[O] Org Tutorials need more structure

[Carsten Dominik]

Hi everyone,

today I looked at our tutorial page at

http://orgmode.org/worg/org-tutorials/index.html

and came away with the feeling that that this page has become
somewhat useless for people who are really new to Org.  I think
the page should start with a section of true recommendations
for beginners, a path we tell every new users to take in order to
learn about Org mode.

Can we have a discussion here on how this path should look like?
When you came to Org-mode as a newby, what were the three resources
that really made an impression on by being accessible and
providing feel and promise for digging deeper?

- Carsten


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Re: [O] how to provide feedback to the org documentation on the website?

[Nick Dokos]

t...@tsdye.com (Thomas S. Dye) writes:
> Jason Lewis  writes:
>> I noticed a word that is probably wrong in the org doco online. What's
>> the general procedure for providing feedback? It's not editable like a
>> wiki is it?
>>
>> Specifically on the page http://orgmode.org/manual/Beamer-export.html
>>
>> " Eventually, every plain list has support" should read "Finally, every
>> plain list has support"
>>
> It is editable! You can find how to register and use git for editing
> Worg here:
>
> http://orgmode.org/worg/worg-about.html
>
> It's actually a pleasure to work on its org-mode files.
>

That's true for worg files but Jason was talking about the org-mode
manual. I believe that's not editable except by developers. The easiest
way to make a change is to send a bug report. It's also possible to post
a patch to the list - in the same way that one would provide a patch for
code (with all the conditions that this implies: TINY change, FSF
copyright assignment, following conventions etc.). For details, see

 http://orgmode.org/worg/org-contribute.html

-- 
Nick

[O] EXPORT_FILE_NAME when exporting the entire org file ?

[Martin Leduc]

Hi everyone,   when exporting only a subtree to pdf, we can set the output file 
such as:
* Some headline:PROPERTIES::EXPORT_FILE_NAME: /path/filename:END:  Is it 
possible to set the output path/filename when exporting the entire org file ? 
(e.g. in the heading #+OPTIONS)
Thanks !Martin

Re: [O] how to provide feedback to the org documentation on the website?

[Thomas S. Dye]

Hi Jason,

It is editable! You can find how to register and use git for editing
Worg here:

http://orgmode.org/worg/worg-about.html

It's actually a pleasure to work on its org-mode files.

All the best,
Tom

Jason Lewis  writes:

> Hi,
>
> I noticed a word that is probably wrong in the org doco online. What's
> the general procedure for providing feedback? It's not editable like a
> wiki is it?
>
> Specifically on the page http://orgmode.org/manual/Beamer-export.html
>
> " Eventually, every plain list has support" should read "Finally, every
> plain list has support"
>
> Jason
>
> -- 
> Jason Lewis
> http://emacstragic.net
>
> Hi,
>
> I noticed a word that is probably wrong in the org doco online. What's
> the general procedure for providing feedback? It's not editable like a
> wiki is it?
>
> Specifically on the page http://orgmode.org/manual/Beamer-export.html
>
> " Eventually, every plain list has support" should read "Finally,
> every plain list has support"
>
> Jason

-- 
Thomas S. Dye
http://www.tsdye.com

[O] how to provide feedback to the org documentation on the website?

[Jason Lewis]

Hi,

I noticed a word that is probably wrong in the org doco online. What's
the general procedure for providing feedback? It's not editable like a
wiki is it?

Specifically on the page http://orgmode.org/manual/Beamer-export.html

" Eventually, every plain list has support" should read "Finally, every
plain list has support"

Jason

-- 
Jason Lewis
http://emacstragic.net



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[O] Transpose or open functions for table cells

[Suvayu Ali]

Hi,

I was wondering if there are any transpose functions for table cells;
something akin to transpose-lines, or transpose-words.  I am also
looking for something like org-open-line, but only for a table cell.
This is my use case:

| col 1 | col 2 |   | col 1 | col 2 |
|---+---+   +---+---|
| 1 | a |   | 1 | a |
| 2 | b |  -->  | 2 | b |
| 3 | d |   | 3 |   |
| 4 | e |   | 4 | d |
| 5 |   |   | 5 | e |

If neither exists, any thoughts how might one go about writing one?

Thanks for any ideas.

-- 
Suvayu

Open source is the future. It sets us free.

[O] Table of Contents Title header

[Ciaran Mulloy]

Hi,
I am using Org-mode for writing product manuals and documentation and
exporting to PDF using the Latex Export. (I'm still using Org-Mode 7.8 as
I've been a little apprehensive about upgrading to the new Latex Export
version). 

I am using the fancy header package: 
#+LATEX_HEADER: \usepackage{fancyhdr}
#+LATEX_HEADER: \pagestyle{fancy}
#+LATEX_HEADER:
\fancyhead[RO,RE]{\includegraphics[width=1.5cm]{company_logo.pdf}} 

It outputs a nice section header together with the company logo nicely
positioned at the top of the page.

My only problem is that I want to include a table of contents which I do as
follows in the title header:

#+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t


However the Table of Contents section title 'Contents' overwrites the
section header 'contents' at the top of the page. Is there a way of being
able to suppress the Table of Contents title 'Contents'.

I know that in Latex one can have an additional option of how a section
header is displayed and just show a blank text. However I haven't been able
to do that. 

Any suggestions would be very welcome!

Ciaran

Re: [O] org-debbugs.el

[Suvayu Ali]

On Fri, Sep 27, 2013 at 09:28:00PM +0200, Michael Albinus wrote:
> Hi,
> 
> I have produced a very first shot of org-debbugs.el. It shows you bug
> reports from debbugs.gnu.org as TODO items. It needs the debbugs package
> from the GNU ELPA repository.
> 
> If you want to try it, you could call
> 
>   (org-debbugs nil '("org-mode"))
> 
> You will see a list of TODO items which belong to the org-mode bugs on
> debbugs.gnu.org. The last link of such an item, [[Messages]], shows you
> all corresponding messages for that bug.
> 
> If you want to see a bulk of bug reports, call
> 
>   (org-debbugs
> '("serious" "important" "normal")
> '("emacs"))
> 
> This returns much more bugs (from the "emacs" project), presented as
> chunk of 500 TODO items. If you follow the link at the very end of the
> buffer, you will get the next 500 items. And so on.
> 
> You can call it also interactively, via "M-x org-debbugs" or "C-u M-x
> org-debbugs".
> 
> Have fun!

I did not do extensive testing, but from a quick look, absolutely
amazing!  This package should definitely go into contrib.

Thanks a lot Michael.

:)

-- 
Suvayu

Open source is the future. It sets us free.

[O] org-debbugs.el

[Michael Albinus]

Hi,

I have produced a very first shot of org-debbugs.el. It shows you bug
reports from debbugs.gnu.org as TODO items. It needs the debbugs package
from the GNU ELPA repository.

If you want to try it, you could call

  (org-debbugs nil '("org-mode"))

You will see a list of TODO items which belong to the org-mode bugs on
debbugs.gnu.org. The last link of such an item, [[Messages]], shows you
all corresponding messages for that bug.

If you want to see a bulk of bug reports, call

  (org-debbugs
'("serious" "important" "normal")
'("emacs"))

This returns much more bugs (from the "emacs" project), presented as
chunk of 500 TODO items. If you follow the link at the very end of the
buffer, you will get the next 500 items. And so on.

You can call it also interactively, via "M-x org-debbugs" or "C-u M-x
org-debbugs".

Have fun!

Best regards, Michael.



org-debbugs.el
Description: application/emacs-lisp

[O] `orgstruct++-mode',`fill-paragraph', and `mail-mode'

[Rene]

I like the intuitive way the Org mode structure editing and list
formatting works.  Thus I turn it on in mail-mode with 

 (add-hook 'mail-mode-hook 'turn-on-orgstruct)

This works alright.

But when I use `orgstruct++-mode'

 (add-hook 'mail-mode-hook 'turn-on-orgstruct++)

Then `fill-paragraph' (M-q) doesn't behave correctly anymore when
applied to the paragraph right below the `mail-header-separator'
("--text follows this line--").  All the above lines get rearranged.

I just realized that with `orgstruct-mode' the regexp
`paragraph-separate' contains the `mail-header-separator', whereas
with `orgstruct++-mode' this regexp does NOT contain the
`mail-header-separator'.  

The value of `paragraph-separate' is predefined in `sendmail.el'.

`orgstruct-mode' appends new regexps to `paragraph-separate', whereas
`orgstruct++-mode' replaces the initial value (given within
`sendmail.el') by orgmode specific ones.

--
Rene

[O] Exporting C++ code block to html

[Xavier Garrido]

Dear Orgers,

I face a problem when I want to 'html' export a pretty simple org file : 
test.org contains the following lines


#+BEGIN_SRC c++
int j= 1;
#+END_SRC

If I do
emacs --batch -q --eval '(require (quote org))' --visit test.org \ 
--funcall org-html-export-to-html


I get
Loading vc-git...
Loading cc-langs...
Symbol's function definition is void: nil

I have also activated the debug mode but the messages are quite cryptic 
for me (attached file). The point is that it only crashes with C/C++ 
languages but works with python, awk, sh, emacs-lisp ...


I'm using orgmode 8.2-35 from the git repository.

Thanks for your help,
Xavier
oading vc-git...
Loading cc-langs...
Debugger entered--Lisp error: (void-function nil)
  nil(1 12 nil)
  c-font-lock-fontify-region(1 12 nil)
  font-lock-fontify-region(1 12 nil)
  byte-code("\212\303 \304\216\305ed	#\210\306 \210\307\211+\207" [save-match-data-internal verbose font-lock-fontified match-data ((byte-code "\30\302\"\207" [save-match-data-internal set-match-data evaporate] 3)) font-lock-fontify-region font-lock-after-fontify-buffer t] 4)
  font-lock-default-fontify-buffer()
  font-lock-fontify-buffer()
  org-html-fontify-code("int j = 1;\n" "c++")
  org-html-do-format-code("int j = 1;\n" "c++" nil t nil)
  org-html-format-code((src-block (:language "c++" :switches nil :parameters nil :begin 1 :end 39 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :hiddenp nil :value "int j = 1;\n" :post-blank 0 :post-affiliated 1 :parent (section (:begin 1 :end 39 :contents-begin 1 :contents-end 39 :post-blank 0 :parent (org-data nil #2)) #0))) (:export-options nil :input-file "/home/garrido/Teachdir/C++.test/test.org" :title "test" :html-extension "html" :html-link-org-as-html t :html-doctype "xhtml-strict" :html-container "div" :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :html-head-include-default-style t :html-head-include-scripts t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-tags ("" . "") :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-inline-images t :creator "http://www.gnu.org/software/emacs/\";>Emacs 24.3.1 (http://orgmode.org\";>Org mode 8.2)" :with-latex t :author nil ...))
  org-html-src-block((src-block (:language "c++" :switches nil :parameters nil :begin 1 :end 39 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :hiddenp nil :value "int j = 1;\n" :post-blank 0 :post-affiliated 1 :parent (section (:begin 1 :end 39 :contents-begin 1 :contents-end 39 :post-blank 0 :parent (org-data nil #2)) #0))) nil (:export-options nil :input-file "/home/garrido/Teachdir/C++.test/test.org" :title "test" :html-extension "html" :html-link-org-as-html t :html-doctype "xhtml-strict" :html-container "div" :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :html-head-include-default-style t :html-head-include-scripts t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-tags ("" . "") :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-inline-images t :creator "http://www.gnu.org/software/emacs/\";>Emacs 24.3.1 (http://orgmode.org\";>Org mode 8.2)" :with-latex t :author nil ...))
  org-export-data((src-block (:language "c++" :switches nil :parameters nil :begin 1 :end 39 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :hiddenp nil :value "int j = 1;\n" :post-blank 0 :post-affiliated 1 :parent (section (:begin 1 :end 39 :contents-begin 1 :contents-end 39 :post-blank 0 :parent (org-data nil #2)) #0))) (:export-options nil :input-file "/home/garrido/Teachdir/C++.test/test.org" :title "test" :html-extension "html" :html-link-org-as-html t :html-doctype "xhtml-strict" :html-container "div" :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :html-head-include-default-style t :html-head-include-scripts t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-tags ("" . "") :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-inline-images t :creator "http://www.gnu.org/software/emacs/\";>Emacs 24.3.1 (http://orgmode.org\";>Org mode 8.2)" :with-latex t :author nil ...))
  #[(element) "\302 \"\207" [element info org-export-data] 3]((src-block (:language "c++" :switches nil :parameters nil :begin 1 :end 39 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :hiddenp nil :value "int j = 1;\n" :post-blank 0 :post-affiliated 1 :parent (section

Re: [O] example filter for code blocks?

[John Kitchin]

That is a pretty interesting pdf. I cannot think of a way to do this
simply. I think that filters get an info argument, which contains the parse
tree. Maybe you could use that to build up a table of which blocks refer to
each other somehow. I guess you would need some syntax in the src-block to
indicate which blocks were referred to. then, use filters to modify the
output of the rendered src-block by inserting the links in.

From: "Sebastien Vauban" 
To: emacs-orgmode@gnu.org
Cc:
Date: Fri, 27 Sep 2013 09:42:39 +0200
Subject: Re: [O] example filter for code blocks?
Hello,

John Kitchin wrote:
> Thanks for  the tips in using export filters for code blocks. I thought I
> would share my current solution. The goal was to export all the code
blocks
> in an org-file to files systematically named part1/script-%d.py where %d
is
> a number. I didnot want to tangle exactly, because I wanted to avoid
naming
> the code block tangle files.
>
> Then, I wanted to insert a pdf link that would open the file, after the
> syntax highlighted code.

Thanks for sharing your wonderful solution!

Related to such things, something I'd like to have for long (but never found
time investigating it more) is that the PDF produced by Org would resemble
more
the PDF produced by Noweb.

In the attached example file (sent on this ML in... 2009), you see that the
Noweb extension to LaTeX

- generated a code block number: page number + order (if there are multiple
  code blocks on the same page);

- for each code block, attached a reference to all code blocks using it.

In the example, you see that code block "sql-init.sql" (defined on page 2)
gets
the number 2a (in that export [1]), and is used in code blocks 2c and 3. And
all those references are hyperlinks.

I found that very handy for reading your LP (or RR) document.

Best regards,
  Seb

[1] It could change if text or code is added in the documentation.

--
Sebastien Vauban
John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu

Re: [O] Exploring data that is in org-mode format

[John Hendy]

On Fri, Sep 27, 2013 at 3:18 AM, Alan Schmitt
 wrote:
> Hello,
>
> This question is slightly off-topic, but it may be of interest to people
> who have a lot of data entered in org-mode.
>
> The short version: what tools are available to explore data, typically
> stored in org-mode tables?

[snip]

> So I collect all this data because it's something I enjoy doing, and I
> would really like to explore it, from the comfortable position of my own
> computer. All of this data is in org-mode tables (or can be easily
> converted to org-mode table). Hence my questions: are there tools you
> would recommend? I'm not afraid of programming (I suspect an answer will
> be 'R'), but I would like pointers to tutorials to do these kind of
> things. The kind of things I would like to do are:
> - extract weekly or monthly tallies or estimation from data collected at
> irregular intervals;
> - compare data sources against each other;
> - estimate future trends based on past data (how much will my gas bill be?);
> - display the result in some kind of dashboard.
>

For simple exploration, you might have a look at ggobi? [1] It allows
you to do some really quick/easy exploration by plotting and being
able to check which variables to use for X and Y, coloring, filtering,
changing plot type, and so on. There's an R package which allows you
to call ggobi on an R data object, which you could easily create with
babel and your existing org tables with the #+name option for the
table and :var specification in the babel block header.

I'd also highly recommend taking a look at shiny via R-Studio.[2] Not
sure if you can call it from Org-mode, but even if you can't... not
*everything* has to be done with Org. You could use the file to do
some data munging/summarization/etc., save it as a new data set (.csv
or similar), and then read that into Shiny. It could be *awesome* for
something like this. I only recently started playing with it but it's
just fantastic and would make for the ability to subset, change
scales/time ranges, and much more in an interactive web app.

I applied for a public server account with RStudio and got it so that
as I learn and do more, I can make them public. As a result of an SO
question, I repaid the answerer by creating an app from his reply:
- Post: 
http://stackoverflow.com/questions/17958730/faceting-a-set-of-contour-plots-in-ggplot-r
- Shiny app: http://spark.rstudio.com/jwhendy/interactive-contour/


Good luck!
John

[1] http://www.ggobi.org/
[2] http://www.rstudio.com/shiny/


> Thanks a lot,
>
> Alan
>

[O] Fwd: epresent issue

[Rustom Mody]

On Fri, Sep 27, 2013 at 9:58 PM, Rustom Mody  wrote:

> On Fri, Sep 27, 2013 at 3:13 PM, Eric Schulte wrote:
>
>> Rustom Mody  writes:
>>
>> > On Fri, Sep 27, 2013 at 7:20 AM, Rustom Mody 
>> wrote:
>> >
>> >> Hi
>> >>
>> >> I am trying to use epresent for presentation.
>> >> Start epresent with M-x epresent-run
>> >>
>> >> I seem to need to press one more q to get out of epresenting and then
>> that
>> >> q gets into the file.
>> >>
>>
>> I can't reproduce this problem with a recent version of epresent and
>> Org-mode.  For example with the following minimal Emacs invocation
>> (without any configuration, run from the epresent directory).
>>
>> emacs -Q --eval "(progn (add-to-list 'load-path
>> \"~/src/org-mode/lisp\") (require 'org))" -l epresent.el present.org
>>
>
> I tried this (with my-path adjustments); and a just-downloaded epresent
> from above link; still the same behavior
>
> In more detail:
>
> 0. Run command
>
> emacs -Q --eval "(progn (add-to-list 'load-path \"~/pdsw/org-mode/lisp\")
> (require 'org))" -l ~/.emacs.d/downloads/epresent.el  lastLect.org
> and then in emacs:
>
> 1. Start with epresent-run
> The buffer changes form half-way -- ie
> a. it becomes full-screen,
> b the menu line vanishes but
> c. the mode line is present
> d. the fonts are still small
>
> 2. After than whatever key I press (including q) it becomes like a
> presentation -- ie no mode-line and large fonts
>
> 3. One more q and it quits with the q appearing where point was last
>


Also just checked with this trivial 4-line file in case there was something
in my org file.  Still the same
--
* H1
** H11
** H12
* H2
---

I just wonder if its to do with
1. emacs version 23.4.1
2. I am using xfce not the more common gnome/kde etc
Thinking of the second because there is a kind of lag in the full-screening
of the window -- something which seems related to the window manager??



-- 
http://www.the-magus.in
http://blog.languager.org

Re: [O] Amazing demonstration by John Kitchin

[John Kitchin]

no problem! I also typed up my notes on setting up blogofile here:
http://jkitchin.github.io/blog/2013/09/27/Installing-and-configuring-blogofile/

I think they are pretty complete, but some of it was from memory.

best wishes,

John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Fri, Sep 27, 2013 at 11:41 AM, Brett Viren  wrote:

> John Kitchin  writes:
>
> > Here is part of how I use org-mode to publish to my blog:
> >
> http://jkitchin.github.io/blog/2013/09/27/Publishing-to-blogofile-using-org-mode/
>
> Thank you very much for typing this up!  I now have some weekend
> entertainment to try and replicate it for myself.
>
> -Brett.
>

Re: [O] epresent issue

[Rustom Mody]

On Fri, Sep 27, 2013 at 3:13 PM, Eric Schulte wrote:

> Rustom Mody  writes:
>
> > On Fri, Sep 27, 2013 at 7:20 AM, Rustom Mody 
> wrote:
> >
> >> Hi
> >>
> >> I am trying to use epresent for presentation.
> >> Start epresent with M-x epresent-run
> >>
> >> I seem to need to press one more q to get out of epresenting and then
> that
> >> q gets into the file.
> >>
>
> I can't reproduce this problem with a recent version of epresent and
> Org-mode.  For example with the following minimal Emacs invocation
> (without any configuration, run from the epresent directory).
>
> emacs -Q --eval "(progn (add-to-list 'load-path
> \"~/src/org-mode/lisp\") (require 'org))" -l epresent.el present.org
>

I tried this (with my-path adjustments); and a just-downloaded epresent
from above link; still the same behavior

In more detail:

0. Run command

emacs -Q --eval "(progn (add-to-list 'load-path \"~/pdsw/org-mode/lisp\")
(require 'org))" -l ~/.emacs.d/downloads/epresent.el  lastLect.org
and then in emacs:

1. Start with epresent-run
The buffer changes form half-way -- ie
a. it becomes full-screen,
b the menu line vanishes but
c. the mode line is present
d. the fonts are still small

2. After than whatever key I press (including q) it becomes like a
presentation -- ie no mode-line and large fonts

3. One more q and it quits with the q appearing where point was last

[O] Needing help on org-gnus + LaTeX export -

[Joseph Vidal-Rosset]

Hi,

I would be very happy to use LaTeX in gnus in scientific correspondence,
instead of using LaTeX it with Thunderbird.

I know that it is possible with org-mode , but I have difficulties to find
a clear tutorial to help me in this task.

My question is twofold: how concretely making links between my gnus and my
org-mode installation, and once is done, how can I use it to write an email
with every feature  that gives me LaTeX (with texlive)?

I would be very thankful to everyone trying to help me.

In advance, thanks.

Jo.

Re: [O] Amazing demonstration by John Kitchin

[Brett Viren]

John Kitchin  writes:

> Here is part of how I use org-mode to publish to my blog:
> http://jkitchin.github.io/blog/2013/09/27/Publishing-to-blogofile-using-org-mode/

Thank you very much for typing this up!  I now have some weekend
entertainment to try and replicate it for myself.

-Brett.


pgpEelfEMRLq4.pgp
Description: PGP signature

Re: [O] example filter for code blocks?

[John Kitchin]

It works in Adobe Reader, Adobe, and Bluebeam Revu. I haven't tried any
others.

John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Fri, Sep 27, 2013 at 11:24 AM, Alan Schmitt <
alan.schm...@polytechnique.org> wrote:

> Hi John,
>
> jkitc...@andrew.cmu.edu writes:
>
> > Actually, it turns out the publisher did put up the pdf with embedded
> > files, you just can't open them in a pdf in a browser. If you download
> the
> > file and open in a good pdf reader, you can open the embedded files. It
> > just made my day to figure that out!
> >
> > This link:
> >
> http://pubs.acs.org/doi/suppl/10.1021/ie400582a/suppl_file/ie400582a_si_001.pdf
>
> I tried opening it with both Skim, Preview, and PdfPen and I don't see
> the pushpin I'm supposed to double-click. I see the pushpins when
> opening the file with emacs, but I cannot click them. Should I use a
> specific PDF viewer?
>
> Thanks,
>
> Alan
>

Re: [O] example filter for code blocks?

[Alan Schmitt]

Hi John,

jkitc...@andrew.cmu.edu writes:

> Actually, it turns out the publisher did put up the pdf with embedded
> files, you just can't open them in a pdf in a browser. If you download the
> file and open in a good pdf reader, you can open the embedded files. It
> just made my day to figure that out!
>
> This link:
> http://pubs.acs.org/doi/suppl/10.1021/ie400582a/suppl_file/ie400582a_si_001.pdf

I tried opening it with both Skim, Preview, and PdfPen and I don't see
the pushpin I'm supposed to double-click. I see the pushpins when
opening the file with emacs, but I cannot click them. Should I use a
specific PDF viewer?

Thanks,

Alan

Re: [O] Amazing demonstration by John Kitchin

[John Kitchin]

Here is part of how I use org-mode to publish to my blog:
http://jkitchin.github.io/blog/2013/09/27/Publishing-to-blogofile-using-org-mode/

My approach is pretty automated, but I have left some manual steps in
place. Basically I write a post as a heading in some org-file, press a key,
which generates the html post in the required format and in the right
place. Then I build the blog, and push it to github. All that could happen
with a key press, but sometimes I like to inspect the content before
pushing.

I will try to describe the actual blog setup another time. I use blogofile,
which is a static blog generator, so it is quite different from using
wordpress, or other blog systems that you publish to via rss, xml-rpc,
etc...



John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Fri, Sep 27, 2013 at 9:55 AM, Brett Viren  wrote:

> John, I finally got a chance to watch your really nice SciPy talk last
> night.
>
> I've been trying to incorporate Reproducible Research methods with org
> into my own work.  I strive to do more and what you are doing looks to
> provide a wealth of examples.  I hope more researchers follow this
> methodology.
>
> One thing I've yet to get a good handle on is publishing org content in
> an automated (and beautiful) way.  I was very taken with your github.io
> pages and would like to try to set up something similar for myself.
>
> Do you have a write-up or other guidance on this that I might follow?
> I've started to go through your related github repositories to figure
> out what you do but if something more guided exists it would help.
>
> Thanks,
> -Brett.
>
> Carsten Dominik  writes:
>
> > Hi,
> >
> > I don't know if this has been linked to before on this mailing
> > list.  At SciPy 2013, John Kitchin has made an amazing
> > demonstration of Org-mode as a tool for reproducible research.
> > Really amazing to watch.
> >
> > http://www.youtube.com/watch?v=1-dUkyn_fZA
> >
> > - Carsten
>

Re: [O] [Babel] Padlines

[Sebastien Vauban]

Hi Eric,

Eric Schulte wrote:
> "Sebastien Vauban"  writes:
>> Eric Schulte wrote:
>>> aditya siram  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

The blank line which was inserted between blocks isn't anymore for me.

ECM:

--8<---cut here---start->8---
* Tangle these blocks
  :PROPERTIES:
  :tangle:   yes
  :padline:  yes
  :END:

#+begin_src emacs-lisp :file test.csv
  "data"
#+end_src

#+begin_src emacs-lisp :file test.csv
  "datb"
#+end_src
--8<---cut here---end--->8---

results in:

--8<---cut here---start->8---
  "data"
  "datb"
--8<---cut here---end--->8---

Note that I tried adding ":padline" to yes, but I normally should not, as it is
the default.

Best regards,
  Seb

-- 
Sebastien Vauban

[O] Round-tripping data between org-mode table and sqlite db using python

[Colin Hall]

Hi,

I've written an org file in which I use org tables and ob-python blocks
to manipulate an sqlite database. Updates to the database are a mix of
manual data entry and computed values. I'm using org-8.0.3 at the
moment.

I was going to post asking how to do this but I managed to develop a
working solution this morning, see the attached org file and the ascii
export below. I'm sure it could be improved, so I'm interested in advice
on how to go about that.

My main issue is that I wish to export the ob-python code as well as the
org-table showing the data, but present them under separate topics. So,
I would like the freedom to place the org-table anywhere within the org
file, preferably as a named table in a topic without an org-babel block
above it. Also, in my application the tables have about 100 rows and
having org-babel blocks hanging around add visual clutter when I'm
performing the edits.

I've not posted to this list much (at all?) so if there is a better way
to present the org example, let me know.

Cheers,
Colin.



Round trip table of data through an ob-python block
===

  I'd like to edit values in tables, store them to an Sqlite database,
  update the table from the Sqlite database, make changes, and store
  them back to the database.

  Here is an example table (I don't know any Hungarian):

  
   Hungarian  English 
  
   alpha  matches 
   beta   station 
   gamma  tobacco 
  


Data entry and Retrieval from Sqlite database
=

  Before making any edits run retrieveFromSqliteDb to update the data
  entry table.


  ,
  | #!/usr/bin/env python
  | import sqlite3
  | con = sqlite3.connect('/var/tmp/test.db')
  | cur = con.cursor()
  | cur.execute("SELECT * FROM translations")
  | rows = cur.fetchall()
  | print '|-+-|'
  | print '| Hungarian | English |'
  | print '|-+-|'
  | for row in rows:
  | id, hungarian, english = row
  | print '| {hungarian} | {english} 
|'.format(hungarian=hungarian,english=english)
  | 
  | print '|-+-|'
  | con.close()
  `
  Listing 1: Retrieve records from database on disk, update data entry
  table

  
   Hungarian  English 
  
   onetwo 
   three  four
  

  Table 1: Data entry table for Hungarian-English translation

  I placed a calls here to make it a bit handier for running the write
  to database block.


Writing data to the Sqlite database
===

  Run this ob-python block to update the Sqlite database

  ,
  | #!/usr/bin/env python
  | import sqlite3
  | con = sqlite3.connect('/var/tmp/test.db')
  | c = con.cursor()
  | c.execute("DROP TABLE IF EXISTS translations")
  | c.execute('''CREATE TABLE translations (
  |   id INTEGER PRIMARY KEY AUTOINCREMENT,
  |   hungarian TEXT,
  |   english TEXT);
  |   ''')
  | c.executemany('INSERT INTO translations (hungarian,english) VALUES (?,?)', 
inData)
  | con.commit()
  | con.close()
  `
  Listing 2: Write records from table to database on disk


Utilities for working with the database
===

  ,
  | #!/usr/bin/env python
  | import sqlite3
  | con = sqlite3.connect('/var/tmp/test.db')
  | c = con.cursor()
  | c.execute("DROP TABLE IF EXISTS translations")
  | c.execute('''CREATE TABLE translations (
  |   id INTEGER PRIMARY KEY AUTOINCREMENT,
  |   hungarian TEXT,
  |   english TEXT);
  |   ''')
  | con.commit()
  | con.close()
  `
  Listing 3: Creating an empty database

  ,
  | .mode column
  | .headers on
  | select * from translations;
  `
  Listing 4: Dump records from the database on disk


#+TITLE: Round trip table of data through an ob-python block
#+AUTHOR:Colin Hall
#+EMAIL: colingh...@gmail.com
#+DATE:  <2013-09-27 Fri>
#+DESCRIPTION: An example of round tripping data from org through an Sqlite database
#+LANGUAGE:  en
#+OPTIONS:   H:1 num:nil toc:nil \n:nil @:t ::t |:t ^:{} -:t f:nil *:t <:nil
#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:nil pri:nil tags:nil
#+STARTUP: overview
#+STARTUP: hidestars

* Round trip table of data through an ob-python block
  
  I'd like to edit values in tables, store them to an Sqlite database,
  update the table from the Sqlite database, make changes, and store
  them back to the database.

  Here is an example table (I don't know any Hungarian):

  #+attr_html: :border 2 :rules all :frame border
  |---+-|
  | Hungarian | English |
  |---+-|
  | alpha | matches |
  | beta  | station |
  | gamma | tobacco |
  |---+-|

* Data entry and Retrieval from Sqlite database
  Before making any

Re: [O] Convention for tags and properties

[Sebastien Vauban]

Nicolas Goaziou wrote:
> "Sebastien Vauban" writes:
>
>> Following those conventions, I guess that:
>>
>> - The `crypt' tag should be "renamed" `CRYPT'
>>
>> - The `Effort' property should be "renamed" `EFFORT'
>>
>> Right?
>
> FWIW, I think you're correct.

Would such a patch be accepted, then, if I can make it?

Best regards,
  Seb

-- 
Sebastien Vauban

Re: [O] Amazing demonstration by John Kitchin

[Brett Viren]

John, I finally got a chance to watch your really nice SciPy talk last
night.

I've been trying to incorporate Reproducible Research methods with org
into my own work.  I strive to do more and what you are doing looks to
provide a wealth of examples.  I hope more researchers follow this
methodology.

One thing I've yet to get a good handle on is publishing org content in
an automated (and beautiful) way.  I was very taken with your github.io
pages and would like to try to set up something similar for myself.

Do you have a write-up or other guidance on this that I might follow?
I've started to go through your related github repositories to figure
out what you do but if something more guided exists it would help.

Thanks,
-Brett.

Carsten Dominik  writes:

> Hi,
>
> I don't know if this has been linked to before on this mailing
> list.  At SciPy 2013, John Kitchin has made an amazing
> demonstration of Org-mode as a tool for reproducible research.
> Really amazing to watch.
>
> http://www.youtube.com/watch?v=1-dUkyn_fZA
>
> - Carsten


pgp7cZIYAKeld.pgp
Description: PGP signature

Re: [O] A tutorial on using ox-rss.el to publish an Emacs-made blog

[Bastien]

Suvayu Ali  writes:

> On Fri, Sep 27, 2013 at 03:38:01PM +0200, Bastien wrote:
>> Hi flammable (?),
>
> The post was signed Basile.  :-p

Yep, sorry Basile !

-- 
 Bastien

Re: [O] [BABEL] BUG - error on tangling - disappears when changing the filename

[Rainer M Krug]

OK - narrowed it down to a post tangle hook which I need for proper
debugging of R (jumping to source line in org file and not tangled R file):

,
| #+begin_src emacs-lisp
| (defvar org-babel-tangled-file nil
|   "If non-nill, current file was tangled with org-babel-tangle")
| (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
| 
| (defun org-babel-mark-file-as-tangled ()
|   (when  (string-match "[.]R" (buffer-file-name))
| (add-file-local-variable 'org-babel-tangled-file t)
| (add-file-local-variable 'buffer-read-only t)
| (add-file-local-variable 'eval: '(auto-revert-mode))
| (basic-save-buffer)))
| 
| (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
| #+end_src
`

The question is now why is this function org-babel-mark-file-as-tangled
receives NULL as a buffer-file-name? 
I can't remove the "when" as I am also tangling some files which do not
have any comment characters (DESCRIPTION file in R packages).

Any suggestions welcome,

Rainer


Rainer M Krug  writes:

> Forgot: tried with 8.2 stable release and with version from git - both
> the same.
>
> Rainer M Krug  writes:
>
>> Hi
>>
>> I have a strange error when tangling.
>>
>> I have a large org file with several code blocks tangling in about
>> 20 R files and one bash file. Usually tangling works perfectly, but
>> sometimes one code block does not tangle a code block to a file. These
>> are different blocks. When I change the name of the fiole to be tangled
>> to, it works again. After d=some time, I can rename it again and it
>> works again.
>>
>> The last time it happened, I was debugging the function. But even when
>> deleting all the content of the code block, the problem persists.
>>
>> This persists over restarts of org.
>>
>> The code block looks as follow:
>>
>> ,
>> | *** dispProb2D (./R/dispProd2D.R) 
>> | :PROPERTIES:
>> | :tangle:   ./R/dispProd2D.R
>> | :comments: yes
>> | :no-expand: TRUE
>> | :END: 
>> | #+begin_src R
>> | cat(5)
>> | #+end_src  
>> `
>>
>> In the original version, there is obviously code in it, but the error
>> occurs even in the empty block. I just renamed the block, and it is
>> working again.
>>
>> Any idea what is causing this?
>>
>> Please find the backtrace below.
>>
>> Cheers,
>>
>> Rainer
>>
>> ,
>> | ebugger entered--Lisp error: (wrong-type-argument stringp nil)
>> |   set-buffer(nil)
>> |   (save-current-buffer (set-buffer (get-file-buffer file)) (revert-buffer 
>> t t t))
>> |   org-babel-find-file-noselect-refresh("./R/dispProd2D.R")
>> |   (let* ((temp-path file) (visited-p (get-file-buffer temp-path))
>> | temp-result temp-file) (org-babel-find-file-noselect-refresh
>> | temp-path) (setq temp-file (get-file-buffer temp-path))
>> | (save-current-buffer (set-buffer temp-file) (setq temp-result (progn
>> | (run-hooks (quote org-babel-post-tangle-hook) (if visited-p nil
>> | (kill-buffer temp-file)) temp-result)
>> |   (lambda (file) (let* ((temp-path file) (visited-p (get-file-buffer
>> | temp-path)) temp-result temp-file)
>> | (org-babel-find-file-noselect-refresh temp-path) (setq temp-file
>> | (get-file-buffer temp-path)) (save-current-buffer (set-buffer
>> | temp-file) (setq temp-result (progn (run-hooks (quote
>> | org-babel-post-tangle-hook) (if visited-p nil (kill-buffer
>> | temp-file)) temp-result))("./R/dispProd2D.R")
>> |   mapc((lambda (file) (let* ((temp-path file) (visited-p
>> | (get-file-buffer temp-path)) temp-result temp-file)
>> | (org-babel-find-file-noselect-refresh temp-path) (setq temp-file
>> | (get-file-buffer temp-path)) (save-current-buffer (set-buffer
>> | temp-file) (setq temp-result (progn (run-hooks (quote
>> | org-babel-post-tangle-hook) (if visited-p nil (kill-buffer
>> | temp-file)) temp-result)) ("postTangleScript.sh" "./.gitignore"
>> | "./DESCRIPTION" "./.Rbuildignore" "./R/parmsFire.R"
>> | "./R/parmsPinus.R" "./R/parmsAcacia.R" "./R/parmsRubus.R"
>> | "./R/parmsBudget.R" "./R/parameter.R" "./R/endYear.R"
>> | "./R/germEst.R" "./R/seedDispersal.R" "./R/seedProduction.R"
>> | "./R/fireAliens.R" "./R/clearAliens.R" "./R/prioritisation.R"
>> | "./R/beginYear.R" "./R/main.R" "./R/cumulativeDc.R"
>> | "./R/dcToIndLayer.R" "./R/competition.R" "./R/dispProd2D.R"
>> | "./R/initfun.R" "./R/newInDrak.R" "./R/resetOptions.R" "./R/stats.R"
>> | "./R/layerIO.R" "./R/layerNames.R" "./R/onLoad.R" "./NAMESPACE"
>> | "./R/package.R"))
>> |   (progn (mapc (function (lambda (file) (let* ((temp-path file)
>> | (visited-p (get-file-buffer temp-path)) temp-result temp-file)
>> | (org-babel-find-file-noselect-refresh temp-path) (setq temp-file
>> | (get-file-buffer temp-path)) (save-current-buffer (set-buffer
>> | temp-file) (setq temp-result (progn ...))) (if visited-p nil
>> | (kill-buffer temp-file)) temp-result))) (mapcar (function car)
>> | path-collector)))
>> |   (if org-babel-post-tangle-hook (progn (mapc (function (lambda
>> | (file) (let* ((temp-path file) (visited-p ...) temp-result
>> | temp-file) (or

Re: [O] A tutorial on using ox-rss.el to publish an Emacs-made blog

[Suvayu Ali]

On Fri, Sep 27, 2013 at 03:38:01PM +0200, Bastien wrote:
> Hi flammable (?),
> 

The post was signed Basile.  :-p

-- 
Suvayu

Open source is the future. It sets us free.

Re: [O] A tutorial on using ox-rss.el to publish an Emacs-made blog

[Bastien]

Hi flammable (?),

flammable project  writes:

> * EMACS
> You need to have an Emacs version greater than 24.2.1. The function
> 'url-encode-url' must be present to generate successfully the RSS
> feed. Since I'm using Xubuntu 13.4. I had to add the PAA of Damien
> CASSOU to my apt config. Then I installed Emacs 24.3.1. The command
> 'url-encode-url' was listed in.

Thanks -- I updated the blog post to mention this constraint.

> * ORG Files
> You should take care about the PROPERTIES section you use in your
> org_files or section used to generate the RSS feeed.
>
> the CATEGORY might be usefull to manage multiple feeds. Personnaly I
> don't try it but with Liferea RSS reader this option is visible.

(I don't use the CATEGORY property myself but maybe will.)

> Personnaly, I put the same date for the DATE and PUBDATE options. The
> date are correctly displayed in my RSS reader.

Why do you need the :DATE: ?  :PUBDATE: is automatically added if not
already present, and should be enough for the feed to know about the
publication date.

Thanks for testing!

-- 
 Bastien

Re: [O] [BABEL] BUG - error on tangling - disappears when changing the filename

[Rainer M Krug]

Forgot: tried with 8.2 stable release and with version from git - both
the same.

Rainer M Krug  writes:

> Hi
>
> I have a strange error when tangling.
>
> I have a large org file with several code blocks tangling in about
> 20 R files and one bash file. Usually tangling works perfectly, but
> sometimes one code block does not tangle a code block to a file. These
> are different blocks. When I change the name of the fiole to be tangled
> to, it works again. After d=some time, I can rename it again and it
> works again.
>
> The last time it happened, I was debugging the function. But even when
> deleting all the content of the code block, the problem persists.
>
> This persists over restarts of org.
>
> The code block looks as follow:
>
> ,
> | *** dispProb2D (./R/dispProd2D.R) 
> | :PROPERTIES:
> | :tangle:   ./R/dispProd2D.R
> | :comments: yes
> | :no-expand: TRUE
> | :END: 
> | #+begin_src R
> | cat(5)
> | #+end_src  
> `
>
> In the original version, there is obviously code in it, but the error
> occurs even in the empty block. I just renamed the block, and it is
> working again.
>
> Any idea what is causing this?
>
> Please find the backtrace below.
>
> Cheers,
>
> Rainer
>
> ,
> | ebugger entered--Lisp error: (wrong-type-argument stringp nil)
> |   set-buffer(nil)
> |   (save-current-buffer (set-buffer (get-file-buffer file)) (revert-buffer t 
> t t))
> |   org-babel-find-file-noselect-refresh("./R/dispProd2D.R")
> |   (let* ((temp-path file) (visited-p (get-file-buffer temp-path))
> | temp-result temp-file) (org-babel-find-file-noselect-refresh
> | temp-path) (setq temp-file (get-file-buffer temp-path))
> | (save-current-buffer (set-buffer temp-file) (setq temp-result (progn
> | (run-hooks (quote org-babel-post-tangle-hook) (if visited-p nil
> | (kill-buffer temp-file)) temp-result)
> |   (lambda (file) (let* ((temp-path file) (visited-p (get-file-buffer
> | temp-path)) temp-result temp-file)
> | (org-babel-find-file-noselect-refresh temp-path) (setq temp-file
> | (get-file-buffer temp-path)) (save-current-buffer (set-buffer
> | temp-file) (setq temp-result (progn (run-hooks (quote
> | org-babel-post-tangle-hook) (if visited-p nil (kill-buffer
> | temp-file)) temp-result))("./R/dispProd2D.R")
> |   mapc((lambda (file) (let* ((temp-path file) (visited-p
> | (get-file-buffer temp-path)) temp-result temp-file)
> | (org-babel-find-file-noselect-refresh temp-path) (setq temp-file
> | (get-file-buffer temp-path)) (save-current-buffer (set-buffer
> | temp-file) (setq temp-result (progn (run-hooks (quote
> | org-babel-post-tangle-hook) (if visited-p nil (kill-buffer
> | temp-file)) temp-result)) ("postTangleScript.sh" "./.gitignore"
> | "./DESCRIPTION" "./.Rbuildignore" "./R/parmsFire.R"
> | "./R/parmsPinus.R" "./R/parmsAcacia.R" "./R/parmsRubus.R"
> | "./R/parmsBudget.R" "./R/parameter.R" "./R/endYear.R"
> | "./R/germEst.R" "./R/seedDispersal.R" "./R/seedProduction.R"
> | "./R/fireAliens.R" "./R/clearAliens.R" "./R/prioritisation.R"
> | "./R/beginYear.R" "./R/main.R" "./R/cumulativeDc.R"
> | "./R/dcToIndLayer.R" "./R/competition.R" "./R/dispProd2D.R"
> | "./R/initfun.R" "./R/newInDrak.R" "./R/resetOptions.R" "./R/stats.R"
> | "./R/layerIO.R" "./R/layerNames.R" "./R/onLoad.R" "./NAMESPACE"
> | "./R/package.R"))
> |   (progn (mapc (function (lambda (file) (let* ((temp-path file)
> | (visited-p (get-file-buffer temp-path)) temp-result temp-file)
> | (org-babel-find-file-noselect-refresh temp-path) (setq temp-file
> | (get-file-buffer temp-path)) (save-current-buffer (set-buffer
> | temp-file) (setq temp-result (progn ...))) (if visited-p nil
> | (kill-buffer temp-file)) temp-result))) (mapcar (function car)
> | path-collector)))
> |   (if org-babel-post-tangle-hook (progn (mapc (function (lambda
> | (file) (let* ((temp-path file) (visited-p ...) temp-result
> | temp-file) (org-babel-find-file-noselect-refresh temp-path) (setq
> | temp-file (get-file-buffer temp-path)) (save-current-buffer
> | (set-buffer temp-file) (setq temp-result ...)) (if visited-p nil
> | (kill-buffer temp-file)) temp-result))) (mapcar (function car)
> | path-collector
> |   (let ((block-counter 0) (org-babel-default-header-args (if
> | target-file (org-babel-merge-params org-babel-default-header-args
> | (list (cons :tangle target-file))) org-babel-default-header-args))
> | (tangle-file (if (equal arg (quote (16))) (progn (or (cdr (assoc
> | :tangle ...)) (user-error "Point is not in a source code block")
> | path-collector) (mapc (function (lambda (by-lang) (let* ((lang (car
> | by-lang)) (specs (cdr by-lang)) (ext (or ... lang)) (lang-f (intern
> | ...)) she-banged) (mapc (function (lambda ... ...)) specs (if
> | (equal arg (quote (4))) (org-babel-tangle-single-block 1 t)
> | (org-babel-tangle-collect-blocks lang tangle-file))) (message
> | "Tangled %d code block%s from %s" block-counter (if (= block-counter
> | 1) "" "s") (file-name-nondirectory (buffer-file-name (or
> | (buffer-base-buffer) (curre

Re: [O] [BUG] Colored tags generate an error when C-x C-w'ing the agenda

[Carsten Dominik]

On Sep 27, 2013, at 1:35 PM, Sebastien Vauban  wrote:

> Hi Carsten,
> 
> Carsten Dominik wrote:
>> On 11.9.2013, at 14:48, Sebastien Vauban  wrote:
>>> If you have colors for tags:
>>> 
>>> --8<---cut here---start->8---
>>> ;; faces for specific tags
>>> (setq org-tag-faces
>>>   '(("home" .
>>>  (:slant italic
>>>   :foreground "#5C88D3" :background "#BBDDFF"))
>>> ("work" .
>>>  (:slant italic
>>>   :foreground "#5F7C43" :background "#C1D996"
>>> --8<---cut here---end--->8---
>>> 
>>> you can't export the agenda views anymore; they all generate the following
>>> error:
>> 
>> It does seem to work if you specify the faces like this (without the dot).
>> 
>> (setq org-tag-faces
>>   '(("home" 
>>  (:slant italic
>>   :foreground "#5C88D3" :background "#BBDDFF"))
>> ("work" 
>>  (:slant italic
>>   :foreground "#5F7C43" :background "#C1D996"
> 
> Without the dot [1], I confirm that I can export both to HTML and PDF with no
> error.
> 
> Though, in the PDF, these tags have a white background, not the one specified.
> This is a small annoyance...
> 
>> Since Emacs does display correctly with this way to specify a font, I'd say
>> this is a bug in ps-print and should be reported to Emacs as such.
> 
> ... which I'll report (with your analysis) to Emacs.

Thank you!

- Carsten

> 
> Thanks for your help!
> 
> Best regards,
>  Seb
> 
> [1] I'd never ever have thought to remove the "dot". How did you discover or
> know that?
> 
> -- 
> Sebastien Vauban
> 
> 



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Re: [O] How to trigger the clockcheck in an agenda view.

[Carsten Dominik]

On 10.9.2013, at 17:07, Nicolas Girard  wrote:

> 2013/8/5 Sebastien Vauban :
>> 
>> Except the above, I definitely don't understand why it wouldn't work for you.
>> Can you reproduce the problem with a minimal Emacs config file (adding the
>> require of `org' and `org-agenda' before)?
>> 
> 
> I think I understand why Rainer has a problem.
> 
> According to the docstring from `org-agenda-custom-commands', there
> are two acceptable syntaxes for defining a command:
> - the "simple" one : (key desc type match settings files)
> - and the "complex" or "composite" one : (key desc (cmd1 cmd2 ...)
> general-settings-for-whole-set files).
> 
> Now, the following code defines two commands, who are functionally
> identical, but syntactically different. The first one uses the "simple"
> syntax, and the second one, the "complex" syntax.
> 
> If you evaluate the code and trigger the agenda, you'll see that the
> first command *doesn't* work as expected, while the second works.
> 
> (I just borrowed your scissors to delimit my code, hope you don't mind ;-) )
> 
> --8<---cut here---start->8---
>  (setq org-agenda-custom-commands nil)
>  (setq org-agenda-custom-commands
>(append
> org-agenda-custom-commands '(
> ("G" "Good: Clock Review"
>  ((agenda ""
>   ((org-agenda-show-log 'clockcheck)
>(org-agenda-clockreport-mode t)
> ("B"  "Bad: Clock Review"
>  agenda ""
>  ((org-agenda-show-log 'clockcheck)
>   (org-agenda-clockreport-mode t))
> --8<---cut here---end--->8---

There are a couple of subtle issues here.

First of all, do not bind org-agenda-clockreport-mode or org-agenda-show-log in 
this way, these are internal variables and meant for a mode that is toggled 
interactively.  Use org-agenda-start-with-clockreport-mode and 
org-agenda-start-with-log-mode  instead.  These are the values chosen when a 
new agenda buffer is created, and at that time its value is copied into 
internal variables.

Second, because this happens when the agenda buffer is created, these need to 
be in the global list of variables, not the local ones for the agenda list, 
when you use a list of commands.  So the example below will work in both cases:

 (setq org-agenda-custom-commands
   (append
org-agenda-custom-commands '(
("H" "Good: Clock Review"
 ((agenda ""))
 ((org-agenda-start-with-log-mode 'clockcheck)
  (org-agenda-start-with-clockreport-mode t)))
("C"  "Bad: Clock Review"
 agenda ""
 ((org-agenda-start-with-log-mode 'clockcheck)
  (org-agenda-start-with-clockreport-mode t))



Hope this helps.

- Carsten



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Re: [O] example filter for code blocks?

[John Kitchin]

Actually, it turns out the publisher did put up the pdf with embedded
files, you just can't open them in a pdf in a browser. If you download the
file and open in a good pdf reader, you can open the embedded files. It
just made my day to figure that out!

This link:
http://pubs.acs.org/doi/suppl/10.1021/ie400582a/suppl_file/ie400582a_si_001.pdf

is a supporting information file created from org-mode, with embedded excel
sheets, and the org-file that was exported to the pdf! It contains all of
the data used to make the figures in the paper, along with the python
scripts we used to make the figures.  It is probably our most complete
supplemental file ever. And, this file is freely available (although the
manuscript requires a subscription to the journal).

We actually wrote the manuscript in org-mode too, and submitted the latex
source that was exported from the org-file. Now, if we can just get
publishers to let us embed the org-source of the manuscript in the
supporting information file so at least the content is available for free...


John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Thu, Sep 26, 2013 at 4:58 PM, Thomas S. Dye  wrote:

> Hi John,
>
> Terrific! There go my plans for the weekend ... :)
>
> Good luck with the heavy-handed journal processor.  It seems worth
> pursuing to me.
>
> All the best,
> Tom
>
> John Kitchin  writes:
>
> > I think it is so interesting, we have actually tried a variation of it! I
> > set up an org-file that exported a supplementary information file, using
> > attachfile to embed data files and scripts in the pdf. Unfortunately, the
> > journal "processed" the pdf file, and stripped those files out ;( We
> > haven't tried to see if we can get our original supplemental pdf
> accepted.
> >
> >
> > John
> >
> > ---
> > John Kitchin
> > Associate Professor
> > Doherty Hall A207F
> > Department of Chemical Engineering
> > Carnegie Mellon University
> > Pittsburgh, PA 15213
> > 412-268-7803
> > http://kitchingroup.cheme.cmu.edu
> >
> >
> >
> > On Thu, Sep 26, 2013 at 3:43 PM, Thomas S. Dye  wrote:
> >
> >> Hi John,
> >>
> >> John Kitchin  writes:
> >>
> >> > Hi everyone,
> >> > Thanks for  the tips in using export filters for code blocks. I
> thought I
> >> > would share my current solution. The goal was to export all the code
> >> blocks
> >> > in an org-file to files systematically named part1/script-%d.py where
> %d
> >> is
> >> > a number. I didnot want to tangle exactly, because I wanted to avoid
> >> naming
> >> > the code block tangle files.
> >> >
> >> > Then, I wanted to insert a pdf link that would open the file, after
> the
> >> > syntax highlighted code.
> >> >
> >> > I wanted this because it is not convenient to copy and paste the
> >> > syntax-highlighted code into an editor. I teach from the pdf that is
> >> > generated, and it would be convenient to just open the code, edit and
> >> rerun
> >> > to explore solutions.
> >>
> >> This seems like it might be an elegant way to distribute a piece of
> >> reproducible research. I suspect most readers would prefer to have a pdf
> >> entry point into a compendium over an Org-mode entry point. Instead of
> >> distributing the Org-mode file that is configured to make a pdf file,
> >> carry out calculations, draw figures, etc., one could distribute a
> >> ready-made pdf file with an appendix of Supplementary Material that has
> >> all the code for calculations, figures, etc.
> >>
> >> What do you think?
> >>
> >> All the best,
> >> Tom
> >>
> >> --
> >> Thomas S. Dye
> >> http://www.tsdye.com
> >>
> > I think it is so interesting, we have actually tried a variation of
> > it! I set up an org-file that exported a supplementary information
> > file, using attachfile to embed data files and scripts in the pdf.
> > Unfortunately, the journal "processed" the pdf file, and stripped
> > those files out ;( We haven't tried to see if we can get our original
> > supplemental pdf accepted.
> >
> > John
> >
> > ---
> > John Kitchin
> > Associate Professor
> > Doherty Hall A207F
> > Department of Chemical Engineering
> > Carnegie Mellon University
> > Pittsburgh, PA 15213
> > 412-268-7803
> > http://kitchingroup.cheme.cmu.edu
> >
> > On Thu, Sep 26, 2013 at 3:43 PM, Thomas S. Dye  wrote:
> >
> > Hi John,
> >
> >
> > John Kitchin  writes:
> >
> > > Hi everyone,
> > > Thanks for the tips in using export filters for code blocks. I
> > thought I
> > > would share my current solution. The goal was to export all the
> > code blocks
> > > in an org-file to files systematically named part1/script-%d.py
> > where %d is
> > > a number. I didnot want to tangle exactly, because I wanted to
> > avoid naming
> > > the code block tangle files.
> > >
> > > 

Re: [O] Elpa color-theme with emacs24

[Suvayu Ali]

Hi Rene,

On Fri, Sep 27, 2013 at 02:08:43AM +, Rene wrote:
> Sebastien Vauban  writes:
> 
> > For the sake of completion, I think that, starting with Emacs 24, it's 
> > better
> > to use their new "custom theme" mechanism, which is more general than the
> > `color-theme' package (and offers the same services regarding color themes).
> 
> You're right.  "DefTheme" is the way to go and should be advised on the worg
> page: http://orgmode.org/worg/org-color-themes.html

At least one of the themes on that page has an updated version using
def-theme:

  

I'm the maintainer.

-- 
Suvayu

Open source is the future. It sets us free.

Re: [O] Exploring data that is in org-mode format

[Nick Dokos]

Alan Schmitt  writes:

> Hello,
>
> This question is slightly off-topic, but it may be of interest to people
> who have a lot of data entered in org-mode.
>
> The short version: what tools are available to explore data, typically
> stored in org-mode tables?
>
> The long version: I've tried an interesting website
> (https://tictrac.com/) whose goal is to gain some insight about
> ourselves by exploring some data we collect (think quantified self). I'm
> not happy with this site for three reasons:
> - I need to send it the data;
> - it focuses on health / activity data whereas there is much more that
> interests me (I for instance have weekly records of natural gas use in my
> gas-heated house and daily record of temperature average outside which I
> would love to compare);
> - it won't let you input arbitrary data (I asked about importing a CSV
> of my daily coffee consumption, they answered they require an external
> service to integrate the data).
>
> So I collect all this data because it's something I enjoy doing, and I
> would really like to explore it, from the comfortable position of my own
> computer. All of this data is in org-mode tables (or can be easily
> converted to org-mode table). Hence my questions: are there tools you
> would recommend? I'm not afraid of programming (I suspect an answer will
> be 'R'), but I would like pointers to tutorials to do these kind of
> things. The kind of things I would like to do are:
> - extract weekly or monthly tallies or estimation from data collected at
> irregular intervals;
> - compare data sources against each other;
> - estimate future trends based on past data (how much will my gas bill be?);
> - display the result in some kind of dashboard.
>

Not org-related and not even emacs-related (sorry Marcin!) but
applicable to the question:

Apart from R and Matlab, there is also ... Python: I'm currently reading 
a very nice book that uses Python, Numpy, Pandas and Matplotlib for
data exploration. It is called "Python for Data Analysis", by Wes
McKinney (the original developer of Pandas). I'm about a third of the
way through it and I can recommend it. You can find a link to the book
at the Pandas site:

   http://pandas.pydata.org/

Just in case the question arises: no, I'm not a paid endorser - just a
satisfied customer :-)

-- 
Nick

Re: [O] Lots of \n in ox-html output

[Thorsten Jolitz]

Suvayu Ali  writes:

> On Fri, Sep 27, 2013 at 11:29:57AM +0200, Thorsten Jolitz wrote:
>> Nicolas Goaziou  writes:
>> 
>>  Hello,
>> 
>> > Thorsten Jolitz  writes:
>> >
>> >> although I did not update recently, html-export of this test org-file
>> >> suddenly includes lots of \n in the html output.
>> >
>> > I cannot reproduce it. Does it also happen with a minimal configuration
>> > file?
>> 
>> It must be something emacsclient/server related, since it does not
>> happen when I call (pseudocode):
>> 
>> ,---
>> | emacs -Q -l init.el -e org-export- ...
>> `---
>> 
>> but does happen with 
>> 
>> ,--
>> | emacs -Q --daemon=myserver -l init.el
>> | emacsclient -e org-export-...
>> `--
>> 
>> where init.el does _nothing_ but setting load-path and requiring the
>> necessary libs. 
>
> Can you try emacs -Q -l init.el where you start the server with
> server-start in init.el?

I tried, but to no avail. Seems like emacsclient somehow fiddles with
the linefeed encoding ...

-- 
cheers,
Thorsten

Re: [O] AUCTeX key bindings within Org documents

[Marcin Borkowski]

Dnia 2013-09-27, o godz. 13:21:40
"Fabrice Niessen"  napisał(a):

> Hello,
> 
> Due to a friend's request, I've tried to offer AUCTeX key bindings
> within Org documents via a minor mode, called "org-auctex-keys".
> 
> If you're interested, check it out at
> https://github.com/fniessen/org-auctex-key-bindings.
> 
> Note that I'm willing to add extra AUCTeX keys -- but I don't use
> AUCTeX enough to know what's important to transfer to Org.

Interesting idea - for me, especially C-c C-f bindings might be
useful.  What might be missing:

C-c C-f C-e emphasize, might just be equivalent to C-c C-f C-i
C-c C-j new item, might be equivalent to C-RET or something
C-c C-c in AUCTeX, this just runs a TeX job.  Here it initiate export
or something like that.

> Best regards,
> Fabrice

Best,

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

[O] [BABEL] BUG - error on tangling - disappears when changing the filename

[Rainer M Krug]

Hi

I have a strange error when tangling.

I have a large org file with several code blocks tangling in about
20 R files and one bash file. Usually tangling works perfectly, but
sometimes one code block does not tangle a code block to a file. These
are different blocks. When I change the name of the fiole to be tangled
to, it works again. After d=some time, I can rename it again and it
works again.

The last time it happened, I was debugging the function. But even when
deleting all the content of the code block, the problem persists.

This persists over restarts of org.

The code block looks as follow:

,
| *** dispProb2D (./R/dispProd2D.R) 
| :PROPERTIES:
| :tangle:   ./R/dispProd2D.R
| :comments: yes
| :no-expand: TRUE
| :END: 
| #+begin_src R
| cat(5)
| #+end_src  
`

In the original version, there is obviously code in it, but the error
occurs even in the empty block. I just renamed the block, and it is
working again.

Any idea what is causing this?

Please find the backtrace below.

Cheers,

Rainer

,
| ebugger entered--Lisp error: (wrong-type-argument stringp nil)
|   set-buffer(nil)
|   (save-current-buffer (set-buffer (get-file-buffer file)) (revert-buffer t t 
t))
|   org-babel-find-file-noselect-refresh("./R/dispProd2D.R")
|   (let* ((temp-path file) (visited-p (get-file-buffer temp-path)) temp-result 
temp-file) (org-babel-find-file-noselect-refresh temp-path) (setq temp-file 
(get-file-buffer temp-path)) (save-current-buffer (set-buffer temp-file) (setq 
temp-result (progn (run-hooks (quote org-babel-post-tangle-hook) (if 
visited-p nil (kill-buffer temp-file)) temp-result)
|   (lambda (file) (let* ((temp-path file) (visited-p (get-file-buffer 
temp-path)) temp-result temp-file) (org-babel-find-file-noselect-refresh 
temp-path) (setq temp-file (get-file-buffer temp-path)) (save-current-buffer 
(set-buffer temp-file) (setq temp-result (progn (run-hooks (quote 
org-babel-post-tangle-hook) (if visited-p nil (kill-buffer temp-file)) 
temp-result))("./R/dispProd2D.R")
|   mapc((lambda (file) (let* ((temp-path file) (visited-p (get-file-buffer 
temp-path)) temp-result temp-file) (org-babel-find-file-noselect-refresh 
temp-path) (setq temp-file (get-file-buffer temp-path)) (save-current-buffer 
(set-buffer temp-file) (setq temp-result (progn (run-hooks (quote 
org-babel-post-tangle-hook) (if visited-p nil (kill-buffer temp-file)) 
temp-result)) ("postTangleScript.sh" "./.gitignore" "./DESCRIPTION" 
"./.Rbuildignore" "./R/parmsFire.R" "./R/parmsPinus.R" "./R/parmsAcacia.R" 
"./R/parmsRubus.R" "./R/parmsBudget.R" "./R/parameter.R" "./R/endYear.R" 
"./R/germEst.R" "./R/seedDispersal.R" "./R/seedProduction.R" "./R/fireAliens.R" 
"./R/clearAliens.R" "./R/prioritisation.R" "./R/beginYear.R" "./R/main.R" 
"./R/cumulativeDc.R" "./R/dcToIndLayer.R" "./R/competition.R" 
"./R/dispProd2D.R" "./R/initfun.R" "./R/newInDrak.R" "./R/resetOptions.R" 
"./R/stats.R" "./R/layerIO.R" "./R/layerNames.R" "./R/onLoad.R" "./NAMESPACE" 
"./R/package.R"))
|   (progn (mapc (function (lambda (file) (let* ((temp-path file) (visited-p 
(get-file-buffer temp-path)) temp-result temp-file) 
(org-babel-find-file-noselect-refresh temp-path) (setq temp-file 
(get-file-buffer temp-path)) (save-current-buffer (set-buffer temp-file) (setq 
temp-result (progn ...))) (if visited-p nil (kill-buffer temp-file)) 
temp-result))) (mapcar (function car) path-collector)))
|   (if org-babel-post-tangle-hook (progn (mapc (function (lambda (file) (let* 
((temp-path file) (visited-p ...) temp-result temp-file) 
(org-babel-find-file-noselect-refresh temp-path) (setq temp-file 
(get-file-buffer temp-path)) (save-current-buffer (set-buffer temp-file) (setq 
temp-result ...)) (if visited-p nil (kill-buffer temp-file)) temp-result))) 
(mapcar (function car) path-collector
|   (let ((block-counter 0) (org-babel-default-header-args (if target-file 
(org-babel-merge-params org-babel-default-header-args (list (cons :tangle 
target-file))) org-babel-default-header-args)) (tangle-file (if (equal arg 
(quote (16))) (progn (or (cdr (assoc :tangle ...)) (user-error "Point is not in 
a source code block") path-collector) (mapc (function (lambda (by-lang) 
(let* ((lang (car by-lang)) (specs (cdr by-lang)) (ext (or ... lang)) (lang-f 
(intern ...)) she-banged) (mapc (function (lambda ... ...)) specs (if 
(equal arg (quote (4))) (org-babel-tangle-single-block 1 t) 
(org-babel-tangle-collect-blocks lang tangle-file))) (message "Tangled %d code 
block%s from %s" block-counter (if (= block-counter 1) "" "s") 
(file-name-nondirectory (buffer-file-name (or (buffer-base-buffer) 
(current-buffer) (if org-babel-post-tangle-hook (progn (mapc (function 
(lambda (file) (let* (... ... temp-result temp-file) 
(org-babel-find-file-noselect-refresh temp-path) (setq temp-file ...) 
(save-current-buffer ... ...) (if visited-p nil ...) temp-result))) (mapcar 
(function car) path-collector (mapc (function (lambda (pair) (if (cdr pair) 
(progn (set

[O] Bug: *bold* text isn't fontified unless text is changed on the same line [8.1 (release_8.1-3-ga005db)]

[Oleh]

Hi,

The font-lock works fine as I type, but when I re-open the file,
or call `revert-buffer', the *bold* text loses its fontification.
Note that all others, like /italic/ or =code=, work fine.
Only *bold* is affected.

I attach a test file.

* Emphasis test
** bold
test *bold*
** italic
test /italic/
** underlined
test _underlined_
** code 
test =code=
** verbatim
test ~verbatim~
** strike-through
test +strike-through+


Tested with org-mode from git, as well as with emacs -q.

regards,
Oleh

Re: [O] AUCTeX key bindings within Org documents

[Nicolas Richard]

Hello Fabrice,

"Fabrice Niessen" 
writes:
> Due to a friend's request, I've tried to offer AUCTeX key bindings within Org
> documents via a minor mode, called "org-auctex-keys".

I checked that out because I often find myself doing C-c C-e while in
org-mode, but I expected it would insert
#+BEGIN_SRC latex
  \begin{prompted_env}

  \end{prompted_env}
#+END_SRC
instead of a new item.

OTOH, I don't really want such a feature, because when I do this, I
usually realize that it's time for me to export the tree to LaTeX and go
on from there.

> If you're interested, check it out at
> https://github.com/fniessen/org-auctex-key-bindings.

I see no licence, which I think (though IANAL) is equal to a strict and
super restrictive copyright ; is that intended ?

Best wishes,

-- 
Nicolas.

Re: [O] org mode R remote code evaluation

[Michael Albinus]

Eric Schulte  writes:

> I'd rather not hard-code the value of "/tmp/".  Perhaps you could rework
> the patch so that it introduces a new customizable variable (including a
> documentation string) so that users can set the value for their system.
>
> Also, please package the patch with git format-patch.

Patch is appended.

> Thanks,

Best regards, Michael.

>From 2b8db5486de75ec35c2c0d3e6063847cf582ace7 Mon Sep 17 00:00:00 2001
From: Michael Albinus 
Date: Fri, 27 Sep 2013 13:34:03 +0200
Subject: [PATCH] * ob-core.el (org-babel-local-file-name): Simplify.
 (org-babel-process-file-name): Apply `expand-file-name' first.
 (org-babel-remote-temporary-directory): New defcustom. (org-babel-temp-file):
 Use it.

---
 lisp/ob-core.el | 19 ---
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 5a032a1..a7c227b 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2680,11 +2680,7 @@ Fixes a bug in `tramp-handle-call-process-region'."
 
 (defun org-babel-local-file-name (file)
   "Return the local name component of FILE."
-  (if (file-remote-p file)
-  (let (localname)
-	(with-parsed-tramp-file-name file nil
- localname))
-file))
+  (or (file-remote-p file 'localname) file))
 
 (defun org-babel-process-file-name (name &optional no-quote-p)
   "Prepare NAME to be used in an external process.
@@ -2694,7 +2690,10 @@ remotely.  The file name is then processed by `expand-file-name'.
 Unless second argument NO-QUOTE-P is non-nil, the file name is
 additionally processed by `shell-quote-argument'"
   ((lambda (f) (if no-quote-p f (shell-quote-argument f)))
-   (expand-file-name (org-babel-local-file-name name
+   ;; We must apply `expand-file-name' on the whole filename.  If we
+   ;; would apply it on the local filename only, undesired effects
+   ;; like prepending a drive letter on MS Windows could happen.
+   (org-babel-local-file-name (expand-file-name name
 
 (defvar org-babel-temporary-directory)
 (unless (or noninteractive (boundp 'org-babel-temporary-directory))
@@ -2707,6 +2706,11 @@ additionally processed by `shell-quote-argument'"
 Used by `org-babel-temp-file'.  This directory will be removed on
 Emacs shutdown."))
 
+(defcustom org-babel-remote-temporary-directory "/tmp/"
+  "Directory to hold temporary files on remote hosts."
+  :group 'org-babel
+  :type 'string)
+
 (defmacro org-babel-result-cond (result-params scalar-form &rest table-forms)
   "Call the code to parse raw string results according to RESULT-PARAMS."
   (declare (indent 1)
@@ -2736,7 +2740,8 @@ of `org-babel-temporary-directory'."
   (if (file-remote-p default-directory)
   (let ((prefix
  (concat (file-remote-p default-directory)
- (expand-file-name prefix temporary-file-directory
+ (expand-file-name
+		  prefix org-babel-remote-temporary-directory
 (make-temp-file prefix nil suffix))
 (let ((temporary-file-directory
 	   (or (and (boundp 'org-babel-temporary-directory)
-- 
1.8.1.2

Re: [O] [BUG] Colored tags generate an error when C-x C-w'ing the agenda

[Sebastien Vauban]

Hi Carsten,

Carsten Dominik wrote:
> On 11.9.2013, at 14:48, Sebastien Vauban  wrote:
>> If you have colors for tags:
>> 
>> --8<---cut here---start->8---
>>  ;; faces for specific tags
>>  (setq org-tag-faces
>>'(("home" .
>>   (:slant italic
>>:foreground "#5C88D3" :background "#BBDDFF"))
>>  ("work" .
>>   (:slant italic
>>:foreground "#5F7C43" :background "#C1D996"
>> --8<---cut here---end--->8---
>> 
>> you can't export the agenda views anymore; they all generate the following
>> error:
>
> It does seem to work if you specify the faces like this (without the dot).
>
>  (setq org-tag-faces
>'(("home" 
>   (:slant italic
>:foreground "#5C88D3" :background "#BBDDFF"))
>  ("work" 
>   (:slant italic
>:foreground "#5F7C43" :background "#C1D996"

Without the dot [1], I confirm that I can export both to HTML and PDF with no
error.

Though, in the PDF, these tags have a white background, not the one specified.
This is a small annoyance...

> Since Emacs does display correctly with this way to specify a font, I'd say
> this is a bug in ps-print and should be reported to Emacs as such.

... which I'll report (with your analysis) to Emacs.

Thanks for your help!

Best regards,
  Seb

[1] I'd never ever have thought to remove the "dot". How did you discover or
know that?

-- 
Sebastien Vauban

[O] AUCTeX key bindings within Org documents

[Fabrice Niessen]

Hello,

Due to a friend's request, I've tried to offer AUCTeX key bindings within Org
documents via a minor mode, called "org-auctex-keys".

If you're interested, check it out at
https://github.com/fniessen/org-auctex-key-bindings.

Note that I'm willing to add extra AUCTeX keys -- but I don't use AUCTeX enough
to know what's important to transfer to Org.

Best regards,
Fabrice

-- 
Fabrice Niessen
Leuven, Belgium

Re: [O] [BUG] Colored tags generate an error when C-x C-w'ing the agenda

[Carsten Dominik]

On 11.9.2013, at 14:48, Sebastien Vauban  wrote:

> Hello,
> 
> If you have colors for tags:
> 
> --8<---cut here---start->8---
>  ;; faces for specific tags
>  (setq org-tag-faces
>'(("home" .
>   (:slant italic
>:foreground "#5C88D3" :background "#BBDDFF"))
>  ("work" .
>   (:slant italic
>:foreground "#5F7C43" :background "#C1D996"
> --8<---cut here---end--->8---
> 
> you can't export the agenda views anymore; they all generate the following
> error:

Since Emacs does display correctly with this way to specify a font, I'd say 
this is a bug in ps-print and should be reported to Emacs as such.

It does seem to work if you specify the faces like this (without the dot).


 (setq org-tag-faces
   '(("home" 
  (:slant italic
   :foreground "#5C88D3" :background "#BBDDFF"))
 ("work" 
  (:slant italic
   :foreground "#5F7C43" :background "#C1D996"

- Carsten

> 
> #+begin_src text
>  Debugger entered--Lisp error: (wrong-type-argument listp "#5C88D3")
>ps-face-attributes("#5C88D3")
>ps-face-attribute-list((:slant italic :foreground "#5C88D3" :background 
> "#BBDDFF"))
>ps-plot-with-face(459 463 (:slant italic :foreground "#5C88D3" :background 
> "#BBDDFF"))
>ps-generate-postscript-with-faces1(1 6850)
>ps-generate-postscript-with-faces(1 6850)
>ps-generate(# 1 6850 ps-generate-postscript-with-faces)
>ps-spool-with-faces(1 6850 nil)
>ps-print-with-faces(1 6850 "~/agenda.ps")
>ps-print-buffer-with-faces("~/agenda.ps")
>...
>command-execute(org-agenda-write)
> #+end_src
> 
> Best regards,
>  Seb
> 
> -- 
> Sebastien Vauban
> 
> 



signature.asc
Description: Message signed with OpenPGP using GPGMail

Re: [O] Special characters in tables (iso-latin-1 or utf-8)

[Marcin Borkowski]

Dnia 2013-09-27, o godz. 11:21:58
Jarmo Hurri  napisał(a):

> 
> Greetings.
> 
> A lot of my tables contain special characters (such as ä and ö)
> because those are used in Finnish names. These are now causing
> problems for me in table formulas.
> 
> Can someone tell me how to fix the table below so that the formula
> will work?
> 
> * testing table
> | string | same string |
> |+-|
> | abc| abc |
> | smörre | #ERROR  |
> #+TBLFM: $2=$1
> 
> When I open a new org-file and type special characters in it, the
> default encoding seems to be iso-latin-1; changing this to utf-8 has
> not helped.

My guess would be that the reason is that calc supports only ASCII
strings.

> All the best,
> 
> Jarmo

Best,

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

Re: [O] Request for write access to Word (noorul)

[Bastien]

Noorul Islam Kamal Malmiyoda  writes:

> Do I have to resend public key to someone to add?

You do have this key on the server:

ssh-rsa B3NzaC1yc2EA...uOJluuy7Fob1dI93uuU0WWQ== noorul@noorul

If this is not the correct one, please send me the new one.

Otherwise please try to clone from the server again (not just update
the remote git locations) and pull/push.

-- 
 Bastien

Re: [O] Lots of \n in ox-html output

[Suvayu Ali]

On Fri, Sep 27, 2013 at 11:29:57AM +0200, Thorsten Jolitz wrote:
> Nicolas Goaziou  writes:
> 
>  Hello,
> 
> > Thorsten Jolitz  writes:
> >
> >> although I did not update recently, html-export of this test org-file
> >> suddenly includes lots of \n in the html output.
> >
> > I cannot reproduce it. Does it also happen with a minimal configuration
> > file?
> 
> It must be something emacsclient/server related, since it does not
> happen when I call (pseudocode):
> 
> ,---
> | emacs -Q -l init.el -e org-export- ...
> `---
> 
> but does happen with 
> 
> ,--
> | emacs -Q --daemon=myserver -l init.el
> | emacsclient -e org-export-...
> `--
> 
> where init.el does _nothing_ but setting load-path and requiring the
> necessary libs. 

Can you try emacs -Q -l init.el where you start the server with
server-start in init.el?

-- 
Suvayu

Open source is the future. It sets us free.

Re: [O] Request for write access to Word (noorul)

[Noorul Islam Kamal Malmiyoda]

On Fri, Sep 27, 2013 at 2:51 PM, Bastien  wrote:
> Noorul Islam Kamal Malmiyoda  writes:
>
>> I am not able to push changes now. Is this now disabled for me?
>
> I don't think so, but you need to push to the orgmode.org server,
> not to repo.or.cz -- please ask for further help on the mailing
> list.
>

I have the remote set as

G |master O| --> git remote -v
origin  w...@orgmode.org:worg.git (fetch)
origin  w...@orgmode.org:worg.git (push)

G |master O| --> git pull
Permission denied (publickey).
fatal: The remote end hung up unexpectedly

Do I have to resend public key to someone to add?

I have that setup on repo.or.cz.

Thanks and Regards
Noorul

Re: [O] epresent issue

[Eric Schulte]

Rustom Mody  writes:

> On Fri, Sep 27, 2013 at 7:20 AM, Rustom Mody  wrote:
>
>> Hi
>>
>> I am trying to use epresent for presentation.
>> Start epresent with M-x epresent-run
>>
>> I seem to need to press one more q to get out of epresenting and then that
>> q gets into the file.
>>

I can't reproduce this problem with a recent version of epresent and
Org-mode.  For example with the following minimal Emacs invocation
(without any configuration, run from the epresent directory).

emacs -Q --eval "(progn (add-to-list 'load-path \"~/src/org-mode/lisp\") 
(require 'org))" -l epresent.el present.org

This is using epresent from https://github.com/eschulte/epresent.

Best,

>>
>> Thanks
>>
>> Rusi
>>
>
> Sorry for the half-complete line:
>> Start epresent with M-x epresent-run
>
> Was meaning to write a scenario but then decided that the one line was
> enough :-)
>
> Did not include usual version stuff (I assumed that I am doing something
> wrong)
> so here it is
>
> Org-mode version 8.2 (release_8.2-34-g33aded
> Emacs 23.4.1
> epresent downloaded yesterday
>
> Rusi

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

Re: [O] [PATCH] [org-table] user-chosen separator in org-table-convert-region

[francois]

On Tue, 24 Sep 2013 15:08:10 +0200, Carsten Dominik 
 wrote:
could you please explain what this does and show an example on how 
this should be used?


It adds the possibility of a string argument used as a regexp for
arbitrary field separator.

It can be used as following :
  (defun my-fjd/convert (beg0 end0 arg)
(interactive "r\nsSeparator: ")
(let* ((beg (min beg0 end0))
   (end (max beg0 end0))
   re)
  (org-table-convert-region beg0 end0 arg)
  ))
  (global-set-key (kbd "T") 'my-fjd/convert)

It permits for example to convert in place csv-like table with
semi-colon separator if I pass ";" as argument.

I modified the patch to add correct documentation in the function.

---
 lisp/org-table.el |3 +++
 1 file changed, 3 insertions(+)

diff --git a/lisp/org-table.el b/lisp/org-table.el
index 246cf8d..4883fc6 100644
--- a/lisp/org-table.el
+++ b/lisp/org-table.el
@@ -548,6 +548,7 @@ (defun org-table-convert-region (beg0 end0 
&optional separator)

 '(4) Use the comma as a field separator
 '(16)Use a TAB as field separator
 integer  When a number, use that many spaces as field separator
+string   When a string, use it as a regexp for field separator
 nil  When nil, the command tries to be smart and figure out the
  separator in the following way:
  - when each line contains a TAB, assume TAB-separated 
material
@@ -591,6 +592,8 @@ (defun org-table-convert-region (beg0 end0 
&optional separator)

 (if (< separator 1)
 (user-error "Number of spaces in separator must be >= 1")
   (format "^ *\\| *\t *\\| \\{%d,\\}" separator)))
+   ((stringp separator)
+  (format "^ *\\|%s" separator))
(t (error "This should not happen"
   (while (re-search-forward re end t)
(replace-match "| " t t)))
--
1.7.10.4

Re: [O] Lots of \n in ox-html output

[Thorsten Jolitz]

Nicolas Goaziou  writes:

 Hello,

> Thorsten Jolitz  writes:
>
>> although I did not update recently, html-export of this test org-file
>> suddenly includes lots of \n in the html output.
>
> I cannot reproduce it. Does it also happen with a minimal configuration
> file?

It must be something emacsclient/server related, since it does not
happen when I call (pseudocode):

,---
| emacs -Q -l init.el -e org-export- ...
`---

but does happen with 

,--
| emacs -Q --daemon=myserver -l init.el
| emacsclient -e org-export-...
`--

where init.el does _nothing_ but setting load-path and requiring the
necessary libs. 

Does emacsclient behave different w.r.t to encoding line-endings or so?

-- 
cheers,
Thorsten

[O] [Bug?] Search string NOT interpreted as individual parts

[Sebastien Vauban]

Hello,

I've observed, with the following minimal Org configuration,

--8<---cut here---start->8---
(require 'org)

(define-key global-map
  (kbd "C-c a") 'org-agenda)

(setq org-agenda-files '("~/ecm.org"))

;; turn on individual word search
(setq org-agenda-search-view-always-boolean t
  org-agenda-search-view-search-words-only t)

;; match part of a word
(setq org-agenda-search-view-force-full-words nil)
--8<---cut here---end--->8---

that the search string is:

- WELL interpreted as individual parts for `C-c a s', but
- NOT interpreted as individual parts for `C-c / /' inside the document itself

You can see (on http://screencast.com/t/JkjcirV2DZ) that the following ECM
document is found when searching

  `C-c a s histo entre RET'.

--8<---cut here---start->8---
#+TITLE: ECM
#+LANGUAGE:  fr

* Opérations

** TODO Ajouter l'historique de l'entreprise

La question "Historique de l'entreprise bon ou pas ?" est inutile dans le
processus...

Intégrer l'*historique PFI de l'entreprise* pour vérifier que ...

** TODO Historique

** TODO Entreprise
--8<---cut here---end--->8---

But, when inside the document,

- `C-c / / histo entre RET' FAILS
- `C-c / / historique entreprise RET' FAILS
- `C-c / / historique de l'entreprise RET' works
- `C-c / / rique de l'entreprise RET' works

That is:

- (setq org-agenda-search-view-always-boolean t)
  is only honored for `C-c a s', NOT for `C-c / /'

- (setq org-agenda-search-view-force-full-words nil)
  is honored for both `C-c a s' and `C-c / /'

Best regards,
  Seb

-- 
Sebastien Vauban

Re: [O] Special characters in tables (iso-latin-1 or utf-8)

[Michael Brand]

Hi Jarmo

On Fri, Sep 27, 2013 at 10:21 AM, Jarmo Hurri  wrote:
> | string | same string |
> |+-|
> | abc| abc |
> | smörre | #ERROR  |
> #+TBLFM: $2=$1

A lisp formula is the easiest way to just copy fields:
#+TBLFM: $2 = '(identity $1)

See also the ERT test-org-table/copy-field in testing/lisp/test-org-table.el:
http://orgmode.org/w/org-mode.git?p=org-mode.git;a=blob_plain;f=testing/lisp/test-org-table.el

Michael

Re: [O] Exploring data that is in org-mode format

[Karl Voit]

* Alan Schmitt  wrote:
> Hello,

Hi Alan!

> The short version: what tools are available to explore data, typically
> stored in org-mode tables?

Great question!

I did some very basic R-scripts to derive boxplots by myself.

> The long version: I've tried an interesting website
> (https://tictrac.com/) whose goal is to gain some insight about
> ourselves by exploring some data we collect (think quantified self). I'm
> not happy with this site for three reasons:
> - I need to send it the data;

I dislike cloud-based services which are not under my control.

> - it focuses on health / activity data whereas there is much more that
> interests me (I for instance have weekly records of natural gas use in my
> gas-heated house and daily record of temperature average outside which I
> would love to compare);

Absolutely!

> - it won't let you input arbitrary data (I asked about importing a CSV
> of my daily coffee consumption, they answered they require an external
> service to integrate the data).

I understand.

> So I collect all this data because it's something I enjoy doing, and I
> would really like to explore it, from the comfortable position of my own
> computer. All of this data is in org-mode tables (or can be easily
> converted to org-mode table). Hence my questions: are there tools you
> would recommend? I'm not afraid of programming (I suspect an answer will
> be 'R'), but I would like pointers to tutorials to do these kind of
> things. The kind of things I would like to do are:
> - extract weekly or monthly tallies or estimation from data collected at
> irregular intervals;
> - compare data sources against each other;
> - estimate future trends based on past data (how much will my gas bill be?);
> - display the result in some kind of dashboard.

I collect much data about myself using Memacs (see signature).
However, I did not derive anything else but some boxplots from it
(visualizing time-differences between periodic events).

Something generic which I can feed Org-mode files (most preferably
in Memacs-like Org-mode format) and derive some standard graphics
(where I pick those that make sense) would be very great!

-- 
mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML to Org-mode:
   > get Memacs from https://github.com/novoid/Memacs <

https://github.com/novoid/extract_pdf_annotations_to_orgmode + more on github

Re: [O] Exploring data that is in org-mode format

[Marcin Borkowski]

Dnia 2013-09-27, o godz. 10:18:15
Alan Schmitt  napisał(a):

> Hello,
> 
> This question is slightly off-topic, but it may be of interest to
> people who have a lot of data entered in org-mode.
> 
> The short version: what tools are available to explore data, typically
> stored in org-mode tables?
> 
> The long version: I've tried an interesting website
> (https://tictrac.com/) whose goal is to gain some insight about
> ourselves by exploring some data we collect (think quantified self).
> I'm not happy with this site for three reasons:
> - I need to send it the data;
> - it focuses on health / activity data whereas there is much more that
> interests me (I for instance have weekly records of natural gas use
> in my gas-heated house and daily record of temperature average
> outside which I would love to compare);
> - it won't let you input arbitrary data (I asked about importing a CSV
> of my daily coffee consumption, they answered they require an external
> service to integrate the data).
> 
> So I collect all this data because it's something I enjoy doing, and I
> would really like to explore it, from the comfortable position of my
> own computer. All of this data is in org-mode tables (or can be easily
> converted to org-mode table). Hence my questions: are there tools you
> would recommend? I'm not afraid of programming (I suspect an answer
> will be 'R'), but I would like pointers to tutorials to do these kind
> of things. The kind of things I would like to do are:
> - extract weekly or monthly tallies or estimation from data collected
> at irregular intervals;
> - compare data sources against each other;
> - estimate future trends based on past data (how much will my gas
> bill be?);
> - display the result in some kind of dashboard.
> 
> Thanks a lot,

Interesting question.  And although it is probably of no use for me,
I'd love to see an Emacs-based tool to do that...

> Alan

Best,

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

[O] Special characters in tables (iso-latin-1 or utf-8)

[Jarmo Hurri]

Greetings.

A lot of my tables contain special characters (such as ä and ö) because
those are used in Finnish names. These are now causing problems for me
in table formulas.

Can someone tell me how to fix the table below so that the formula will
work?

* testing table
| string | same string |
|+-|
| abc| abc |
| smörre | #ERROR  |
#+TBLFM: $2=$1

When I open a new org-file and type special characters in it, the
default encoding seems to be iso-latin-1; changing this to utf-8 has not
helped.

All the best,

Jarmo

[O] Exploring data that is in org-mode format

[Alan Schmitt]

Hello,

This question is slightly off-topic, but it may be of interest to people
who have a lot of data entered in org-mode.

The short version: what tools are available to explore data, typically
stored in org-mode tables?

The long version: I've tried an interesting website
(https://tictrac.com/) whose goal is to gain some insight about
ourselves by exploring some data we collect (think quantified self). I'm
not happy with this site for three reasons:
- I need to send it the data;
- it focuses on health / activity data whereas there is much more that
interests me (I for instance have weekly records of natural gas use in my
gas-heated house and daily record of temperature average outside which I
would love to compare);
- it won't let you input arbitrary data (I asked about importing a CSV
of my daily coffee consumption, they answered they require an external
service to integrate the data).

So I collect all this data because it's something I enjoy doing, and I
would really like to explore it, from the comfortable position of my own
computer. All of this data is in org-mode tables (or can be easily
converted to org-mode table). Hence my questions: are there tools you
would recommend? I'm not afraid of programming (I suspect an answer will
be 'R'), but I would like pointers to tutorials to do these kind of
things. The kind of things I would like to do are:
- extract weekly or monthly tallies or estimation from data collected at
irregular intervals;
- compare data sources against each other;
- estimate future trends based on past data (how much will my gas bill be?);
- display the result in some kind of dashboard.

Thanks a lot,

Alan

Re: [O] Lots of \n in ox-html output

[Nicolas Goaziou]

Hello,

Thorsten Jolitz  writes:

> although I did not update recently, html-export of this test org-file
> suddenly includes lots of \n in the html output.

I cannot reproduce it. Does it also happen with a minimal configuration
file?


Regards,

-- 
Nicolas Goaziou

Re: [O] Using Variable Width Fonts for org-mode and Fixed Width forTabless

[Alan Schmitt]

Hi Ian,

li...@wilkesley.net writes:

> I am struggling to get this to work. In my init files I have:
>
> (set-default-font "DejaVu Serif Italic")
>
> I have followed the advice on StackOverflow 
> http://stackoverflow.com/questions/3758139/variable-pitch-for-org-mode-fixed-pitch-for-tables
>  
> and customized my Init file to include:
>
> (set-face-attribute 'org-table nil :inherit 'fixed-pitch)
>
> However, table formatting is still screwed up. C-u C-x = shows
>
>  xft:-unknown-IM FELL DW 
> Pica-normal-italic-normal-*-15-*-*-*-*-0-iso10646-1 (#x29)
>
> Character code properties: customize what to show
>name: LATIN CAPITAL LETTER F
>general-category: Lu (Letter, Uppercase)
>decomposition: (70) ('F')
>
> There are text properties here:
>face org-table
>fontifiedt
>line-prefix  [Show]
>wrap-prefix  [Show]
>
> I have tried setting the font for org-table using Emacs Customize 
> Interface, but without any success. Ideally I want tables to use a 
> monospace font like Inconsolata or DejaVu mono. Can anyone provide an 
> example of how to set org-table to use a specified fixed width font.

I've played a little with this, and here is what I have (straight from
my config file).

First, I set up the font for variable pitch, and I tell emacs to use it
for text modes.

** setup
#+BEGIN_SRC emacs-lisp
  (set-face-attribute 'variable-pitch nil :family "Ubuntu")
  (set-face-attribute 'variable-pitch nil :height 140)
  
  (add-hook 'text-mode-hook 'variable-pitch-mode)
#+END_SRC

Then I set up exceptions for some faces in some modes. I have exceptions
for info, mu4e, and org mode. Here are the ones for org mode.

** org
from 
http://yoo2080.wordpress.com/2013/05/30/monospace-font-in-tables-and-source-code-blocks-in-org-mode-proportional-font-in-other-parts/

#+BEGIN_SRC emacs-lisp
  (defun my-adjoin-to-list-or-symbol (element list-or-symbol)
(let ((list (if (not (listp list-or-symbol))
(list list-or-symbol)
  list-or-symbol)))
  (require 'cl-lib)
  (cl-adjoin element list)))
  
  (mapc
   (lambda (face)
 (set-face-attribute
  face nil
  :inherit
  (my-adjoin-to-list-or-symbol
   'fixed-pitch
   (face-attribute face :inherit
   (list 'org-code 'org-block 'org-table 'org-block-background 'org-date 
'org-link 'org-footnote))
#+END_SRC

What this says is: use fixed-pitch for the faces in the list at the
end. I have to include dates, links, and footnotes because I use them in
tables and I don't know how to conditionally change a face (i.e., use
fixed-pitch for links in tables but not for links in other places).

Hopefully this will work for you.

Alan