Re: [O] whether in drawer?

[Derek Feichtinger]

Hi

Samuel Wales  gmail.com> writes:

> 
> can one tell whether point is in a drawer?
> 
> 
By coincidence just posted a patch request which contains the functionality
you desire. I use org-element-at-point and then test for drawer/property drawer:

(defun org-open-if-in-drawer ()
  (let ((element (org-element-at-point)))
(while (and element
(not (memq (org-element-type element)
   '(drawer property-drawer
  (setq element (org-element-property :parent element)))
(when element
  (let ((pos (point)))
(goto-char (org-element-property :begin element))
(org-flag-drawer nil)
(goto-char pos)


Cheers,
Derek

[O] PATCH: invoking RET on agenda clock log line ends up with point in closed clock drawer

[Derek Feichtinger]

Hello

A longer time ago, hitting RET on an agenda clock log line brought up the
respective org buffer with the cursor positioned on the clock line. At some
point this stopped to work cleanly, at least when using clock drawers. The
clock drawer would always be closed (even when it was opened in the org
buffer before jumping.) with the cursor being in the hidden drawer. So, it
became impossible to find the target clock line for e.g. modifying it.

I had fixed it for myself a longer time ago and forgot to submit my proposal
for a patch, until yesterday another user raised my attention to it.

My proposal for a patch is


;; when jumping to the agenda from a log message, the point ends up at
;; a CLOCK item in a LOGBOOK drawer, but the drawer gets closed, even
;; if the drawer was open before. I add a drawer opening function to
;; the respective agenda hook
(defun org-open-if-in-drawer ()
  (let ((element (org-element-at-point)))
(while (and element
(not (memq (org-element-type element)
   '(drawer property-drawer
  (setq element (org-element-property :parent element)))
(when element
  (let ((pos (point)))
(goto-char (org-element-property :begin element))
(org-flag-drawer nil)
(goto-char pos)

(add-hook 'org-agenda-after-show-hook #'org-open-if-in-drawer)


Best regards,
Derek

Re: [O] M-x cfw:open-org-calendar not working

[Paul James Harper]

Adam

Thanks. I got it working. But I'll note that method for troubleshooting
in future.

Regards,

Paul
On 2016-04-28 01:16:55, Adam Porter wrote:
> I would try opening the el files and eval-buffer in each one, then see
> if the commands are available.

Re: [O] Special alignment in org-mode

[David Cao]

Hi!

This solution works fairly well with the headers themselves, but the actual
content beneath the headers stays to the side of the buffer (as pictured:
http://i.imgur.com/nGv8XBI.png).
Would there be any way to fix this?

David

On Wed, Apr 27, 2016 at 9:47 AM John Kitchin 
wrote:

> I think this does approximately what you want:
>
> #+BEGIN_SRC emacs-lisp :results none
> (require 'ov)
>
> (defun org-max-heading-depth ()
>   "Get maximum depth of a heading."
>   (let ((max-depth 0)
> depth)
> (org-map-entries (lambda ()
>(when (> (setq depth (car
> (org-heading-components))) max-depth)
>  (setq max-depth depth
> max-depth))
>
>
> (defun org-right-align-overlay ()
>   "Put an overlay on headline * to right align to maximum depth.
> Should be run while on the headline."
>   (interactive)
>   (let* ((diff (- (org-max-heading-depth) (car (org-heading-components
>  ov)
> (while (and (setq ov (ov-at (match-beginning 1)))
>(overlay-get ov 'right-align))
>   (delete-overlay ov))
>
> ;; (setq ov (make-overlay (line-beginning-position) (+ 1
> (line-beginning-position
> (setq ov (make-overlay (match-beginning 1) (+ 1 (match-beginning 1
> (overlay-put ov 'before-string (make-string diff ? ))
> (overlay-put ov 'right-align t)))
>
> (defun org-right-align-clear ()
>   (interactive)
>   (ov-clear 'right-align))
>
> (defun align-matcher ( limit)
>   (while (re-search-forward org-heading-regexp limit t)
> (org-right-align-overlay)))
>
> (add-to-list 'org-font-lock-hook 'align-matcher)
> #+END_SRC
>
> Its only light tested, and may be slow on a long document because it is
> checking the maximum depth each time. You could set this to a constant,
> e.g. 8 if it is too slow.
>
> David Cao writes:
>
> > Hello,
> >
> > I was wondering if there is any way to right-align the header indicators
> > while left-aligning the actual content. Unfortunately I haven't been able
> > to find any mention of such a feature online.
> >
> > For example:
> >
> >   * My fancy org file
> >  ** Header 2
> > Some content here
> > *** Header 3
> >
> > Thanks in advance!
> > David
>
>
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>

[O] whether in drawer?

[Samuel Wales]

can one tell whether point is in a drawer?

Re: [O] How to reorder a footnote list?

[Adam Porter]

I don't understand: you want the footnotes to be in reverse order?  I
know very little about latex, so I'm sorry if this is just noise.

BTW, this won't help now, and is not meant to be snarky, but keeping
your org files in a git repo would help with a situation like this,
because you could find the commit where the change happened and get the
old text back.  I use a combination of real-auto-save-mode, a cron job,
and a "raise-or-run" script that automatically commits my org file
changes to git either every 15 minutes or every time I hide Emacs with
the script.  It has saved me a few times when I accidentally deleted
subtrees without realizing it until days later (probably had a region
marked by accident and then typed over it or something like that).

Re: [O] M-x cfw:open-org-calendar not working

[Adam Porter]

I would try opening the el files and eval-buffer in each one, then see
if the commands are available.

Re: [O] new rule to capitalise the first word in a sentence? but how?

[Samuel Wales]

very old code, maybe can be adjusted slightly to do what you want.

(defun alpha-capitalize-sentences ()
  (interactive)
  (let ((b (region-beginning))
(e (region-end))
;;i always use double spaces but i want sentence movement
;;to be liberal -- that is to count more things as
;;sentences.
(sentence-end-double-space nil)
;;need to make it understand org headlines etc. also.
;;don't know if this will help.  will fail on *bold*.
;;non-idempotent.  use a vector function.
(sentence-end-without-space
 (concat sentence-end-without-space "*")))
(save-excursion
  (goto-char b)
  (loop
while (< (point) (max b e))
do
(when (y-or-n-p "capitalize this sentence?")
  (capitalize-word 1))
;;forward-sentence-incl-org (headlines, items, other)
do
(let ((sentence-end-without-period t))
  (forward-sentence
;;;(replace-regexp "i" "I" t (region-beginning) (region-end))
(save-excursion
  (perform-replace "i" "I"
   nil t t nil nil
   b e

Re: [O] pandoc-style citations

[John Kitchin]

>
> Org-ref does a lot of nice things, but on this particular point is not
> very helpful, and has nothing to add for the case of multiple cites with
> overall and individual pre/posts. The package states that this is low
> priority b/c this style of citation is rare in scientific publishing (by
> which I guess is meant natural sciences; footnotes with multiple
> citations and linking text are of common in humanities and some social
> sciences).

Fair enough. I don't think the standard link syntax is rich enough for this.

I worked out the basis for an alternative approach here:
http://kitchingroup.cheme.cmu.edu/blog/2015/02/05/Extending-the-org-mode-link-syntax-with-attributes/
that might also be adaptable for your use case. It basically gets
towards the cite syntax but doesn't require adding new elements and
other things.


I updated the org-ref docs on why we don't currently do more than the
simple pre/post text. I don't have anything against supporting more, I
just don't know how to do it, or when it would be right ;)

>
> thanks again and best wishes
> alex


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

Re: [O] new rule to capitalise the first word in a sentence? but how?

[Marcin Borkowski]

On 2016-04-27, at 19:36, Sharon Kimble  wrote:

> How can I have a rule that will capitalise the first word of a new
> sentence, with the previous sentence concluding with a full stop and
> then one space please? This would be extremely useful for me as I tend
> to forget to capitalise the first word, but how can it be done please?

Would this help?

https://www.emacswiki.org/emacs/auto-capitalize.el

> Thanks
> Sharon.

Hth,

-- 
Marcin Borkowski
http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
Faculty of Mathematics and Computer Science
Adam Mickiewicz University

[O] How to reorder a footnote list?

[Sharon Kimble]

Something has happened to my list of footnotes which are now numbered in
order of 1,2,3, etc, instead of its more normal 50, 49, 48, etc. I don't
know exactly when it happened but I'm not able now to export my document
to latex because its looking for [fn:1] at the bottom of the list
but [fn:1] is now at the top of the list!

So how can I reorder the list please? I've googled but without success.

Thanks
Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.4, fluxbox 1.3.7, emacs 25.0.93


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Re: [O] pandoc-style citations

[Alex Fenton]

On 27/04/16 21:41, John Kitchin wrote:

you might also checkout helm-bibtex. A recent note indicated "Support
for pre- and postnotes for pandoc-citeproc citations."


Thanks, I already use helm-bibtex together with org-ref so will have a look.

this exports out of the org-ref box to:
blah blah blah \cite[][, p.23]{ref1}, also \cite{ref2}, for a contrary
view see \cite[][ pp148-152]{ref3}.

I don't use this style of citations, so I don't know if it is right.


Not quite unfortunately, this would mean that in the two styles I use, 
Harvard (common in social science) referencing, the references appear in 
separate parentheses, or footnote (common in e.g. history) in separate 
footnotes, when they should be together in a single one. I appreciate 
that the style in medicine and many natural sciences is often just an 
author/year abbreviation or number, which works much better plopped into 
normal running text.


best
alex

Re: [O] pandoc-style citations

[Alex Fenton]

Hi Richard

On 27/04/16 16:09, Richard Lawrence wrote:

As far as Elisp implementations go, I know of no specific parser for
Pandoc citation syntax.  But there is support for a Pandoc-like syntax
(discussed in the threads you read) in the wip-cite branch of Org's
repository.



https://github.com/wyleyr/org-mode/


Thanks for your reply, and for all your work on specifying and 
developing this. It looks like that for now I can adapt some of the 
parsing in org-element.el (org-element-citation-reference-parser and 
org-element-citation-parser etc) to get something that works for now in 
standard mainline org.




Export is where efforts stalled last year.


That's understandable, given that, as you say, it's a complex problem 
given the range of citation styles and output formats. It's still a 
shame given the work that you (pl.) have put into integrating citations 
into the org parser & element tree so they are first class objects.


I don't know whether it's conceivable that the data structures and 
parsing could be integrated into org, with the (presumably) relatively 
easy latex output, which I suspect is the commonest use case, and then 
with some kind of "adequate" output for other targets (html, text, odt) 
- perhaps an output that would require further post-processing by a 
third-party tool such as citeproc or pandoc.


Latex-outputters would be better off and other targets no worse off than 
present, and it might act as a spur to solve the other target formats 
one by one way. But I can see that this has been to some extent 
considered and can also see the arguments against.




You may also want to look at John Kitchin's org-ref, which I believe
works similar to your homebrew link solution, but has a lot of features
and may provide a better interface for what you're trying to do:


Org-ref does a lot of nice things, but on this particular point is not 
very helpful, and has nothing to add for the case of multiple cites with 
overall and individual pre/posts. The package states that this is low 
priority b/c this style of citation is rare in scientific publishing (by 
which I guess is meant natural sciences; footnotes with multiple 
citations and linking text are of common in humanities and some social 
sciences).


thanks again and best wishes
alex

Re: [O] M-x cfw:open-org-calendar not working - Solved

[Paul Harper]

Can't remember where I got this from. But this config got Calfw and
Org-gcal working with Gmail.

#+BEGIN_SRC emacs-lisp
(require 'calfw-cal)
(require 'calfw-ical)
(require 'calfw-howm)
(require 'calfw-org)

(defun my-open-calendar ()
  (interactive)
  (cfw:open-calendar-buffer
   :contents-sources
   (list
(cfw:org-create-source "Green")  ; orgmode source
   )))

;; Org-Gcal
(require 'org-gcal)
(setq org-gcal-client-id "mysecretclientid.googleusercontent.com"
  org-gcal-client-secret "myreallysecret"
  org-gcal-file-alist '(("myem...@gmail.com" .
"~/Dropbox/org/calendars/schedule.org")
  ))

#+END_SRC

I hope it helps somebody out.

On 27 April 2016 at 06:41, Paul Harper  wrote:

>
> I am following this article "Taming Google Calendar With Org-Mode" to
> try to get sync going with my Google
> Calendar. http://jameswilliams.be/blog/2016/01/11/Taming-Your-GCal.html
>
> I've installed Calfw and Org-Gcal with  the package manager. But when I
> M-x cfw:open-org-calendar it does not find the command. Mx cf  only
> finds cfengine.
>
> What is the best way for me to troubleshoot this? My setup is identical
> to the article except for:
>
> (add-to-list 'load-path "/home/username/.emacs.d/elpa/calfw-20160302.1858")
> (require 'calfw)
> (require 'calfw-org)
>
> Regards
>
>
> Paul
> --
> Sent with my mu4e
>



-- 
Regards,


Paul

about.me/pauljamesharper

GnuPG Fingerprint: B3C2 6A80 BB3E 8D4D 126E  4FBE 5F62 4195 17D3 CB75


“Wisdom consists in being able to distinguish among dangers and make a
choice of the least harmful.” — Niccolo Machiavelli, The Prince

“The user’s going to pick dancing pigs over security every time.” — Bruce
Schneier

Re: [O] pandoc-style citations

[John Kitchin]

you might also checkout helm-bibtex. A recent note indicated "Support
for pre- and postnotes for pandoc-citeproc citations."

I haven't tried it, so I am not sure how it works for org-mode. org-ref
supports [[cite:somekey][pre-text::post-text]] syntax, without folding
the link on itself so you can see it.

I think your example would look like:

blah blah blah [[cite:ref1][::, p.23]], also cite:ref2, for a contrary
view see [[cite:ref3][:: pp148-152]]

this exports out of the org-ref box to:
blah blah blah \cite[][, p.23]{ref1}, also \cite{ref2}, for a contrary
view see \cite[][ pp148-152]{ref3}.

I don't use this style of citations, so I don't know if it is right.

Alex Fenton writes:

> Hello,
>
> I see that there were several extensive and fruitful discussions on this
> list last year on citation syntax. There seemed to be a reasonable
> degree of consensus that pandoc-style citation syntax was at the least a
> good model.
>
> I'd like to know if there are any implementations out there of elisp to
> parse pandoc citation syntax and turn it into latex \cites. My question
> is not so much "when/if this will be in org mode" but rather whether
> there's something I can drop in now (likely as a link type).
>
> I have a lot of longish citations with multiple references each with
> their own pre- and post- ("'blah blah blah @ref1, p.23, also @ref2, for
> a contrary view see @ref3 pp148-152") that end up as \cites. However my
> home-brew link solution, stuffing the multiple pre- and posts- with
> separator into the link description is unwieldy - difficult to write,
> hard to read and easy to get wrong or breaking output.
>
> thanks
> alex


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

[O] new rule to capitalise the first word in a sentence? but how?

[Sharon Kimble]

How can I have a rule that will capitalise the first word of a new
sentence, with the previous sentence concluding with a full stop and
then one space please? This would be extremely useful for me as I tend
to forget to capitalise the first word, but how can it be done please?

Thanks
Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.4, fluxbox 1.3.7, emacs 25.0.93


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Re: [O] org-passwords.el and encryption

[Julien Cubizolles]

Eric S Fraga  writes:

> On Wednesday, 27 Apr 2016 at 16:24, Julien Cubizolles wrote:
>> there must be something wrong with my setup: keychain complains:
>>
>> * Adding 1 gpg key(s): 370D5DFF
>> * Error: Problem adding (is pinentry installed?); giving up
>
> Which version(s) of pinentry do you have installed?

I have pinentry-gnome3, pinentry-curses, pinentry-tty, and I try with
all 3 of them, setup with update-alternatives. The error remains the
same.

> And is this error from your .profile (i.e. console login) 

yes (from .bash_profile actually)

> or is it when you try manually?

also, running:
--8<---cut here---start->8---
keychain --eval --agents ssh,gpg id_rsa MYGPGKEY
--8<---cut here---end--->8---
in a non login shell.

Regards,

Julien.

[O] TaskJuggler exporting TODO tasks as complete?

[Erik Wickstrom]

Hi,

I've noticed that if I export a project with a list of TODOs, the
taskjuggler gantt chart shows all of the tasks' taskbars as "complete"
(ie a filled status bar.) unless I manually add a ":Complete: 0"
property to each TODO item.

This happens because if the TODO isn't  in a DONE state, and there
isn't a :complete: property, then the "complete" attribute won't be
set in the .tjp file att all.

There should probably be a customizable variable with a default value
for this situation (ie the user can set it to 0, or 100 depending on
their display preference).  Basically, I want to set my tasks to
"complete 0" if it isn't overridden by the TODO state or property.

Additionally, any TODO in a state other than DONE should have the .tjp
complete property set to something other than 100.  In fact, it would
be really cool for those who customize their TODO states
(TODO|INPROGRESS|WAITING|DONE...) if the user could map them to
completion percentages in the org file.

Thoughts?

Erik

[O] make org-agenda-to-appt run a shell command also

[Samuel Wales]

i currently use org-agenda-to-appt to make emacs make an emacs window
pop up when a timed task shows up.  this works well!

however, for some of these tasks i want to do something in
addition.  i want to run a shell command.

i'd put the shell command in the properties drawer like

#+begin_quote
:PROPERTIES:
:Appt-shell-command: "mycommand whatever whatever"
:END:
#+end_quote

the windows would pop up as normal, but also the shell
command would run.  there woudn't be any change to the
window layout; the shell command would run silently.

can anybody design this?  i have no clue.


samuel

-- 
The Kafka Pandemic: http://thekafkapandemic.blogspot.com

The disease DOES progress.  MANY people have died from it.  And
ANYBODY can get it.

Denmark: free Karina Hansen NOW.

Re: [O] bug: export prints bogus link

[Samuel Wales]

thanks, nicolas.

-- 
The Kafka Pandemic: http://thekafkapandemic.blogspot.com

The disease DOES progress.  MANY people have died from it.  And
ANYBODY can get it.

Denmark: free Karina Hansen NOW.

Re: [O] exported table has text overflowing off the pdf page

[Thomas S. Dye]

Aloha Sharon,

Sharon Kimble writes:

> Thanks Eduardo, as I said I'm converting a latex document into org-mode,
> so I've already got quite complex tables working in latex, so I'm just
> pasting them into my org document and then having a '#+begin_latex'
> before the latexed table and a '#+end_latex' after the table, and its
> working quite well except I am, so far, unable to have a 'list of
> tables' which isn't a real problem.

This gives me a list of tables:

#+TOC: tables

All the best,
Tom

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

Re: [O] org-passwords.el and encryption

[Eric S Fraga]

On Wednesday, 27 Apr 2016 at 16:24, Julien Cubizolles wrote:
> there must be something wrong with my setup: keychain complains:
>
> * Adding 1 gpg key(s): 370D5DFF
> * Error: Problem adding (is pinentry installed?); giving up

Which version(s) of pinentry do you have installed?  And is this error
from your .profile (i.e. console login) or from lightdm, or is it when
you try manually?

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.92.1, Org release_8.3.4-739-g789412

[O] Using source blocks instead of Ansible

[William Denton]

Is anyone using Org for remote configuration management instead of a tool like 
Ansible?


For example:  I like to install R from source to /usr/local/src/R/ so that I 
always have the latest version.  I do this (changing the version numbers as 
needed, though looking at it now I see I should set the version number as a 
variable):


#+BEGIN_SRC shell
cd /usr/local/src/R
curl -O http://cran.utstat.utoronto.ca/src/base/R-3/R-3.2.4.tar.gz
tar xzvf R-3.2.4.tar.gz
cd R-3.2.4
./configure
make
make check
cd ..
rm -f R Rscript
ln -s R-3.2.4/bin/R R
ln -s R-3.2.4/bin/Rscript Rscript
#+END_SRC

I do that on a few machines and copy and paste as needed.  Now, I could use

:dir /me@remote:

to run that on another machine.  And if I want to run that on multiple machines 
I could change the target as needed.


Has anyone taken this to the next level so it's easier to manage tasks like 
this, more reproducible, tidier, and closer to Ansible or Chef?  If so I'd love 
to see an example.  Or if anyone's tried and found it's just easier to use a 
proper purpose-built system, that's good to know too.


Looking in the archives I see there was mention a couple of years ago of 
org-converge, but it's idle:


https://github.com/wallyqs/org-converge

Cheers,

Bill
--
William Denton ↔  Toronto, Canada ↔  https://www.miskatonic.org/

Re: [O] exported table has text overflowing off the pdf page

[Sharon Kimble]

Eduardo Mercovich  writes:

> Dear Sharon.
>
 I'm running into problems exporting tables into latex with a 2-column
 3-row table with a large amount of text to go into the cells, but when
 its exported the text is taking over and overflowing off the pdf page.
>
> I'm a newbie and confronted to this same situation found this latex
> options (from the org-manual, but not obvious when you don't know what
> you're searching):
>
> #+CAPTION: This is your table caption (of course, it's optional). 
> #+NAME:   table:yourtableid
>
> #+ATTR_LATEX: :environment longtable :width 1\textwidth :font \small 
> \raggedright :align >{\raggedright}p{9cm} p{3cm}
> | Here | comes | your | table |
> |--+---+--+---|
> | and  | some  | text | cells |
>
> Let's break this into pieces:
>
> :environment longtable
>  breaks across pages if too long. 
>
> :width 1\textwidth
>  it has the width of the text block
>
> :font \small
>  assuming your latex class has a "small" font size definition,
>  can be tiny, miniscule, etc. 
>
> : \raggedright
>  don't justify a few words in short width columns, looks much better
>
> :align >{\raggedright}p{9cm} p{3cm}
>  this defines the column align and width. 
>
> Try it, see what happens and let's optimize this together. :)
>

Thanks Eduardo, as I said I'm converting a latex document into org-mode,
so I've already got quite complex tables working in latex, so I'm just
pasting them into my org document and then having a '#+begin_latex'
before the latexed table and a '#+end_latex' after the table, and its
working quite well except I am, so far, unable to have a 'list of
tables' which isn't a real problem.

Thanks
Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.4, fluxbox 1.3.7, emacs 25.0.93


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Re: [O] How to have a controllable popup?

[Sharon Kimble]

John Kitchin  writes:

> It sounds like helm could do what you want.
>
> Here is an example of making a simple helm source:
> http://kitchingroup.cheme.cmu.edu/blog/2015/01/24/Anatomy-of-a-helm-source/
>
> I guess you would run M-x your-helm-command where you want it, and the
> information would appear in a helm buffer. you select what you want and
> make it get inserted.
>

Thanks John, I've been able to make a work-around by using tabbar-ruler
to create tabs and then copy my 'reference list' into a small temporary
buffer which is next to my working document so its easy to switch too. I
can add reference numbers to it and at the end of the day I copy them
back into my main reference list. I'm finding the org-mode document is
ideal for keeping urls, and also reference notes at the end of the
document after my latex command ending the document.

Thanks
Sharon.

>
> Sharon Kimble writes:
>
>> I'm not sure whether this is the right place for this or if I should be
>> looking elsewhere for it, so sorry if its the wrong place.
>>
>> I'm converting a large latex file of 780 pages when its in a pdf file,
>> but I'm converting from latex to org-mode. I'm also taking the
>> opportunity of revising it and standardising it. And I'm also rebuilding
>> the bibliography database held in a bib file.
>>
>> So I have a section in the org-mode file which has the old bibliography
>> index number alongside the new number. How can I have a popup just
>> showing those numbers which I can look at and then input a certain
>> number into the main body of the file, and then close the popup until I
>> need to call it again? The popup would need to be scrollable and appear
>> in the right third of the page.
>>
>> I've tried to set it up with workgroups, and also tabs of the relevant
>> files next to each other in tabbar, but neither of these really worked.
>>
>> Thanks
>> Sharon.
>
>
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu

-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.4, fluxbox 1.3.7, emacs 25.0.93


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Re: [O] Special alignment in org-mode

[John Kitchin]

I think this does approximately what you want:

#+BEGIN_SRC emacs-lisp :results none
(require 'ov)

(defun org-max-heading-depth ()
  "Get maximum depth of a heading."
  (let ((max-depth 0)
depth)
(org-map-entries (lambda ()
   (when (> (setq depth (car (org-heading-components))) 
max-depth)
 (setq max-depth depth
max-depth))


(defun org-right-align-overlay ()
  "Put an overlay on headline * to right align to maximum depth.
Should be run while on the headline."
  (interactive)
  (let* ((diff (- (org-max-heading-depth) (car (org-heading-components
 ov)
(while (and (setq ov (ov-at (match-beginning 1)))
   (overlay-get ov 'right-align))
  (delete-overlay ov))

;; (setq ov (make-overlay (line-beginning-position) (+ 1 
(line-beginning-position
(setq ov (make-overlay (match-beginning 1) (+ 1 (match-beginning 1
(overlay-put ov 'before-string (make-string diff ? ))
(overlay-put ov 'right-align t)))

(defun org-right-align-clear ()
  (interactive)
  (ov-clear 'right-align))

(defun align-matcher ( limit)
  (while (re-search-forward org-heading-regexp limit t)
(org-right-align-overlay)))

(add-to-list 'org-font-lock-hook 'align-matcher)
#+END_SRC

Its only light tested, and may be slow on a long document because it is
checking the maximum depth each time. You could set this to a constant,
e.g. 8 if it is too slow.

David Cao writes:

> Hello,
>
> I was wondering if there is any way to right-align the header indicators
> while left-aligning the actual content. Unfortunately I haven't been able
> to find any mention of such a feature online.
>
> For example:
>
>   * My fancy org file
>  ** Header 2
> Some content here
> *** Header 3
>
> Thanks in advance!
> David


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

Re: [O] How to have a controllable popup?

[John Kitchin]

It sounds like helm could do what you want.

Here is an example of making a simple helm source:
http://kitchingroup.cheme.cmu.edu/blog/2015/01/24/Anatomy-of-a-helm-source/

I guess you would run M-x your-helm-command where you want it, and the
information would appear in a helm buffer. you select what you want and
make it get inserted.


Sharon Kimble writes:

> I'm not sure whether this is the right place for this or if I should be
> looking elsewhere for it, so sorry if its the wrong place.
>
> I'm converting a large latex file of 780 pages when its in a pdf file,
> but I'm converting from latex to org-mode. I'm also taking the
> opportunity of revising it and standardising it. And I'm also rebuilding
> the bibliography database held in a bib file.
>
> So I have a section in the org-mode file which has the old bibliography
> index number alongside the new number. How can I have a popup just
> showing those numbers which I can look at and then input a certain
> number into the main body of the file, and then close the popup until I
> need to call it again? The popup would need to be scrollable and appear
> in the right third of the page.
>
> I've tried to set it up with workgroups, and also tabs of the relevant
> files next to each other in tabbar, but neither of these really worked.
>
> Thanks
> Sharon.


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

Re: [O] org-passwords.el and encryption

[Julien Cubizolles]

Eric S Fraga  writes:


> I have keychain in both my .bash_profile (for when I log in in console
> mode or remotely) 

there must be something wrong with my setup: keychain complains:

--8<---cut here---start->8---
* Adding 1 gpg key(s): 370D5DFF
* Error: Problem adding (is pinentry installed?); giving up
--8<---cut here---end--->8---

> eval $(keychain --eval --agents ssh,gpg id_rsa gpgkey )

I have the same here.


I think I'll give up with keychain for now, ssh-agent and gpg-agent are
automatically started when I log in, two passphrases per login are not
too annoying.

Thanks for your help.

[O] Restore org-agenda-undo in the presence of evil and undo-tree

[Christoph LANGE]

Hi all,

I am using evil and undo-tree and therefore have (global-undo-tree-mode 1).

In agenda views, I would like to be able to use org-agenda-undo, but the
usual keyboard shortcuts for org-agenda-undo are occupied by undo-tree-undo.

So I wondered how to disable undo-tree-mode in agenda views and came up
with the following:

  (add-hook 'org-agenda-finalize-hook #'(lambda () (undo-tree-mode -1)))

Nevertheless, undo is not working properly as long as the underlying Org
buffer, which I am editing remotely from the agenda buffer, is in
evil-mode.  If I switch it to Emacs input, undo works.

Can anyone confirm this behaviour?

Cheers, and thanks in advance,

Christoph

-- 
Dr. Christoph Lange, Enterprise Information Systems Department
Applied Computer Science @ University of Bonn; Fraunhofer IAIS
http://langec.wordpress.com/about, Skype duke4701

→ CSCUBS Computer Science Conference for University of Bonn Students
  25 May 2016; submission deadline 28 April – http://cscubs.cs.uni-bonn.de

Re: [O] pandoc-style citations

[Richard Lawrence]

Hi Alex,

Alex Fenton  writes:

> I see that there were several extensive and fruitful discussions on this 
> list last year on citation syntax. There seemed to be a reasonable 
> degree of consensus that pandoc-style citation syntax was at the least a 
> good model.
>
> I'd like to know if there are any implementations out there of elisp to 
> parse pandoc citation syntax and turn it into latex \cites. My question 
> is not so much "when/if this will be in org mode" but rather whether 
> there's something I can drop in now (likely as a link type).

As far as Elisp implementations go, I know of no specific parser for
Pandoc citation syntax.  But there is support for a Pandoc-like syntax
(discussed in the threads you read) in the wip-cite branch of Org's
repository.  This provides support for multi-cite citations in Org
syntax, but it isn't hooked up to the export framework at all.

Export is where efforts stalled last year.  Aaron Ecay, Vaidheeswaran C,
and I all worked on different proof-of-concept implementations to hook
up the citation parser to a citation processor and the various
exporters.  This is a non-trivial problem, and it seems that not many
people have a lot of time to work on it (including me), so if you want
to help, that would be great!  Aaron's work is in the Org repository
(see the wip-cite-awe branch).  Vaidheeswaran's is elsewhere; I don't
know where exactly, but you can search the list for a link.  My own is
here, in the wip-cite-rebase branch:

https://github.com/wyleyr/org-mode/.

There is also Pandoc itself, which can read (some) Org syntax.
Depending on what your document looks like, you might have good luck
just using Pandoc to convert it to LaTeX.

> I have a lot of longish citations with multiple references each with 
> their own pre- and post- ("'blah blah blah @ref1, p.23, also @ref2, for 
> a contrary view see @ref3 pp148-152") that end up as \cites. However my 
> home-brew link solution, stuffing the multiple pre- and posts- with 
> separator into the link description is unwieldy - difficult to write, 
> hard to read and easy to get wrong or breaking output.

You may also want to look at John Kitchin's org-ref, which I believe
works similar to your homebrew link solution, but has a lot of features
and may provide a better interface for what you're trying to do:

https://github.com/jkitchin/org-ref
 
Best,
Richard

Re: [O] New Beamer environment selection problem

[Jarmo Hurri]

Nicolas Goaziou  writes:

>> The newest versions of org (pulled from git) introduced a problem in my
>> use of beamer. Consider the following org file
>>
>> #---
>> #+STARTUP: beamer
>> * foo
>> ** bar
>> #---
>>
>> Earlier, when I moved my cursor to the end of word "bar" and pressed
>> "C-c C-b" for (org-beamer-select-environment), I was able to select a
>> beamer environment. Now I get an error
>>
>> apply: Wrong number of arguments: max, 0
>>
>> Any ideas?
>
> I cannot reproduce it. Could you send a detailed backtrace?

Is this detailed enough?

Debugger entered--Lisp error: (wrong-number-of-arguments max 0)
  max()
  apply(max nil)
  org-fast-tag-selection(nil nil nil nil)
  org-set-tags()
  org-beamer-select-environment()
  call-interactively(org-beamer-select-environment nil nil)
  command-execute(org-beamer-select-environment)

> Could you also check you're not experiencing a mixed installation?

This is a printout of (org-version):

Org-mode version 8.3.4 (release_8.3.4-758-g1daac7 @ 
/home/jarmo/addons/emacs-packages/org/lisp/)

Also, in (list-load-path-shadows) all the directories that hide other
stuff point to the up-to-date org installation. In addition, in my
.emacs, load-path is updated to include the correct org lisp directory
before any org stuff is loaded.

But it is true that this isn't the only weird thing I have seen
recently. I still haven't been able to solve my Babel shell problem I
posted earlier.

Jarmo

Re: [O] Beamer presantation, Abstract and Article in same document - how to structure and how to export?

[Rainer M Krug]

Rasmus  writes:

> Hi,
>
> Rainer M Krug  writes:
>
>> I would like to have one document containing
>>
>> 1) abstract for
>> 2) a presentation and 
>> 3) a resulting paper
>>
>> My question is: how can I structure this an how can I handle the export?
>>
>> Obviously under different top level headers:
>>
>> * Abstract
>> #+begin_abstract
>> Needs top be written
>> #+end_abstract
>>
>> * Presentation
>> ** Title
>> *** first slide
>> ...
>> * Paper
>> ** Abstract
>> How can I refer to the abstract above?
>> ** ...
>
> While you may not necessarily *need* beamerarticle, you might still find
> it enlightening.  See section 21.2 in the beamer manual.
>
> Example:
>
> #+title: beamer example with text not shown
> #+options: h:2
>
> #+latex_class_options: [ignorenonframetext]
> * h1
> text that is not part of any slide 
> ** my first slide
> - a
> - b
>
> Another companion is #+include which you can use to extract named element
> from one file to the other, e.g. to share tables.

Thanks - both good ideas. I will look into them. I have already put the
[ignorenonframetext] option in.

>
>> But what about the specific settings? Can I set them per subtree?
>>
>> #+LaTeX_CLASS: beamer
>> #+LaTeX_CLASS_OPTIONS: [bigger]
>
> Isn't the latex class guess correctly?

I only copied from the work examples - but it is true - I don't need
this - and to leave it out, actually makes life much easier.

>
>> I could than export each subtree separate?
>
> Should be easy to do with a bit of lisp.

I use emacs, org, ess and gnus , but I never managed to get a real grasp
of elisp.

>
>> Can I define the name for the exported document per subtree?
>
>   
> http://orgmode.org/org.html#index-property_002c-EXPORT_005fFILE_005fNAME-1651

OK - thanks - found it.

>
>> How can I switch easily between different settings?
>
> For #+LaTeX_CLASS_OPTIONS I'd maybe use a macro.
> I'd also use this for setting export tags, e.g. 
>
> #+MACRO: exclude-tags (eval (mapconcat 'identity (list "#+EXCLUDE_TAGS:" 
> "noexport" (concat "no" (symbol-name org-export-current-backend))) " "))
>
> You might also find the if clause in this macro interesting:
>
> #+MACRO: abbr (eval (if (org-export-derived-backend-p 
> org-export-current-backend 'html) "@@html: title=\"$2\">@@$1@@html:@@" "$1"))

Thanks - I will look into this. I used macros already - but this looke=s
very interesting.

Cheers,

Rainer

>
> Hope it helps,
> Rasmus

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Description: PGP signature

Re: [O] Beamer presantation, Abstract and Article in same document - how to structure and how to export?

[Rasmus]

Hi,

Rainer M Krug  writes:

> I would like to have one document containing
>
> 1) abstract for
> 2) a presentation and 
> 3) a resulting paper
>
> My question is: how can I structure this an how can I handle the export?
>
> Obviously under different top level headers:
>
> * Abstract
> #+begin_abstract
> Needs top be written
> #+end_abstract
>
> * Presentation
> ** Title
> *** first slide
> ...
> * Paper
> ** Abstract
> How can I refer to the abstract above?
> ** ...

While you may not necessarily *need* beamerarticle, you might still find
it enlightening.  See section 21.2 in the beamer manual.

Example:

#+title: beamer example with text not shown
#+options: h:2
#+latex_class_options: [ignorenonframetext]
* h1
text that is not part of any slide 
** my first slide
- a
- b

Another companion is #+include which you can use to extract named element
from one file to the other, e.g. to share tables.

> But what about the specific settings? Can I set them per subtree?
>
> #+LaTeX_CLASS: beamer
> #+LaTeX_CLASS_OPTIONS: [bigger]

Isn't the latex class guess correctly?

> I could than export each subtree separate?

Should be easy to do with a bit of lisp.

> Can I define the name for the exported document per subtree?

  http://orgmode.org/org.html#index-property_002c-EXPORT_005fFILE_005fNAME-1651

> How can I switch easily between different settings?

For #+LaTeX_CLASS_OPTIONS I'd maybe use a macro.
I'd also use this for setting export tags, e.g. 

#+MACRO: exclude-tags (eval (mapconcat 'identity (list "#+EXCLUDE_TAGS:" 
"noexport" (concat "no" (symbol-name org-export-current-backend))) " "))

You might also find the if clause in this macro interesting:

#+MACRO: abbr (eval (if (org-export-derived-backend-p 
org-export-current-backend 'html) "@@html:@@$1@@html:@@" "$1"))

Hope it helps,
Rasmus

-- 
If you can mix business and politics wonderful things can happen!

Re: [O] [PATCH] new :async feature for org-babel-clojure

[Frederick Giasson]

Hi Nicolas,




Right now, async is really more about "feedback" than "asynchronous".
However it has never been clear is it was possible or not, and if so,
how :)

Any pointers on how this could be done in emacs?

You could start a new Emacs evaluating some code in a subprocess, with
`start-process' and collect return value. You may want to have a look at
`org-export-async-start' or "async.el" library in ELPA.

Unfortunately, it is not yet possible to re-use the latter in Org code,
since it is unavailable in vanilla Emacs.

The hard part, IMO, is to bring the right context in the subprocess
(e.g., the environment should be the same, other blocks may be needed,
etc.).


Yeah, will have to take some more time to check that, I probably have 
much to learn regarding Elisp itself first.


Rethinking about that, would it not be better to remove the confusion by 
changing the terminology I used: ":async"? What it really is is to have 
feedback of the underlying process, and not really an asynchronous process.


I thought about two possibilities:

  (1) creating two new results options: :output-process and 
:value-process. Which means that we output the underlying process of a 
:output or :value :results

  (2) renaming :async by :show-process or something similar.

Then we take the time to check how a real asynchronous system can be put 
in place.


Thoughts?

Thanks,

Fred





Regards,

Re: [O] tables, comment in one line, export to html

[Nicolas Goaziou]

Michael Brand  writes:

> <#> will have to be considered for removal of the line too.

Yes, it is really the same as alignment/width cookies. BTW, it should be
possible to merge them together. E.g., one could write  for
a right aligned 10 characters large column not meant to be exported.

This probably requires some slight changes in org-table.el.

> <#> will have to be fontified like <5> as org-formula (name and
> description of the face are not precise) wich is the easiest part of
> the change. Shouldn't < and > in a table be fontified too?

They should, as long as the first field is "/", unlike to
alignment/width cookies. I wouldn't bother too much though, since
fontification needs to be rewritten using the parser, once the latter
get a more robust cache, that is.

Regards,

Re: [O] org-passwords.el and encryption

[Eric S Fraga]

On Wednesday, 27 Apr 2016 at 09:57, Julien Cubizolles wrote:
> Eric S Fraga  writes:
>
>> I use gpg-agent in conjunction with keychain.  Generally works very
>> well.
>
> I'm trying to set it up but I'm running into problems. Could you precise
> a few details:
>
> + do you run keychain from your ~/.profile, and so how ? If I follow the
>   instructions at http://www.funtoo.org/Keychain, keychain can't start
>   in the login screen of the display manager (lightdm on Ubuntu in my
>   case)

I have keychain in both my .bash_profile (for when I log in in console
mode or remotely) and in my .xinitrc.  The latter is used by lightdm but
only when you have selected a non-standard desktop environment (not sure
which setting but not one of gnome, kde, etc.).  I use ratpoison...

> + do you use keychain to also manage ssh keys? If so does it use a
>   graphical tool to ask for your passphrase ?

Yes.  And yes: pinentry.  I should say that keychain works without fault
for ssh but see below for gpg.

> + how does emacs ask for the gpg passphrase: graphical (pinentry), 
> emacsclient or
>   in a minibuffer ?

Sometimes, emacs will ask and usually does so in the minibuffer.  I
cannot answer more precisely because although I am running Debian
testing on all of my systems, they all behave slightly differently when
it comes to ssh and gpg key management.  I obviously do not have exactly
the same packages installed on all of my systems...

My keychain line in my .xinitrc is:

eval $(keychain --eval --agents ssh,gpg id_rsa gpgkey )

I think the gpgkey needs to be the subkey but I am not sure.

My .bash_profile has essentially the same.

HTH,
eric

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.92.1, Org release_8.3.4-655-g9fb077

Re: [O] tables, comment in one line, export to html

[Michael Brand]

Hi Nicolas

I agree, together all the below makes sense. Some comments added.

Nicolas Goaziou  wrote:

> You are talking about section "3.5 The spreadsheet". I don't think this
> feature is directly related to spreadsheet capabilities.
>
> Actually, / in first column is described earlier in the manual, in "3.3
> Column groups". Besides, there is a similar feature described in "3.2
> Column width and alignment", about lines containing only alignment
> cookies:
>
>  Lines which only contain these formatting cookies will be removed
>   automatically when exporting the document.

<#> will have to be considered for removal of the line too.

> IMO, a better change would be to merge 3.2 and 3.3 as "Column
> operations" or some such, and add "<#>" as a way to ignore columns upon
> exporting. This way, everything related to columns is packed in the same
> subsection, and every column markup uses < or >. Moreover, there is no
> possible confusion with # markup from spreadsheet.
>
> WDYT?

> Another advantage about this is that there is no need for "/" in the
> first column, much like alignments cookies.

<#> will have to be fontified like <5> as org-formula (name and
description of the face are not precise) wich is the easiest part of
the change. Shouldn't < and > in a table be fontified too?

> It makes it simpler to ignore the first column.

Michael

[O] Beamer presantation, Abstract and Article in same document - how to structure and how to export?

[Rainer M Krug]

Hi

I would like to have one document containing

1) abstract for
2) a presentation and 
3) a resulting paper

My question is: how can I structure this an how can I handle the export?

Obviously under different top level headers:

--8<---cut here---start->8---
* Abstract
#+begin_abstract
Needs top be written
#+end_abstract

* Presentation
** Title
*** first slide
...
* Paper
** Abstract
How can I refer to the abstract above?
** ...
--8<---cut here---end--->8---

But what about the specific settings? Can I set them per subtree?

--8<---cut here---start->8---
#+LaTeX_CLASS: beamer
#+LaTeX_CLASS_OPTIONS: [bigger]
--8<---cut here---end--->8---

I could than export each subtree separate?

Can I define the name for the exported document per subtree?

How can I switch easily between different settings?

Any suggestions or examples?

Or should I use publishing (I am always reluctant, as it seems so complicated)?

Thanks,

Rainer

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

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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

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

email:  rai...@krugs.de

Skype:  RMkrug

PGP: 0x0F52F982


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Re: [O] New Beamer environment selection problem

[Nicolas Goaziou]

Hello,

Jarmo Hurri  writes:


> The newest versions of org (pulled from git) introduced a problem in my
> use of beamer. Consider the following org file
>
> #---
> #+STARTUP: beamer
> * foo
> ** bar
> #---
>
> Earlier, when I moved my cursor to the end of word "bar" and pressed
> "C-c C-b" for (org-beamer-select-environment), I was able to select a
> beamer environment. Now I get an error
>
> apply: Wrong number of arguments: max, 0
>
> Any ideas?

I cannot reproduce it. Could you send a detailed backtrace? Could you
also check you're not experiencing a mixed installation?

Regards,

-- 
Nicolas Goaziou

Re: [O] org-passwords.el and encryption

[Julien Cubizolles]

Eric S Fraga  writes:

> I use gpg-agent in conjunction with keychain.  Generally works very
> well.

I'm trying to set it up but I'm running into problems. Could you precise
a few details:

+ do you run keychain from your ~/.profile, and so how ? If I follow the
  instructions at http://www.funtoo.org/Keychain, keychain can't start
  in the login screen of the display manager (lightdm on Ubuntu in my
  case)

+ do you use keychain to also manage ssh keys? If so does it use a
  graphical tool to ask for your passphrase ?

+ how does emacs ask for the gpg passphrase: graphical (pinentry), emacsclient 
or
  in a minibuffer ?

Thanks for you help.

Julien.

[O] New Beamer environment selection problem

[Jarmo Hurri]

Greetings.

The newest versions of org (pulled from git) introduced a problem in my
use of beamer. Consider the following org file

#---
#+STARTUP: beamer
* foo
** bar
#---

Earlier, when I moved my cursor to the end of word "bar" and pressed
"C-c C-b" for (org-beamer-select-environment), I was able to select a
beamer environment. Now I get an error

apply: Wrong number of arguments: max, 0

Any ideas?

Jarmo

Re: [O] tables, comment in one line, export to html

[Nicolas Goaziou]

Completing myself,

> IMO, a better change would be to merge 3.2 and 3.3 as "Column
> operations" or some such, and add "<#>" as a way to ignore columns upon
> exporting. This way, everything related to columns is packed in the same
> subsection, and every column markup uses < or >. Moreover, there is no
> possible confusion with # markup from spreadsheet.

Another advantage about this is that there is no need for "/" in the
first column, much like alignments cookies. It makes it simpler to
ignore the first column.

Re: [O] tables, comment in one line, export to html

[Nicolas Goaziou]

Hello,

Michael Brand  writes:

> To have similar things look similar and make it clear in the manual I
> suggest to change the long existing
>
>   ~/~
>  Do not export this line.  Useful for lines that contain the
>  narrowing `' markers or column group markers.
>
>   Finally, just to whet your appetite [...]
>
> to
>
>   ~/~
>  Do not export this row or column.  In the first column ~/~ means
>  do not export this row which is useful for rows that contain the
>  narrowing ~~ markers, column group markers or markers to not
>  export a column.  In all other columns ~/~ means do not export
>  this column if also the first column is marked with ~/~.  When
>  the first column should not be exported move its content other
>  than markers into an other column.
>
>   When more than one marker is needed in a column put each in an own
>   row with ~/~ in the first column.
>
>   Finally, just to wet your appetite [...]

You are talking about section "3.5 The spreadsheet". I don't think this
feature is directly related to spreadsheet capabilities.

Actually, / in first column is described earlier in the manual, in "3.3
Column groups". Besides, there is a similar feature described in "3.2
Column width and alignment", about lines containing only alignment
cookies:

 Lines which only contain these formatting cookies will be removed
  automatically when exporting the document.

IMO, a better change would be to merge 3.2 and 3.3 as "Column
operations" or some such, and add "<#>" as a way to ignore columns upon
exporting. This way, everything related to columns is packed in the same
subsection, and every column markup uses < or >. Moreover, there is no
possible confusion with # markup from spreadsheet.

WDYT?

Regards,

-- 
Nicolas Goaziou