 
 Sebastien Vauban
 
 



signature.asc
Description: Message signed with OpenPGP using GPGMail


Re: [O] Strange Behaviour while rescheduling date

2013-09-23 Thread G. Martin Butz

Hello Sebastian,

Am 23.09.2013 09:46, schrieb Sebastien Vauban:

Hello,

G. Martin Butz wrote:

In case I try to reschedule a date from the weekly agenda view I get the
following backtrace; I am under the impression, that this seems not to be the
bug, which I have tried to describe in the last message, but at least it
shows, that something is wrong (with my setup/emacs/org?)

Debugger entered--Lisp error: (error Before first headline at position 1 in
buffer date.org)


FYI, I also experience that (annoying) message now and then, but I never
understood which conditions did make it appear -- and, no, it's not an advised
split-window in my case ;-(.


well, I am not entirely sure, that the backtrace I manage to get  was 
actually directly related to the initially described behaviour. Seemed 
to be two differnt things but somehow connected. As I could not savely 
reproduce the rescheduling and replacing of an org-buffer by the 
calendar (no backtrace/no 'official' error) I did use the rescheduling 
of a date starting from the agenda buffer as a test case. This led to 
the offendig config /split-window/.


Now everything seems to work fine.

So far
Martin


Best regards,
   Seb




--

| G. Martin Butz, m...@mkblog.org, 0421 98749324, www.mkblog.org |




Re: [O] C-u C-u C-c ! inserts an active timestamp.

2013-09-23 Thread Nicolas Richard
Carsten Dominik carsten.domi...@gmail.com writes:

 Applied

I noticed that the whole mail went into the commit msg (commit
12de6223dcd736c0958eca874def052b407ff5d1) ; did I send the patch
incorrectly ?

I used git format-patch then inserted the result at the end of the email
I wrote. The page http://orgmode.org/worg/org-contribute.html#sec-4 is
not very explicit about how to send the result of `git format-patch',
but I seem to remember it was ok to just yank the content at the end of
a mail. Is that a wrong assumption ?

-- 
Nicolas



Re: [O] C-u C-u C-c ! inserts an active timestamp.

2013-09-23 Thread Suvayu Ali
On Mon, Sep 23, 2013 at 10:51:33AM +0200, Nicolas Richard wrote:
 Carsten Dominik carsten.domi...@gmail.com writes:
 
  Applied
 
 I noticed that the whole mail went into the commit msg (commit
 12de6223dcd736c0958eca874def052b407ff5d1) ; did I send the patch
 incorrectly ?
 
 I used git format-patch then inserted the result at the end of the email
 I wrote. The page http://orgmode.org/worg/org-contribute.html#sec-4 is
 not very explicit about how to send the result of `git format-patch',
 but I seem to remember it was ok to just yank the content at the end of
 a mail. Is that a wrong assumption ?

Simply attaching the patch as a text attachment should do fine I think.

-- 
Suvayu

Open source is the future. It sets us free.



Re: [O] C-u C-u C-c ! inserts an active timestamp.

2013-09-23 Thread Sebastien Vauban
Hello Suvayu,

Suvayu Ali wrote:
 On Mon, Sep 23, 2013 at 10:51:33AM +0200, Nicolas Richard wrote:
 Carsten Dominik carsten.domi...@gmail.com writes:
 
  Applied
 
 I noticed that the whole mail went into the commit msg (commit
 12de6223dcd736c0958eca874def052b407ff5d1) ; did I send the patch
 incorrectly ?
 
 I used git format-patch then inserted the result at the end of the email
 I wrote. The page http://orgmode.org/worg/org-contribute.html#sec-4 is
 not very explicit about how to send the result of `git format-patch',
 but I seem to remember it was ok to just yank the content at the end of
 a mail. Is that a wrong assumption ?

 Simply attaching the patch as a text attachment should do fine I think.

Though, many guidelines tell:

  Do not attach your patch, but submit it inline in the mail body,
  /unless you cannot teach your mailer to leave the formatting
  of the patch alone/.

That allows for easy reviews... and easy comments (after every chunk of code).

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] File-local export filters

2013-09-23 Thread Rasmus
Hi Carsten,

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

 Have I overlooked an easy way to do this, or would this be
 something others would like to use as well.

Can't you identify it by the folder name?  Or with a
special #+DESCRIPTION or #+KEYWORDS?

Like this: 

#+TITLE: MySpecialFile.org

#+begin_src emacs-lisp
(defun rasmus/match-buffer (text backend info)
  Match only some buffers identified by 
  (if (and
   (string-match MySpecialFile (plist-get info :input-file))
   (org-export-derived-backend-p backend 'latex))
  Match! text)) 

(add-to-list 'org-export-filter-final-output-functions
 'rasmus/match-buffer) 
#+end_src

Otherwise I'd also bind the value locally and maintain the code in a
SETUPFILE or in a * lisp :noexport: heading.

–Rasmus


-- 
I almost cut my hair, it happened just the other day




[O] convenience sort function

2013-09-23 Thread Christian Wittern

Dear org users,

I would like to define a convenience sort function to sort on a certain 
property (e.g PRE), which I can assign to a key, so that I can avoid having 
to type


C-^ r PRE RET

It seems that I want to call org-sort-entries, which has the following 
signature:


(defun org-sort-entries
  (optional with-case sorting-type getkey-func compare-func property)

From the docstring, I learn that I have to use ?r to sort on properties and 
the last parameter is the property to sort on, PRE in this case.  However, 
what I do not understand is what I should give for getkey-func and 
compare-func.

Something like this
(org-sort-entries t ?r t t PRE)
or this
(org-sort-entries t ?r nil nil PRE)
does not work, and reading the source does not give me any clues (probably 
because I do not understand what is going on)


Any help would be apprectiated,

Christian


--
Christian Wittern, Kyoto




Re: [O] Bug: Wrong type argument: arrayp, nil when exporting to beamer [8.2 (8.2-elpa @ /Users/jason/.emacs.d/elpa/org-20130919/)]

2013-09-23 Thread Nicolas Goaziou
Hello,

Jason Lewis ja...@dickson.st writes:

 Thanks. The error message is not very clear and this is an easy
 mistake for a beginner to make.

I think that nesting frames is a strange error to make.

Anyway, here is the relevant part of the manual:

   - Headlines become frames when their level is equal to
 'org-beamer-frame-level' or 'H' value in an 'OPTIONS' line (*note
 Export settings::).

 Though, if a headline in the current tree has a 'BEAMER_ENV'
 property set to either to 'frame' or 'fullframe', its level
 overrides the variable.  A 'fullframe' is a frame with an empty
 (ignored) title.

Do you think it should be reformulated? If so, could you suggest what
would be needed?


Regards,

-- 
Nicolas Goaziou



[O] Non-interactive org-schedule

2013-09-23 Thread Marcin Borkowski
Hi all,

I'd like to call org-schedule from an Elisp function.  I'd like it to,
say, insert today's date by default, and as a bonus, a repeater (I'm
writing a custom org-insert-habit function, so that I can automate
setting the STYLE and LOGGING proerties).  Calling just (org-schedule)
did not work.  How to do that?

Best,

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



[O] A custom exporter

2013-09-23 Thread Marcin Borkowski
Hi all,

I'm toying with an idea of writing my own exporter backend, based on the
html one.  My question is: what should I read to learn how to do this?
I am aware of http://orgmode.org/worg/exporters/ox-overview.html, but
ox-\(element-\)?docstrings look a bit scary.  I thought that reading
the source code of some existing backend alongside the docstrings might
be helpful.  Am I right?  Do you have any suggestions as to which one to
choose first?  How did the authors of existing backends start learning
how to do that, and do they have any tips for their younger colleague;)?

Best,

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



Re: [O] C-u C-u C-c ! inserts an active timestamp.

2013-09-23 Thread Suvayu Ali
On Mon, Sep 23, 2013 at 11:16:25AM +0200, Sebastien Vauban wrote:
 Hello Suvayu,
 
 Suvayu Ali wrote:
  On Mon, Sep 23, 2013 at 10:51:33AM +0200, Nicolas Richard wrote:
  Carsten Dominik carsten.domi...@gmail.com writes:
  
   Applied
  
  I noticed that the whole mail went into the commit msg (commit
  12de6223dcd736c0958eca874def052b407ff5d1) ; did I send the patch
  incorrectly ?
  
  I used git format-patch then inserted the result at the end of the email
  I wrote. The page http://orgmode.org/worg/org-contribute.html#sec-4 is
  not very explicit about how to send the result of `git format-patch',
  but I seem to remember it was ok to just yank the content at the end of
  a mail. Is that a wrong assumption ?
 
  Simply attaching the patch as a text attachment should do fine I think.
 
 Though, many guidelines tell:
 
   Do not attach your patch, but submit it inline in the mail body,
   /unless you cannot teach your mailer to leave the formatting
   of the patch alone/.
 
 That allows for easy reviews... and easy comments (after every chunk of code).

Valid point.  In that case maybe the problem was Nicolas's patch was
inlined after the signature marker, -- .

-- 
Suvayu

Open source is the future. It sets us free.



[O] [Babel] Lisp error: (wrong-type-argument listp hline)

2013-09-23 Thread Sebastien Vauban
Hello Eric,

This ECM does generate an error, when run with :hlines yes.

#+name: table
| Key | Value |
|-+---|
| ABJ | 1 |
| DEK | 2 |

As you can see, there is one header and one horizontal line in the input
table.

* Set :hlines to no

Adding `:hlines no' strips the horizontal line, but does keep the header.

  #+begin_src emacs-lisp :var data=table :results output :hlines no
  (mapc (lambda (item) (princ (format UPDATE dim SET val=%s WHERE code='%s'\n
  (nth 1 item) (nth 0 item
   data)
  #+end_src

  #+results:
  #+begin_example
  UPDATE dim SET val=Value WHERE code = 'Key'   LINE NOT WANTED
  UPDATE dim SET val=1 WHERE code = 'ABJ'
  UPDATE dim SET val=2 WHERE code = 'DEK'
  #+end_example

* Set :hlines to yes

`:hlines yes' should leave the horizontal line, but generates an error.

  #+begin_src emacs-lisp :var data=table :results output :hlines yes
  (mapc (lambda (item) (princ (format UPDATE dim SET val=%s WHERE code='%s'\n
  (nth 1 item) (nth 0 item
   data)
  #+end_src

--8---cut here---start-8---
  Debugger entered--Lisp error: (wrong-type-argument listp hline)
nth(1 hline)
(format UPDATE dim SET val=%s WHERE code='%s'\n (nth 1 item) (nth 0 item))
(princ (format UPDATE dim SET val=%s WHERE code='%s'\n (nth 1 item) (nth 
0 item)))
(lambda (item) (princ (format UPDATE dim SET val=%s WHERE code='%s'\n 
(nth 1 item) (nth 0 item(hline)
mapc((lambda (item) (princ (format UPDATE dim SET val=%s WHERE 
code='%s'\n (nth 1 item) (nth 0 item ((Key Value) hline (ABJ 1) 
(DEK 2)))
...
call-interactively(org-self-insert-command nil nil)
--8---cut here---end---8---

* Ignore the table header

Finally, how am I then supposed to *ignore the header line*?  By adding

  #+begin_src emacs-lisp
  (setq table (cdr table))
  #+end_src

?

Do I have to do that explicitly in my code block, or is there an option for
telling that to Babel?

Best regards,
  Seb

-- 
Sebastien Vauban




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

2013-09-23 Thread Paul Stansell
Hi Eric,

There appears to be a slight bug in the way gnuplot handles blocked
data with missing entries.

An example is provided in the org script at then end of this note.

In the code block gnuplot_1 the use of ':missing ?' seems to cause
the exported data file to lack the blanks lines that are essential
for the plot.  The plot from this code block is incorrect.

In gnuplot_2 ':missing' is not used, but instead 'set datafile missing
?' is set explicitly in the gnuplot code block.  The plot from this
code block is correct.

Surely gnuplot_1 should produce exactly the same plot as gnuplot_2.

Kind regards,

Paul


Exported data file does not include blank lines.
#+name: gnuplot_1
#+begin_src gnuplot :var d=block_data_missing :missing ? :results silent
  set ticslevel 0
  splot d index 0 u 1:2:3 w lp pt 6 ps 5, d index 1 u 1:2:3 w lp pt 6 ps 5
#+end_src

Exported data file includes blank lines.
#+name: gnuplot_2
#+begin_src gnuplot :var d=block_data_missing :results silent
  set datafile missing ?
  set ticslevel 0
  splot d index 0 u 1:2:3 w lp pt 6 ps 5, d index 1 u 1:2:3 w lp pt 6 ps 5
#+end_src

#+name: block_data_missing
| 1 | 1 |  2 |
| 1 | 2 |  5 |
| 1 | 3 | 10 |
|   |   ||
| 2 | 1 |  5 |
| 2 | 2 | 10 |
| 2 | 3 | 13 |
|   |   ||
| 3 | 1 | 10 |
| 3 | 2 |  ? |
| 3 | 3 | 18 |
|   |   ||
|   |   ||
| 1 | 1 | 12 |
| 1 | 2 | 15 |
| 1 | 3 | 20 |
|   |   ||
| 2 | 1 | 15 |
| 2 | 2 | 18 |
| 2 | 3 | 23 |
|   |   ||
| 3 | 1 |  ? |
| 3 | 2 | 23 |
| 3 | 3 | 28 |







Re: [O] A custom exporter

2013-09-23 Thread Josiah Schwab

 I'm toying with an idea of writing my own exporter backend, based on the
 html one.  My question is: what should I read to learn how to do this?
 I am aware of http://orgmode.org/worg/exporters/ox-overview.html, but
 ox-\(element-\)?docstrings look a bit scary.  I thought that reading
 the source code of some existing backend alongside the docstrings might
 be helpful.  Am I right?  Do you have any suggestions as to which one to
 choose first?  How did the authors of existing backends start learning
 how to do that, and do they have any tips for their younger colleague;)?

I'm also very much in the inexperienced camp, but I did find that
reading though a derived exporter (I read the ox-md.el) was useful.
Between that and asking couple of questions on this mailing list, I was
able to write the minimal exporter I needed.

Best,
Josiah



Re: [O] org mode R remote code evaluation

2013-09-23 Thread Alexander Vorobiev
The :results output doesn't help in my setup (I'm on Windows, the remote
system is linux, access is via putty/plink)

#+BEGIN_SRC sh :results output :dir /grid:
  ls
#+END_SRC

executing Sh code block...
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY...done
byte-code: Couldn't write region to
`/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY', decode
using `tramp_perl_decode_with_module %s' failed

The /Users directory obviously does not exist on linux.

Tramp itself works in my configuration, I can open files, etc. I have the
latest org-mode from elpa.

Thanks,
Alex


On Thu, Aug 29, 2013 at 5:42 AM, Johannes Rainer 
johannes.rai...@i-med.ac.at wrote:

 thanks! so the :results output does the trick.




 On Thu, Aug 29, 2013 at 10:25 AM, Loris Bennett 
 loris.benn...@fu-berlin.de wrote:

 Johannes Rainer johannes.rai...@gmail.com writes:

  dear all,
 
  I have some computation intense R-code that I want to run remotely on
 my server,
  and, according to the org manual that should be possible with the :dir
  parameter. so I went on and tried the following (user/server masked):
 
  #+BEGIN_SRC R :dir /xx@xxx:
system(hostname)
  #+END_SRC
 
  when I execute it I get the error:
 
  Tramp: Encoding region using function `base64-encode-region'...done
  Tramp: Decoding region into remote file
  /ssh:xx@xxx
 :/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs...done
  byte-code: Couldn't write region to
  `/ssh:xx@xxx
 :/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs',
  decode using `base64 -d -i %s' failed
 
  apparently, this temp folder does not exist on the linux server, it is
 actually
  the temp folder from my local machine.
 
  I get the same error when I try to execute remote shell code, so it's
 not R
  related.
 
  I also tried to start a ssh session using M-x ssh and used the source
 block
 
  #+BEGIN_SRC R :exports both :session *ssh xxx*
  system(hostname)
  #+END_SRC
 
  on the server it executes the command but it can not write the results:
 
  xxx
  Warning message:
  In file.rename(tfile, transfer.file) :
cannot rename file '/tmp/RtmpsirjGl/file51c8f6ce4ec' to
 
 '/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/babel-46345zSH/R-46345a4N',
  reason 'No such file or directory'
 
 
  I am using emacs 24.3 and Org-mode version 8.0.7
 (release_8.0.7-384-g6fdc23)
 
  I would be helpful for any suggestions how I could solve this problem.
 
  thanks in advance

 The following works for me:

 #+BEGIN_SRC R :results output :dir /xxx@x:
 system(hostname)
 #+END_SRC

 with Emacs 24.2.1 and 8.0.7 (8.0.7-6-g13cb28-elpaplus)

 Cheers,

 Loris

 --
 This signature is currently under construction.





 --
 Johannes Rainer, PhD
 Applied Bioinformatics Group,
 Division Molecular Pathophysiology,
 Biocenter, Medical University Innsbruck,
 Innrain 80/82 II, 6020 Innsbruck, Austria
 and
 Tyrolean Cancer Research Institute
 Innrain 66, 6020 Innsbruck, Austria

 Tel.: +43 (0)512 9003 70961
 Email:  johannes.rai...@i-med.ac.at
 johannes.rai...@tcri.at
 URL:   http://bioinfo.i-med.ac.at





[O] [PATCH] Markdown: Add publishing in markdown

2013-09-23 Thread Brice Waegenire
* lisp/ox-md.el

Add  the possibility to publish in Markdown by using the function
org-md-publish-to-md.

TINYCHANGE
---
diff --git a/lisp/ox-md.el b/lisp/ox-md.el
index f7e4875..71759ac 100644
--- a/lisp/ox-md.el
+++ b/lisp/ox-md.el
@@ -31,7 +31,7 @@

 (eval-when-compile (require 'cl))
 (require 'ox-html)
-
+(require 'ox-publish)

 ^L
 ;;; User-Configurable Variables
@@ -477,6 +477,17 @@ Return output file's name.
 (org-export-to-file 'md outfile async subtreep visible-only)))


+;;;###autoload
+(defun org-md-publish-to-md (plist filename pub-dir)
+  Publish an org file to Markdown.
+
+FILENAME is the filename of the Org file to be published.  PLIST
+is the property list for the given project.  PUB-DIR is the
+publishing directory.
+
+Return output file name.
+  (org-publish-org-to 'md filename .md plist pub-dir))
+
 (provide 'ox-md)

 ;; Local variables:



[O] [PATCH] Markdown: add publishing in markdown

2013-09-23 Thread Brice Waegenire
* lisp/ox-md.el

Add  the possibility to publish in Markdown by using the function
org-md-publish-to-md.

TINYCHANGE
---
diff --git a/lisp/ox-md.el b/lisp/ox-md.el
index f7e4875..71759ac 100644
--- a/lisp/ox-md.el
+++ b/lisp/ox-md.el
@@ -31,7 +31,7 @@

 (eval-when-compile (require 'cl))
 (require 'ox-html)
-
+(require 'ox-publish)

 ^L
 ;;; User-Configurable Variables
@@ -477,6 +477,17 @@ Return output file's name.
 (org-export-to-file 'md outfile async subtreep visible-only)))


+;;;###autoload
+(defun org-md-publish-to-md (plist filename pub-dir)
+  Publish an org file to Markdown.
+
+FILENAME is the filename of the Org file to be published.  PLIST
+is the property list for the given project.  PUB-DIR is the
+publishing directory.
+
+Return output file name.
+  (org-publish-org-to 'md filename .md plist pub-dir))
+
 (provide 'ox-md)

 ;; Local variables:



Re: [O] Bug: subtree LaTeX export problems after upgrade [8.1 (8.1-elpa @ /home/brian/.emacs.d/elpa/org-20130906/)]

2013-09-23 Thread Brian Zbriger
Please disregard my recent bug report re: LaTeX exports... the problem was
entirely on my end.


[O] Bug: subtree LaTeX export problems after upgrade [8.1 (8.1-elpa @ /home/brian/.emacs.d/elpa/org-20130906/)]

2013-09-23 Thread Brian Zbriger
I just upgraded to org-mode 8.1 using 'package-install' and I think I am
encountering some bugs when
exporting to LaTeX. I am using the following tags
in the header of my orgmode files:

#+AUTHOR:[my name]
#+DATE:  %B %e, %Y

If I am exporting an entire buffer, %B %e, %Y now shows up verbatim
instead of as a date like it used to.

If I am exporting a subtree, I am also forced to re-specify the author and
date with :EXPORT_DATE: and :EXPORT_AUTHOR: or else the name is changed to
Charles Cave and the date something like 01-01-2009.


Emacs  : GNU Emacs 24.2.1 (i686-pc-linux-gnu, GTK+ Version 3.6.4)
 of 2013-04-09 on komainu, modified by Debian
Package: Org-mode version 8.1 (8.1-elpa @
/home/brian/.emacs.d/elpa/org-20130906/)

current state:
==
(setq
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
  org-babel-execute-safely-maybe)
 org-latex-format-headline-function
'org-latex-format-headline-default-function
 org-export-with-drawers '(not LOGBOOK)
 org-export-copy-to-kill-ring 'if-interactive
 org-archive-location ::*Archived Tasks
 org-export-date-timestamp-format nil
 org-export-with-tags t
 org-tab-first-hook '(org-hide-block-toggle-maybe
  org-src-native-tab-command-maybe
  org-babel-hide-result-toggle-maybe
  org-babel-header-arg-expand)
 org-refile-targets '((org-agenda-files :maxlevel . 3))
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
  org-cycle-hide-inline-tasks org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-speed-command-hook '(org-speed-command-default-hook
  org-babel-speed-command-hook)
 org-babel-pre-tangle-hook '(save-buffer)
 org-occur-hook '(org-first-headline-recenter)
 org-export-email-info t
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-capture-templates '((t Task entry
  (file+headline ~/MasterFile.org Tasks)
  * TODO %? %i %a)
 (n General Note entry
  (file+headline ~/MasterFile.org Notes)
  * %? %i %a :kill-buffer t)
 )
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-log-refile 'time
 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)
 org-directory ~/Documents/
 org-export-creator-info nil
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-agenda-files '(~/Documents/area_paper2/area_paper2.org
~/MasterFile.org)
 org-file-apps '((auto-mode . emacs) (\\.mm\\' . default)
 (\\.x?html?\\' . default) (\\.pdf\\' . evince %s))
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
 org-src-mode-configure-edit-buffer)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-confirm-shell-link-function 'yes-or-no-p
 )


Re: [O] [OT] mail followup to (was Re: M-x fill-region equivalent for lists?)

2013-09-23 Thread Eric S Fraga
Sebastien Vauban sva-n...@mygooglest.com writes:

[...]

 Yes, you must have something along that line:

   ;; addresses to prune (disable `Cc:' to myself) when doing wide replies
   (setq message-dont-reply-to-names gnus-ignored-from-addresses)

I do indeed!
Gnus has everything basically... :-)
Back to org now although gnus+org rules my days.

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.3.50.1, Org release_8.1.1-7-gaecdf5




Re: [O] Non-interactive org-schedule

2013-09-23 Thread Marcin Borkowski
Dnia 2013-09-23, o godz. 12:46:35
Marcin Borkowski mb...@wmi.amu.edu.pl napisał(a):

 I'd like to call org-schedule from an Elisp function.  I'd like it to,
 say, insert today's date by default, and as a bonus, a repeater (I'm
 writing a custom org-insert-habit function, so that I can automate
 setting the STYLE and LOGGING proerties).  Calling just (org-schedule)
 did not work.  How to do that?

OK, so I did my homework.  (I had done it previously, too, but I ran
(apropos today) which wasn't exactly what was needed;).)  Here's the
code:

(org-schedule nil (format-time-string %Y-%m-%d (current-time)))

Adding a repeater seems to require something along the lines of

(save-excursion
  (search-forward )
  (backward-char)
  (insert (concat
 .+
(read-string Minimum interval: )
/
(read-string Maximum interval: 

(I realize that this is *very* crude implementation, but remember that
it's a quick-and-dirty hack to be used once every few days at most, so
coding it in an elegant way would be a bit of waste of time...)

 Best,

Cheers,

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



Re: [O] Non-interactive org-schedule

2013-09-23 Thread Marcin Borkowski
Dnia 2013-09-23, o godz. 21:46:10
Marcin Borkowski mb...@wmi.amu.edu.pl napisał(a):

 [...] 
 (I'm writing a custom org-insert-habit function, so that I can
 [...] 

#+BEGIN_SHAMELESS_PLUG
Just in case someone might need something like this.  (Not that it's
difficult, but why reinvent the wheel.)  The code is ugly and crude,
and not very general, but works for me.

http://mbork.pl/2013-09-23_Automatic_insertion_of_habit_templates_%28en%29
#+END_SHAMELESS_PLUG

Best,

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



Re: [O] [PATCH] Markdown: add publishing in markdown

2013-09-23 Thread Nicolas Goaziou
Hello,

Brice Waegenire brice@gmail.com writes:

 * lisp/ox-md.el

 Add  the possibility to publish in Markdown by using the function
 org-md-publish-to-md.

 TINYCHANGE

Thank you for your patch.

Would you mind posting it again using git format-patch? Also the commit
message could be:

  ox-md: Add publishing function to back-end

  * lisp/ox-md.el: Add the possibility to publish in Markdown by using
the function `org-md-publish-to-md'.


Regards,

-- 
Nicolas Goaziou



Re: [O] [Babel] Lisp error: (wrong-type-argument listp hline)

2013-09-23 Thread Eric Schulte
Hi Seb,

I think you're confused by headers which are re-added by the colnames
machinery.  See the following which returns scalar output avoiding any
colnames post-processing.

#+Property: results scalar

#+name: table
| Key | Value |
|-+---|
| ABJ | 1 |
| DEK | 2 |

#+begin_src emacs-lisp :var data=table :hlines no
  data
#+end_src

#+RESULTS:
: ((Key Value) (ABJ 1) (DEK 2))

#+begin_src emacs-lisp :var data=table :hlines yes
  data
#+end_src

#+RESULTS:
: ((Key Value) hline (ABJ 1) (DEK 2))

 * Set :hlines to yes

 `:hlines yes' should leave the horizontal line, but generates an error.

   #+begin_src emacs-lisp :var data=table :results output :hlines yes
   (mapc (lambda (item) (princ (format UPDATE dim SET val=%s WHERE 
 code='%s'\n
   (nth 1 item) (nth 0 item
data)
   #+end_src

This is not a babel error, this is an error in your code block body,
which assumes that every element of `data' will be a list.  The symbol
`hline' is not a list.


 Finally, how am I then supposed to *ignore the header line*?  By adding

   #+begin_src emacs-lisp
   (setq table (cdr table))
   #+end_src

 ?

 Do I have to do that explicitly in my code block, or is there an option for
 telling that to Babel?


Use the :colnames processing to strip the headings.

#+begin_src emacs-lisp :var data=table :colnames yes
  data
#+end_src

#+RESULTS:
: ((ABJ 1) (DEK 2))

Best,


 Best regards,
   Seb

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D


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

2013-09-23 Thread Eric Schulte
Paul Stansell paulstans...@gmail.com writes:

 Hi Eric,

 There appears to be a slight bug in the way gnuplot handles blocked
 data with missing entries.

 An example is provided in the org script at then end of this note.

 In the code block gnuplot_1 the use of ':missing ?' seems to cause
 the exported data file to lack the blanks lines that are essential
 for the plot.  The plot from this code block is incorrect.

 In gnuplot_2 ':missing' is not used, but instead 'set datafile missing
 ?' is set explicitly in the gnuplot code block.  The plot from this
 code block is correct.

 Surely gnuplot_1 should produce exactly the same plot as gnuplot_2.


Hi Paul,

Currently the :missing header argument for gnuplot code blocks does two
things.  It adds the set datafile missing... line to the code block
body *and* it binds `*org-babel-gnuplot-missing*' to the value of the
:missing header argument when the datafile is written, so empty table
cells are replaced with the value of the :missing header argument.

The reason you're not getting a blank line is because it is replaced
with three missing values, in this case ? ? ?.

Do you think this behavior should be changed or split between two header
arguments?

Thanks,


 Kind regards,

 Paul


 Exported data file does not include blank lines.
 #+name: gnuplot_1
 #+begin_src gnuplot :var d=block_data_missing :missing ? :results silent
   set ticslevel 0
   splot d index 0 u 1:2:3 w lp pt 6 ps 5, d index 1 u 1:2:3 w lp pt 6 ps 5
 #+end_src

 Exported data file includes blank lines.
 #+name: gnuplot_2
 #+begin_src gnuplot :var d=block_data_missing :results silent
   set datafile missing ?
   set ticslevel 0
   splot d index 0 u 1:2:3 w lp pt 6 ps 5, d index 1 u 1:2:3 w lp pt 6 ps 5
 #+end_src

 #+name: block_data_missing
 | 1 | 1 |  2 |
 | 1 | 2 |  5 |
 | 1 | 3 | 10 |
 |   |   ||
 | 2 | 1 |  5 |
 | 2 | 2 | 10 |
 | 2 | 3 | 13 |
 |   |   ||
 | 3 | 1 | 10 |
 | 3 | 2 |  ? |
 | 3 | 3 | 18 |
 |   |   ||
 |   |   ||
 | 1 | 1 | 12 |
 | 1 | 2 | 15 |
 | 1 | 3 | 20 |
 |   |   ||
 | 2 | 1 | 15 |
 | 2 | 2 | 18 |
 | 2 | 3 | 23 |
 |   |   ||
 | 3 | 1 |  ? |
 | 3 | 2 | 23 |
 | 3 | 3 | 28 |






-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D