date:20150626

Hello,

Rustom Mody rustompm...@gmail.com writes:

 Bitbucket does not allow html entities in markdown
 See https://bitbucket.org/rustom/vit-projects/wiki/emacs
 and search for #

 So how to turn off html entities in md export?

It depends on where these entities are coming from. 

Anyway, vanilla Markdown supports HTML so anything ox-md cannot
translate into Markdown syntax (e.g., tables) is exported as pure HTML.

 And if thats not available any tips on how to hook say a sed-filter to
 ox-md export?

See filters in (info (org)Advanced configuration).


Regards,

-- 
Nicolas Goaziou

Re: [O] Turn off html entities in md export

2015-06-26 Thread Rustom Mody

On Fri, Jun 26, 2015 at 1:24 PM, Nicolas Goaziou m...@nicolasgoaziou.fr
wrote:

 Hello,

 Rustom Mody rustompm...@gmail.com writes:

  Bitbucket does not allow html entities in markdown
  See https://bitbucket.org/rustom/vit-projects/wiki/emacs
  and search for #
 
  So how to turn off html entities in md export?

 It depends on where these entities are coming from.


Simple basic thing
... becomes …
-- becomes –
etc



 Anyway, vanilla Markdown supports HTML so anything ox-md cannot
 translate into Markdown syntax (e.g., tables) is exported as pure HTML.


For systems (bitbucket is just a common example) that simply does not work
because of security or whatever reasons
See
https://bitbucket.org/site/master/issue/6930/support-some-or-all-html-in-markdown-bb
for BB users clamoring but BB not likely to listen


  And if thats not available any tips on how to hook say a sed-filter to
  ox-md export?

 See filters in (info (org)Advanced configuration).


Thanks
Will try to check that out

Re: [O] Turn off html entities in md export

Rustom Mody rustompm...@gmail.com writes:

 Simple basic thing
 ... becomes …
 -- becomes –
 etc

In this particular case, see `org-export-with-special-strings'.

 For systems (bitbucket is just a common example) that simply does not work
 because of security or whatever reasons
 See
 https://bitbucket.org/site/master/issue/6930/support-some-or-all-html-in-markdown-bb
 for BB users clamoring but BB not likely to listen

In the worst case, you might need to implement a derived export back-end
applying Bitbucket constraints.

Regards,

Re: [O] problem with ox-pandoc export

Hello,

Alan Schmitt alan.schm...@polytechnique.org writes:

 Is there any reason why the options would disappear during export?

Maybe ox-pandoc doesn't handle this meta-data. Perhaps you're doing
a body-only export. Or you have `org-export-with-title' and al. set to
nil...


Regards,

-- 
Nicolas Goaziou

Re: [O] Turn off html entities in md export

2015-06-26 Thread Rustom Mody

On Fri, Jun 26, 2015 at 1:24 PM, Nicolas Goaziou m...@nicolasgoaziou.fr
wrote:

 Hello,

 Rustom Mody rustompm...@gmail.com writes:

  Bitbucket does not allow html entities in markdown
  See https://bitbucket.org/rustom/vit-projects/wiki/emacs
  and search for #
 
  So how to turn off html entities in md export?

 It depends on where these entities are coming from.

 Anyway, vanilla Markdown supports HTML so anything ox-md cannot
 translate into Markdown syntax (e.g., tables) is exported as pure HTML.


As https://bitbucket.org/tutorials/markdowndemo/overview#markdown-header-tab
shows
bitbucket md tables are very similar to org tables (and html table is
disallowed)

How to say (to ox-md) Leave tables as they are  ?

Re: [O] can't assign to hline relative reference:

Hello,

Marijn Schouten (hkBst) hk...@gentoo.org writes:

 Through irc I found someone who tested this with the latest
 development version as of now and it instead produces the error: can't
 assign to hline relative reference. That also does not seem like the
 right behavior to me.

 Could someone shed some light on the situation?

See http://article.gmane.org/gmane.emacs.orgmode/77257.

Regards,

-- 
Nicolas Goaziou

[O] Time-zone in dates

2015-06-26 Thread Oleg Sivokon

Hello, list.

I was looking for a way to add time-zone to the date recrod, something
like: 2015-07-05 Sun 20:00 GMT+0.  I was told that it's very likely
that the functionality isn't there, so I wonder if it's really so, and
if indeed so, then what would it take to add it?

I've asked the same question here:
http://emacs.stackexchange.com/questions/13463/specify-timezone-in-org-date-format
just in case you saw it earlier.

Best.

Oleg

Re: [O] Time-zone in dates

2015-06-26 Thread J. David Boyd

Eric S Fraga e.fr...@ucl.ac.uk writes:

 On Friday, 26 Jun 2015 at 16:40, Oleg Sivokon wrote:
 Hello, list.

 I was looking for a way to add time-zone to the date recrod, something
 like: 2015-07-05 Sun 20:00 GMT+0.  I was told that it's very likely
 that the functionality isn't there, so I wonder if it's really so, and
 if indeed so, then what would it take to add it?

 It is indeed so.  What would it take?  Somebody to program the
 functionality in but this is a major challenge as time stamps are a
 fundamental building block of org and it would likely need to be upwards
 compatible...

I can see that being a real pain.  The simple way would 'just' be to convert
everything to UTC in the background for comparison.

Nothing I want to do!

Dave

[O] [PATCH] org-mobile: Tiny fix in creating index.org file

2015-06-26 Thread Sergey Gordienko

* lisp/org-mobile.el (org-mobile-create-index-file):
Eliminate cloning of `#+READONLY' property in the `index.org' file.
A sublists of `org-todo-keywords' don't need to contain the `|'.

TINYCHANGE
---
 lisp/org-mobile.el | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lisp/org-mobile.el b/lisp/org-mobile.el
index 2c13802..293de79 100644
--- a/lisp/org-mobile.el
+++ b/lisp/org-mobile.el
@@ -439,14 +439,14 @@ agenda view showing the flagged items.
(if org-mobile-use-encryption
org-mobile-encryption-tempfile
  target-file)
+  (insert #+READONLY\n)
   (while (setq entry (pop def-todo))
-   (insert #+READONLY\n)
(setq kwds (mapcar (lambda (x) (if (string-match ( x)
   (substring x 0 (match-beginning 0))
 x))
   (cdr entry)))
(insert #+TODO:  (mapconcat 'identity kwds  ) \n)
-   (setq dwds (member | kwds)
+   (setq dwds (or (member | kwds) (last kwds))
  twds (org-delete-all dwds kwds)
  todo-kwds (org-delete-all twds todo-kwds)
  done-kwds (org-delete-all dwds done-kwds)))
-- 
1.9.5 (Apple Git-50.3)

Re: [O] Turn off html entities in md export

Rustom Mody rustompm...@gmail.com writes:

 As https://bitbucket.org/tutorials/markdowndemo/overview#markdown-header-tab
 shows
 bitbucket md tables are very similar to org tables (and html table is
 disallowed)

 How to say (to ox-md) Leave tables as they are  ?

Write a derived export backend, e.g., ox-md-bb.el that will translate
tables properly according to Bitbucket rules.

You can also use a hook that will turn Org tables into Bitbucket
markdown tables and wrap them within a #+begin_md...#+end_md block.


Regards,

Re: [O] Turn off html entities in md export

2015-06-26 Thread Rasmus

Rustom Mody rustompm...@gmail.com writes:

 How to say (to ox-md) Leave tables as they are  ?

See org-element-interpret-data and e.g. org-org-identity.

Rasmus

-- 
And when I’m finished thinking, I have to die a lot

Re: [O] HTML/images zipped?

Rasmus ras...@gmx.us writes:

 Peter Davis p...@pfdstudio.com writes:

 Is there any way to export HTML with all references images,
 etc. packaged in a ZIP file?

 My guess is that at the moment your best bet is hacking some together with
 ox-publish.  See org-publish-project-alist.

Thanks, Rasmus. I'll take a look when I have a chance, but for now, I'll
have to zip the files by hand.

Thanks!
-pd

Re: [O] helm-bibtex questions

http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-bibliography-files-for-biblatex

I think you need this in your bibtex file:

-*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-

Xebar Saram writes:

thanks so much again John

i did add this line
(bibtex-set-dialect 'biblatex)
in my init but that dosent seem to do much as i still get the journal
mandatory field missing error. anything else i can try?

best

On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin johnrkitc...@gmail.com
wrote:

I believe that is an emacs bibtex issue. You need some kind of line in
your bibtex file to specify it is the biblatex dialect.

On June 25, 2015, at 6:58 AM, Xebar Saram zelt...@gmail.com wrote:

Great, works well. one question though (and this may very well be due to
my inexperience). the jabref export i had used 'journaltitle' instead of
journal to be (to my understanding) compatible with the newer .bib files
used by biblatex (and biber). when i ran org-ref clean it gave an error on
journal mandatory field missing. i had to replace all 'journaltitle' to
'journal' to get it to work.
is this by design? does org-ref not support the new biblatex/biber .bib
file format?

kind regards

Itai

On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin jkitc...@andrew.cmu.edu
wrote:

yes, there is a way ;)

First. Make sure you have a backup of the references. I like to keep
mine in a local git repo so you can undo any mistakes that get made.

I suggest you run these first:
%% (bibtex-validate-globally) ; checks for duplicate keys
%% (bibtex-validate)

I also recommend you run bibtex-sort (it is easier to spot duplicates in
a sorted list).

and (org-ref-build-full-bibliography) - makes a pdf of all references.

to make sure everything is compliant and functional.

Then, put this next line at the top of your bibtex file. The t argument to
org-ref-clean-bibtex-entry will preserve your existing keys.

% (bibtex-map-entries (lambda (key start end) (org-ref-clean-bibtex-entry
t)))

Put your cursor at the end of that line, and type C-x C-e to run the
function, and
wait patiently. It took a few minutes on my 1300 entries, and I had to
restart it once on some entry.

when it is done, run (org-ref-build-full-bibliography) again to make
sure it works and review the ~200 page pdf ;). fix errors and repeat
until it builds ;)

Note if you want to change title cases in all entries you can use

% (bibtex-map-entries 'jmax-title-case-article)
% (bibtex-map-entries 'jmax-sentence-case-article)

I hope that helps!

Xebar Saram writes:

John

First of all thanks so much for the excellent org-ref-clean-bibtex-entry
function i love it!
also your blog post on cleaning the bib file is a life saver

i have 800 references, is there a way to auto
make org-ref-clean-bibtex-entry go thorough my whole bib file instead
of me
going and cleaning it 1 by 1?

kind regards

On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg
malsb...@posteo.de
wrote:

Here is my CV in org-mode:

https://gist.github.com/tmalsburg/96084ba82281937c26b7

It’s a pretty straightforward org document except for one thing: the
key
to making this work was biblatex which can be used to create several
lists of references filtered according to keywords, author, etc. This
allowed me to have separate sections for journal articles, conference
presentations, etc. I store the relevant keywords in the tags field of
the BibTeX entries and since biblatex doesn’t know this field, I copy
the tags on-the-fly to the keywords field (see DeclareSourcemap in the
LaTeX headers).

Titus

On 2015-06-22 Mon 07:28, Xebar Saram wrote:
Hi John

a bit off topic, but do you also write your academic CV in orgmode or
lateX? in anycase would you mind sharing your org/latex CV template?
it
would be helpful as a starting point for me if thats possible.

kind regards and thanks so much in advance

On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin
jkitc...@andrew.cmu.edu
wrote:

sweet! I did not know you could do that! I will be refactoring
org-ref
soon to do that instead of redefining the commands!

John

---
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

On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg
malsb...@posteo.de wrote:

On 2015-06-19 Fri 03:56, Xebar Saram wrote:
Hi again Titus

2 quick questions that arose from using helm-bitex today
extensively:

how does one exclude in the search items? for example i want to
search
for
xebar without keyword progress (I want to exclude in progress
articles
not published yet)

is it possible to define default enter

Re: [O] Time-zone in dates

2015-06-26 Thread Eric S Fraga

On Friday, 26 Jun 2015 at 16:40, Oleg Sivokon wrote:
 Hello, list.

 I was looking for a way to add time-zone to the date recrod, something
 like: 2015-07-05 Sun 20:00 GMT+0.  I was told that it's very likely
 that the functionality isn't there, so I wonder if it's really so, and
 if indeed so, then what would it take to add it?

It is indeed so.  What would it take?  Somebody to program the
functionality in but this is a major challenge as time stamps are a
fundamental building block of org and it would likely need to be upwards
compatible...
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-1247-ga833d3

Re: [O] HTML/images zipped?

That is a cool idea. Here is some code for data uris that worked on with
org-mode earlier this summer. You could definitely hack a filter that
embedded the image uri directly into the exported html.

http://kitchingroup.cheme.cmu.edu/blog/2015/05/09/Another-approach-to-embedding-org-source-in-html/

Peter Davis writes:

 phillip.l...@newcastle.ac.uk (Phillip Lord) writes:

 data-uri's is probably what you want. There is no standard format for
 zipping multiple HTML files together, while including images (or video's
 or audio) directly into the HTML works reasonably well.

 I found a snippet to get ox-html to do this -- it would be a good
 feature to add properly though!

 Thanks, Phillip. That sounds like an interesting possibility. I've never
 worked with data-uri's. Can you post or send that snippet? I don't seem
 to be finding it on my initial searches.

 Thanks,
 -pd

--
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] Time-zone in dates

2015-06-26 Thread Left Right

On Fri, Jun 26, 2015 at 5:12 PM, Eric S Fraga e.fr...@ucl.ac.uk wrote:
 Somebody to program the
 functionality in but this is a major challenge as time stamps are a
 fundamental building block of org and it would likely need to be upwards
 compatible...
 --
 : Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-1247-ga833d3

Thanks for the info, Eric. I imagined this wouldn't be easy, but I
would be interested to know whether there might be some suggestions,
possibly to split the work up into stages. For example, perhaps, at
first one could only live with dates typed in in that format, but the
calendar wouldn't offer an interface to input them. Perhaps there
could be even more fine-grained stages. I'm also not entirely sure,
but I have a feeling that that might be a problem as well: does
interoperability with Calc require certain date format? Would Calc
have to also have to support this, once added?

Thanks.

Oleg

[O] old ob-clojure in orgmode.org/elpa/?

2015-06-26 Thread Julien Chastang

Hello

Is there a reason why ob-clojure.el is out-of-date in orgmode.org/elpa/? It
does not have any reference to cider, and is therefore more than a year
old, I believe. It is also out-of-sync with
orgmode.org/cgit.cgi/org-mode.git. Am I missing something concerning how
current orgmode.org/elpa/ should be?

Many Thanks.

-- 
Julien Chastang
Scientific Software Developer
Unidata-UCAR

Re: [O] Time-zone in dates

2015-06-26 Thread Eric S Fraga

On Friday, 26 Jun 2015 at 10:38, J. David Boyd wrote:

[...]

 I can see that being a real pain.  The simple way would 'just' be to convert
 everything to UTC in the background for comparison.

Having spent a year essentially commuting between Australia and the UK a
couple of years ago, I can tell you that there is no simple
solution... :(

The simplest solution for me was firstly to use org (of course :-), then
put in all time stamps as local time and finally ensure that the time
zone setting for the computer itself, e.g. a laptop, matched where I was
at the time.  This turns out to be more human oriented than having to
worry about time zones, especially when it comes to extra complications
like summer time.

In practice, I do not miss having time zone information in org.

YMMV, of course!

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-1247-ga833d3

Re: [O] HTML/images zipped?


Thanks, John. I will take a closer look at both of these.

Cheers,
-pd

On 6/26/15 10:24 AM, John Kitchin wrote:

I did something like this for org-files:
https://github.com/jkitchin/jmax/blob/master/ox-archive.el

You might use that as a starting point for html.

Also, my blogofile code
(https://github.com/jkitchin/jmax/blob/master/user/blogofile.el) does
something like this to publish org to blogofile.



Rasmus writes:


Peter Davis p...@pfdstudio.com writes:


Is there any way to export HTML with all references images,
etc. packaged in a ZIP file?

My guess is that at the moment your best bet is hacking some together with
ox-publish.  See org-publish-project-alist.

Hope it helps,
Rasmus

PS: On the list, we have talked about a .borg format that might serve for
similar situation but it's at an idea stage at the moment.

--
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] HTML/images zipped?

phillip.l...@newcastle.ac.uk (Phillip Lord) writes:

 data-uri's is probably what you want. There is no standard format for
 zipping multiple HTML files together, while including images (or video's
 or audio) directly into the HTML works reasonably well.

 I found a snippet to get ox-html to do this -- it would be a good
 feature to add properly though!

Thanks, Phillip. That sounds like an interesting possibility. I've never
worked with data-uri's. Can you post or send that snippet? I don't seem
to be finding it on my initial searches.

Thanks,
-pd

Re: [O] HTML/images zipped?

I did something like this for org-files:
https://github.com/jkitchin/jmax/blob/master/ox-archive.el

You might use that as a starting point for html.

Also, my blogofile code
(https://github.com/jkitchin/jmax/blob/master/user/blogofile.el) does
something like this to publish org to blogofile.



Rasmus writes:

 Peter Davis p...@pfdstudio.com writes:

 Is there any way to export HTML with all references images,
 etc. packaged in a ZIP file?

 My guess is that at the moment your best bet is hacking some together with
 ox-publish.  See org-publish-project-alist.

 Hope it helps,
 Rasmus

 PS: On the list, we have talked about a .borg format that might serve for
 similar situation but it's at an idea stage at the moment.

--
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] HTML/images zipped?

I am not sure. I have this in my init file:

(require 'ox-org)

maybe that is required for you too?

Peter Davis writes:

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

 I did something like this for org-files:
 https://github.com/jkitchin/jmax/blob/master/ox-archive.el

 You might use that as a starting point for html.

 I'm not lisp-savvy, but I've been experimenting with this. I get an
 error:

 Unknown nil backend: Aborting export

 It seems to be coming from these lines:

   (let ((org-export-filter-link-functions '(ox-mrkup-filter-link)))
   (org-org-export-as-org)))

 I'm not sure how or where backend is supposed to be defined.

 Also, I guess it would take some tweaking to export to HTML and save
 that in the ZIP, instead of the original org file.

 Any hints welcome.

 Thanks!
 -pd

--
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] HTML/images zipped?

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

 I did something like this for org-files:
 https://github.com/jkitchin/jmax/blob/master/ox-archive.el

 You might use that as a starting point for html.

I'm not lisp-savvy, but I've been experimenting with this. I get an
error:

Unknown nil backend: Aborting export

It seems to be coming from these lines:

  (let ((org-export-filter-link-functions '(ox-mrkup-filter-link)))
(org-org-export-as-org)))

I'm not sure how or where backend is supposed to be defined.

Also, I guess it would take some tweaking to export to HTML and save
that in the ZIP, instead of the original org file.

Any hints welcome.

Thanks!
-pd

Re: [O] helm-bibtex questions

In org-ref, I have a function that will copy a bibtex entry to the
clipboard in the helm menu for the cite link actions:

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3363

And here a menu item to insert a bibtex entry and attach its pdf to an
email:

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3382

exactly for those purposes!

 5. i love the insert formatted reference (f5) option and use it often
 sending people references:
 a. does it also auto send that to the clipboard?

 There is currently no way to copy references directly to the
 clipboard.  My recommendation is to use one of Emacs’ mail clients, then
 you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
 when combined with helm-mu).

 b. it cuts most of the authors name and leaves only the first few. is there
 a switch to get it to print all authors. is that a latex cite formatting
 issue?

 Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
 anything in my setup.  Could you please provide an example?  (Perhaps
 this is something for the issue tracker on Github.)

 Best wishes,

   Titus



 best and thanks so much again

 Z

 On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg malsb...@posteo.de
 wrote:



 Here is my CV in org-mode:

   https://gist.github.com/tmalsburg/96084ba82281937c26b7

 It’s a pretty straightforward org document except for one thing: the key
 to making this work was biblatex which can be used to create several
 lists of references filtered according to keywords, author, etc.  This
 allowed me to have separate sections for journal articles, conference
 presentations, etc.  I store the relevant keywords in the tags field of
 the BibTeX entries and since biblatex doesn’t know this field, I copy
 the tags on-the-fly to the keywords field (see DeclareSourcemap in the
 LaTeX headers).

   Titus

 On 2015-06-22 Mon 07:28, Xebar Saram wrote:
  Hi John
 
  a bit off topic, but do you also write your academic CV in orgmode or
  lateX? in anycase would you mind sharing your org/latex CV template? it
  would be helpful as a starting point for me if thats possible.
 
  kind regards and thanks so much in advance
 
  Z
 
  On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin jkitc...@andrew.cmu.edu
  wrote:
 
  sweet! I did not know you could do that! I will be refactoring org-ref
  soon to do that instead of redefining the commands!
 
  John
 
  ---
  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
 
 
  On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg 
  malsb...@posteo.de wrote:
 
 
  On 2015-06-19 Fri 03:56, Xebar Saram wrote:
   Hi again Titus
  
   2 quick questions that arose from using helm-bitex today extensively:
  
   how does one exclude in the search items? for example i want to
 search
  for
   xebar without keyword progress (I want to exclude in progress
 articles
   not published yet)
  
   is it possible to define default enter command in helm-bibtex ?
 
  Yes.  Helm uses the first action as the default action.  To move an
  action to the top of the list you can use the following code:
 
(helm-delete-action-from-source Insert BibTeX key
 helm-source-bibtex)
(helm-add-action-to-source Insert BibTeX key
 'helm-bibtex-insert-key
  helm-source-bibtex 0)
 
  The second argument in the second line is the function that executes
 the
  action.  Here is a list of all actions and their functions:
 
Open PDF file (if present): helm-bibtex-open-pdf
Open URL or DOI in browser: helm-bibtex-open-url-or-doi
Insert citation: helm-bibtex-insert-citation
Insert reference: helm-bibtex-insert-reference
Insert BibTeX key: helm-bibtex-insert-key
Insert BibTeX entry: helm-bibtex-insert-bibtex
Attach PDF to email: helm-bibtex-add-PDF-attachment
Edit notes: helm-bibtex-edit-notes
Show entry: helm-bibtex-show-entry
 
  Best,
 
Titus
 
  
   best
  
   Z
  
   On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg 
  malsb...@posteo.de
   wrote:
  
  
   On 2015-06-18 Thu 04:32, Xebar Saram wrote:
Hi Titus and thx so much for the answers!
   
i will in the future use the github page to make requests.
   
The number of matches will be displayed in the mode line. 
   
i see that now thx! :) the problem was(is) that its colored black
 on
  my
black modline BG which makes it invisible ;-) i assume thats an
 helm
   config
i need to change
   
   
If you don’t want to type these search expressions, you could
  create a
command that invokes helm-bibtex with a default search expression
 and
   that
command could be bound to a keyboard shortcut.
   
that would be prefect for me and a solution to my issue. would you
  mind
giving an example of such a code chunk. unfortunately i dont know
  elisp
   though
as

Re: [O] helm-bibtex questions

2015-06-26 Thread Titus von der Malsburg


On 2015-06-26 Fri 00:21, Xebar Saram wrote:
 Hi Titus

 Another round of helm-bibtex questions if you dont mind (question come
 since i use it 50 times a day now ;-))

No problem.  I’ve also learned a couple of things though this exchange.

 1. is there a way (or a keybind) to select all entries filtered? now to
 select all my publications for example i have to use C-space
 repeatedly.

Key bindings are inherited from Helm so it’s useful to consult Helm’s
documentation for question of that type.  I just checked and found that
M-a selects all candidates.

 2. what is the syntax for greater then? for example all articles  2012
 (year)

I’m afraid that’s not possible because 2012 is just another string for
the purposes of matching.  But you may want to check Helm’s
documentation and mailing lists.  Helm is full of surprises.

 4. i cant get helm-bibtex to search the biblatex field of pubstate. are
 biblatex (biber) supported/ i have this in my config?

 (setq helm-bibtex-additional-search-fields '(pubstate))

This works on my setup.  Helm-bibtex doesn’t really care whether
something is a BibTeX or a Biblatex field.  You should be able to use
any kind of field whether standard or not.  Note that additional search
fields are not displayed in the results list (they are only used for
matching).  Perhaps that’s why you thought it doesn’t work?

 also on a related issue i assume one can define many fields in the above
 example. since my elisp sucks would the syntax be this

 (setq helm-bibtex-additional-search-fields '(pubstate tags))

This is correct.

 or do you need to qoute them or use a , symbol?

 5. i love the insert formatted reference (f5) option and use it often
 sending people references:
 a. does it also auto send that to the clipboard?

There is currently no way to copy references directly to the
clipboard.  My recommendation is to use one of Emacs’ mail clients, then
you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
when combined with helm-mu).

 b. it cuts most of the authors name and leaves only the first few. is there
 a switch to get it to print all authors. is that a latex cite formatting
 issue?

Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
anything in my setup.  Could you please provide an example?  (Perhaps
this is something for the issue tracker on Github.)

Best wishes,

  Titus



 best and thanks so much again

 Z

 On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg malsb...@posteo.de
 wrote:



 Here is my CV in org-mode:

   https://gist.github.com/tmalsburg/96084ba82281937c26b7

 It’s a pretty straightforward org document except for one thing: the key
 to making this work was biblatex which can be used to create several
 lists of references filtered according to keywords, author, etc.  This
 allowed me to have separate sections for journal articles, conference
 presentations, etc.  I store the relevant keywords in the tags field of
 the BibTeX entries and since biblatex doesn’t know this field, I copy
 the tags on-the-fly to the keywords field (see DeclareSourcemap in the
 LaTeX headers).

   Titus

 On 2015-06-22 Mon 07:28, Xebar Saram wrote:
  Hi John
 
  a bit off topic, but do you also write your academic CV in orgmode or
  lateX? in anycase would you mind sharing your org/latex CV template? it
  would be helpful as a starting point for me if thats possible.
 
  kind regards and thanks so much in advance
 
  Z
 
  On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin jkitc...@andrew.cmu.edu
  wrote:
 
  sweet! I did not know you could do that! I will be refactoring org-ref
  soon to do that instead of redefining the commands!
 
  John
 
  ---
  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
 
 
  On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg 
  malsb...@posteo.de wrote:
 
 
  On 2015-06-19 Fri 03:56, Xebar Saram wrote:
   Hi again Titus
  
   2 quick questions that arose from using helm-bitex today extensively:
  
   how does one exclude in the search items? for example i want to
 search
  for
   xebar without keyword progress (I want to exclude in progress
 articles
   not published yet)
  
   is it possible to define default enter command in helm-bibtex ?
 
  Yes.  Helm uses the first action as the default action.  To move an
  action to the top of the list you can use the following code:
 
(helm-delete-action-from-source Insert BibTeX key
 helm-source-bibtex)
(helm-add-action-to-source Insert BibTeX key
 'helm-bibtex-insert-key
  helm-source-bibtex 0)
 
  The second argument in the second line is the function that executes
 the
  action.  Here is a list of all actions and their functions:
 
Open PDF file (if present): helm-bibtex-open-pdf
Open URL or DOI in browser: helm-bibtex-open-url-or-doi
Insert citation:

Re: [O] helm-bibtex questions

2015-06-26 Thread Titus von der Malsburg


On 2015-06-26 Fri 10:21, Titus von der Malsburg wrote:
 On 2015-06-26 Fri 00:21, Xebar Saram wrote:
 Hi Titus

 Another round of helm-bibtex questions if you dont mind (question come
 since i use it 50 times a day now ;-))

 No problem.  I’ve also learned a couple of things though this exchange.

 1. is there a way (or a keybind) to select all entries filtered? now to
 select all my publications for example i have to use C-space
 repeatedly.

 Key bindings are inherited from Helm so it’s useful to consult Helm’s
 documentation for question of that type.  I just checked and found that
 M-a selects all candidates.

 2. what is the syntax for greater then? for example all articles  2012
 (year)

 I’m afraid that’s not possible because 2012 is just another string for
 the purposes of matching.  But you may want to check Helm’s
 documentation and mailing lists.  Helm is full of surprises.

Of course you can use regular expressions to search for a range of
years:

  201[2-5]

Almost as good as 2012.


 4. i cant get helm-bibtex to search the biblatex field of pubstate. are
 biblatex (biber) supported/ i have this in my config?

 (setq helm-bibtex-additional-search-fields '(pubstate))

 This works on my setup.  Helm-bibtex doesn’t really care whether
 something is a BibTeX or a Biblatex field.  You should be able to use
 any kind of field whether standard or not.  Note that additional search
 fields are not displayed in the results list (they are only used for
 matching).  Perhaps that’s why you thought it doesn’t work?

 also on a related issue i assume one can define many fields in the above
 example. since my elisp sucks would the syntax be this

 (setq helm-bibtex-additional-search-fields '(pubstate tags))

 This is correct.

 or do you need to qoute them or use a , symbol?

 5. i love the insert formatted reference (f5) option and use it often
 sending people references:
 a. does it also auto send that to the clipboard?

 There is currently no way to copy references directly to the
 clipboard.  My recommendation is to use one of Emacs’ mail clients, then
 you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
 when combined with helm-mu).

 b. it cuts most of the authors name and leaves only the first few. is there
 a switch to get it to print all authors. is that a latex cite formatting
 issue?

 Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
 anything in my setup.  Could you please provide an example?  (Perhaps
 this is something for the issue tracker on Github.)

 Best wishes,

   Titus



 best and thanks so much again

 Z

 On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg malsb...@posteo.de
 wrote:



 Here is my CV in org-mode:

   https://gist.github.com/tmalsburg/96084ba82281937c26b7

 It’s a pretty straightforward org document except for one thing: the key
 to making this work was biblatex which can be used to create several
 lists of references filtered according to keywords, author, etc.  This
 allowed me to have separate sections for journal articles, conference
 presentations, etc.  I store the relevant keywords in the tags field of
 the BibTeX entries and since biblatex doesn’t know this field, I copy
 the tags on-the-fly to the keywords field (see DeclareSourcemap in the
 LaTeX headers).

   Titus

 On 2015-06-22 Mon 07:28, Xebar Saram wrote:
  Hi John
 
  a bit off topic, but do you also write your academic CV in orgmode or
  lateX? in anycase would you mind sharing your org/latex CV template? it
  would be helpful as a starting point for me if thats possible.
 
  kind regards and thanks so much in advance
 
  Z
 
  On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin jkitc...@andrew.cmu.edu
  wrote:
 
  sweet! I did not know you could do that! I will be refactoring org-ref
  soon to do that instead of redefining the commands!
 
  John
 
  ---
  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
 
 
  On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg 
  malsb...@posteo.de wrote:
 
 
  On 2015-06-19 Fri 03:56, Xebar Saram wrote:
   Hi again Titus
  
   2 quick questions that arose from using helm-bitex today extensively:
  
   how does one exclude in the search items? for example i want to
 search
  for
   xebar without keyword progress (I want to exclude in progress
 articles
   not published yet)
  
   is it possible to define default enter command in helm-bibtex ?
 
  Yes.  Helm uses the first action as the default action.  To move an
  action to the top of the list you can use the following code:
 
(helm-delete-action-from-source Insert BibTeX key
 helm-source-bibtex)
(helm-add-action-to-source Insert BibTeX key
 'helm-bibtex-insert-key
  helm-source-bibtex 0)
 
  The second argument in the second line is the function that executes
 the
  action.  Here is a

Re: [O] more helm-bibtex/org-ref questions

You could have multiple file fields I suppose, and adapt [1] to give you
a choice of which one to open.

Personally, I have one pdf per bibtex entry, named by the key of the
entry, in a directory called bibtex-pdfs somewhere defined by
org-ref-pdf-directory. There are ~1300 pdfs in there now. I always
access them through helm bibtex.

admittedly, I don't have the SI or other stuff around usually. I don't
use bibtex to keep track of the directories where I write manuscripts
either.

You could always make links to these other things in the associated
notes entry. or put org-links in a bibtex field, and then you can open
them with C-c o (if you setup links to work everywhere). That way,
opening the pdf is easy, and opening the other things is just opening
the entry and running the link open command.

Ramon Diaz-Uriarte writes:

 Dear All,

 (I am not sure this is the appropriate place, but this is neither a bug
 report nor an feature request about helm-bibtex or org-ref, but a question
 from ignorance and I am learning quite a bit from the other helm-bibtex
 questions).


 How do people deal with multiple files that are logically associated to an
 entry?


 I've been used to keeping the main file, supplementary materials,
 associated code, etc, in a directory per entry. This kind of modus operandi
 is something I adopted (fell into?)  easily with Zotero and Mendeley. But I
 am not sure that this is the best way to proceed.


 If I end up with multiple files per directory, helm-bibtex-find-pdf[1]
 cannot know which one I want to open. I could keep the main file in the
 general directory, so it is found directly by helm-bibtex-find-pdf and
 specify other files (of secondary usage) in the file field (and maybe
 open them via ebib when/if needed)?  But this does not seem
 elegant. Another is to have an entry per file, with unique key, but this
 does not seem right.



 Thanks,

 R.


 [1] Thanks to Titus' help
 (https://github.com/tmalsburg/helm-bibtex/issues/53), opening a PDF that is
 given in the file field with the directory name is now within my reach.

--
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] Time-zone in dates

Hello,

Eric S Fraga e.fr...@ucl.ac.uk writes:

 In practice, I do not miss having time zone information in org.

Time zone information is interesting when users of different areas are
exchanging Org documents.

I think it would be useful to have:

 - a keyword to specify time zone per document. This time zone would
   apply to every time stamp not defining their own time zone. Default
   value could be `local' so we would be backward compatible.

 - a way to specify a time zone per time stamp, overriding the previous
   keyword.

I think it would require to define a proper API for timestamps in order
to ensure, e.g., comparisons are done right.


Regards,

-- 
Nicolas Goaziou

Re: [O] HTML/images zipped?


Thanks, John. That didn't solve it for me. I'll keep digging when I get
a chance.

Thank you.

-pd


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

 I am not sure. I have this in my init file:

 (require 'ox-org)

 maybe that is required for you too?

 Peter Davis writes:

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

 I did something like this for org-files:
 https://github.com/jkitchin/jmax/blob/master/ox-archive.el

 You might use that as a starting point for html.

 I'm not lisp-savvy, but I've been experimenting with this. I get an
 error:

 Unknown nil backend: Aborting export

 It seems to be coming from these lines:

   (let ((org-export-filter-link-functions '(ox-mrkup-filter-link)))
   (org-org-export-as-org)))

 I'm not sure how or where backend is supposed to be defined.

 Also, I guess it would take some tweaking to export to HTML and save
 that in the ZIP, instead of the original org file.

 Any hints welcome.

 Thanks!
 -pd

 --
 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] Time-zone in dates

2015-06-26 Thread francois

Hello,

On Fri, Jun 26, 2015 at 09:20:00PM +0200, Nicolas Goaziou wrote:
 Time zone information is interesting when users of different areas are
 exchanging Org documents.
 
 I think it would be useful to have:
 
  - a keyword to specify time zone per document. This time zone would
apply to every time stamp not defining their own time zone. Default
value could be `local' so we would be backward compatible.
 
  - a way to specify a time zone per time stamp, overriding the previous
keyword.
 
 I think it would require to define a proper API for timestamps in order
 to ensure, e.g., comparisons are done right.

Timezones are strange beasts to deal with.

It is really simpler programmatically to deal with time offsets
instead. The downside is that you cannot manage DST and other similar
peculiarities but the API is much simpler to write.

Just please don't confuse timezones and time offsets especially in
documentation as it is not the same thing and it can lead to
confusion.

I reread from time to time this note from W3C which explains the
difference and why it matters :
http://www.w3.org/TR/2005/NOTE-timezone-20051013/#d2e226 

Regards,
François

[O] more helm-bibtex/org-ref questions

2015-06-26 Thread Ramon Diaz-Uriarte

Dear All,

(I am not sure this is the appropriate place, but this is neither a bug
report nor an feature request about helm-bibtex or org-ref, but a question
from ignorance and I am learning quite a bit from the other helm-bibtex
questions).


How do people deal with multiple files that are logically associated to an
entry?


I've been used to keeping the main file, supplementary materials,
associated code, etc, in a directory per entry. This kind of modus operandi
is something I adopted (fell into?)  easily with Zotero and Mendeley. But I
am not sure that this is the best way to proceed.


If I end up with multiple files per directory, helm-bibtex-find-pdf[1]
cannot know which one I want to open. I could keep the main file in the
general directory, so it is found directly by helm-bibtex-find-pdf and
specify other files (of secondary usage) in the file field (and maybe
open them via ebib when/if needed)?  But this does not seem
elegant. Another is to have an entry per file, with unique key, but this
does not seem right.



Thanks,

R.

 
[1] Thanks to Titus' help
(https://github.com/tmalsburg/helm-bibtex/issues/53), opening a PDF that is
given in the file field with the directory name is now within my reach.

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

Re: [O] Time-zone in dates

Hello,

franc...@avalenn.eu writes:

 Timezones are strange beasts to deal with.

True.

 It is really simpler programmatically to deal with time offsets
 instead. The downside is that you cannot manage DST and other similar
 peculiarities but the API is much simpler to write.

However, time offsets are not very interesting. Org is (also) about
appointments, deadlines... so timezones are more accurate.

Also, Emacs contains timezone.el, which, I assume, should take care of
all the heavy duty concerning these beasts, as far as an API is
concerned.

This requires care, but it should be doable, really, don't you think?

 Just please don't confuse timezones and time offsets especially in
 documentation as it is not the same thing and it can lead to
 confusion.

 I reread from time to time this note from W3C which explains the
 difference and why it matters :
 http://www.w3.org/TR/2005/NOTE-timezone-20051013/#d2e226

Thank you for the reference. I didn't know about it.


Regards,

-- 
Nicolas Goaziou

Re: [O] HTML/images zipped?

2015-06-26 Thread Nick Dokos

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

 I did something like this for org-files:
 https://github.com/jkitchin/jmax/blob/master/ox-archive.el


I tried this on some arbitrary org file (not containing any references) and I 
got an error:

Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  file-name-directory(nil)
  (let* ((temporary-file-directory (file-name-directory (buffer-file-name))) 
(tempname (make-temp-file extract-bib)) (contents (buffer-string)) (cb 
(current-buffer)) basename texfile bibfile results) (find-file tempname) 
(insert contents) (setq basename (file-name-sans-extension 
(file-name-nondirectory buffer-file-name)) texfile (concat tempname .tex) 
bibfile (concat tempname .bib)) (save-excursion (goto-char (point-min)) (if 
(re-search-forward ^bibliography: (point-max) (quote end)) nil (insert 
(format \nbibliography:%s (mapconcat (quote identity) 
reftex-default-bibliography ,) (save-buffer) (org-latex-export-to-latex) 
(find-file texfile) (reftex-parse-all) (reftex-create-bibtex-file bibfile) 
(save-buffer) (setq results (buffer-string)) (kill-buffer (concat basename 
.bib)) (kill-buffer (concat basename .tex)) (kill-buffer basename) 
(delete-file bibfile) (delete-file texfile) (delete-file tempname) 
(switch-to-buffer cb) (if (not (string=  results)) (progn (save-excursion 
(goto-char (point-max)) (insert \n\n) (org-insert-heading) (insert (format  
Bibtex entries\n\n#+BEGIN_SRC text :tangle %s\n%s\n#+END_SRC (concat 
(file-name-sans-extension ...) .bib) results))
  org-ref-extract-bibtex-entries()
  (let* ((org-file (buffer-name)) (org-file-abs-path (buffer-file-name)) 
(base-name (file-name-sans-extension org-file)) (org-archive (if (string= 
zip-base-name ) (concat base-name - (format-time-string %Y-%m-%d 
(current-time))) zip-base-name)) (org-archive-zip (concat org-archive .zip)) 
link-list) (if (file-exists-p org-archive-zip) (progn (delete-file 
org-archive-zip))) (if (file-exists-p org-archive) (progn (delete-directory 
org-archive t))) (make-directory org-archive t) (setq link-list (let 
((parsetree (org-element-parse-buffer)) (counter 0)) (org-element-map parsetree 
(quote link) (function (lambda (link) (let* (... ... ... ... ... ... ... ...) 
(message ...) (cond ... ... ...))) (message (format \n\nlink-list: %s\n\n 
link-list)) (let ((counter 0)) (defalias (quote ox-mrkup-filter-link) (function 
(lambda (text back-end info) (message handing link %s: %s\n counter text) 
(let ((link ...)) (message   %s replacement is %s\n counter link) (if (not 
...) (progn ... ...) (setq output ...)) (setq counter (+ counter 1)) output 
(let ((org-export-filter-link-functions (quote (ox-mrkup-filter-link 
(org-org-export-as-org))) (switch-to-buffer *Org ORG Export*) (insert (format 
# archived from %s on %s\n org-file-abs-path (format-time-string %Y-%m-%d 
(current-time (org-ref-extract-bibtex-entries) (write-file 
(expand-file-name org-file org-archive)) (shell-command (concat zip -v -r  
org-archive-zip  *)) (rename-file org-archive-zip (concat ../ org-archive 
.zip)) (switch-to-buffer org-file) (delete-directory org-archive t) 
org-archive-zip)
  ox-archive-create-zip(foo)
...

I think there is a bug in ox-archive-create-zip:

--8---cut here---start-8---
...
(switch-to-buffer *Org ORG Export*)
(insert (format # archived from %s on %s\n
org-file-abs-path
(format-time-string %Y-%m-%d (current-time

;; add bibliography references if they exist. 
(org-ref-extract-bibtex-entries)
...
--8---cut here---end---8---

because the first thing that org-ref-extract-bibtex-entries does is

--8---cut here---start-8---
  (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
--8---cut here---end---8---

and (buffer-file-name) returns nil on the *Org ORG Export* buffer.
But since you obviously use this code successfully, I wonder why
you don't hit this.

Thanks for any help,
Nick

Re: [O] HTML/images zipped?

hm... maybe it has been a while since I ran that ;) I pushed some
changes that seem to have it working on a small test file.

This code is somewhat on the border of a filter/custom export. There are
probably links that will now work with it, I have not tested it super
thoroughly.

Notably, it does not preserve relative paths, but rather renames files
and images and replaces the links in the org-file with the new
names. It was too hard to figure out how to preserve the paths when I
wrote this originally.

Nick Dokos writes:

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

 I did something like this for org-files:
 https://github.com/jkitchin/jmax/blob/master/ox-archive.el


 I tried this on some arbitrary org file (not containing any references) and I 
 got an error:

 Debugger entered--Lisp error: (wrong-type-argument stringp nil)
   file-name-directory(nil)
   (let* ((temporary-file-directory (file-name-directory (buffer-file-name))) 
 (tempname (make-temp-file extract-bib)) (contents (buffer-string)) (cb 
 (current-buffer)) basename texfile bibfile results) (find-file tempname) 
 (insert contents) (setq basename (file-name-sans-extension 
 (file-name-nondirectory buffer-file-name)) texfile (concat tempname .tex) 
 bibfile (concat tempname .bib)) (save-excursion (goto-char (point-min)) (if 
 (re-search-forward ^bibliography: (point-max) (quote end)) nil (insert 
 (format \nbibliography:%s (mapconcat (quote identity) 
 reftex-default-bibliography ,) (save-buffer) 
 (org-latex-export-to-latex) (find-file texfile) (reftex-parse-all) 
 (reftex-create-bibtex-file bibfile) (save-buffer) (setq results 
 (buffer-string)) (kill-buffer (concat basename .bib)) (kill-buffer (concat 
 basename .tex)) (kill-buffer basename) (delete-file bibfile) (delete-file 
 texfile) (delete-file tempname) (switch-to-buffer cb) (if (not (string=  
 results)) (progn (save-excursion (goto-char (point-max)) (insert \n\n) 
 (org-insert-heading) (insert (format  Bibtex entries\n\n#+BEGIN_SRC text 
 :tangle %s\n%s\n#+END_SRC (concat (file-name-sans-extension ...) .bib) 
 results))
   org-ref-extract-bibtex-entries()
   (let* ((org-file (buffer-name)) (org-file-abs-path (buffer-file-name)) 
 (base-name (file-name-sans-extension org-file)) (org-archive (if (string= 
 zip-base-name ) (concat base-name - (format-time-string %Y-%m-%d 
 (current-time))) zip-base-name)) (org-archive-zip (concat org-archive 
 .zip)) link-list) (if (file-exists-p org-archive-zip) (progn (delete-file 
 org-archive-zip))) (if (file-exists-p org-archive) (progn (delete-directory 
 org-archive t))) (make-directory org-archive t) (setq link-list (let 
 ((parsetree (org-element-parse-buffer)) (counter 0)) (org-element-map 
 parsetree (quote link) (function (lambda (link) (let* (... ... ... ... ... 
 ... ... ...) (message ...) (cond ... ... ...))) (message (format 
 \n\nlink-list: %s\n\n link-list)) (let ((counter 0)) (defalias (quote 
 ox-mrkup-filter-link) (function (lambda (text back-end info) (message 
 handing link %s: %s\n counter text) (let ((link ...)) (message   %s 
 replacement is %s\n counter link) (if (not ...) (progn ... ...) (setq output 
 ...)) (setq counter (+ counter 1)) output (let 
 ((org-export-filter-link-functions (quote (ox-mrkup-filter-link 
 (org-org-export-as-org))) (switch-to-buffer *Org ORG Export*) (insert 
 (format # archived from %s on %s\n org-file-abs-path (format-time-string 
 %Y-%m-%d (current-time (org-ref-extract-bibtex-entries) (write-file 
 (expand-file-name org-file org-archive)) (shell-command (concat zip -v -r  
 org-archive-zip  *)) (rename-file org-archive-zip (concat ../ org-archive 
 .zip)) (switch-to-buffer org-file) (delete-directory org-archive t) 
 org-archive-zip)
   ox-archive-create-zip(foo)
 ...

 I think there is a bug in ox-archive-create-zip:

 --8---cut here---start-8---
 ...
 (switch-to-buffer *Org ORG Export*)
 (insert (format # archived from %s on %s\n
   org-file-abs-path
   (format-time-string %Y-%m-%d (current-time

 ;; add bibliography references if they exist.
 (org-ref-extract-bibtex-entries)
 ...
 --8---cut here---end---8---

 because the first thing that org-ref-extract-bibtex-entries does is

 --8---cut here---start-8---
   (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
 --8---cut here---end---8---

 and (buffer-file-name) returns nil on the *Org ORG Export* buffer.
 But since you obviously use this code successfully, I wonder why
 you don't hit this.

 Thanks for any help,
 Nick

--
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] [PATCH] org-add-planning-info: Improve deletion handling

2015-06-26 Thread Kyle Meyer

Hello,

I've attached a patch that fixes up a few issues I've noticed with
org-add-planning-info.  The main one (in terms what I actually see when
editing Org files) is that, when org-adapt-indentation is nil, closing a
repeating TODO heading adds an extra space before the planning info
entry when it cycles back to TODO.  For example, marking

* TODO h
SCHEDULED: 2015-06-26 Fri +1w

as DONE inserts an extra space before SCHEDULED:

* TODO h
 SCHEDULED: 2015-07-03 Fri +1w
:PROPERTIES:
:LAST_REPEAT: [2015-06-26 Fri 23:38]
:END:
:LOGBOOK:
- State DONE   from TODO   [2015-06-26 Fri 23:38]
:END:

From 6315be9e7a83cd9837807c2eb87ed7b3c6b70997 Mon Sep 17 00:00:00 2001
From: Kyle Meyer k...@kyleam.com
Date: Fri, 26 Jun 2015 21:33:34 -0400
Subject: [PATCH] org-add-planning-info: Improve deletion handling

* lisp/org.el (org-add-planning-info): Reset point before each
  planning entry search.  Clean up extra spaces.

* testing/lisp/test-org.el (test-org/add-planning-info): Add tests.

- Reposition save-excursion call to reset point every dolist
  iteration.  Otherwise, the order of the entries to be removed
  matters, and a call like

  (org-add-planning-info nil nil 'scheduled 'deadline)

  on

  DEADLINE: 2015-06-26 Fri SCHEDULED: 2015-06-26 Fri

  will fail to remove the deadline entry.

- Delete leading white space even when at the beginning of the line so
  that, when org-adapt-indentation is nil, a space is not inserted
  when removing the leading planning info entry.

  This prevents headings with repeating entries like

  SCHEDULED: 2015-06-26 Fri +1w

  from being closed and recycled with an extra space in front of
  SCHEDULED.

- Add leading white space to the planning info entry regexp to prevent
  leftover white space when removing entries other than the first
  entry.
---
 lisp/org.el  |  35 ++-
 testing/lisp/test-org.el | 159 +++
 2 files changed, 178 insertions(+), 16 deletions(-)

diff --git a/lisp/org.el b/lisp/org.el
index 02f5c22..5a7d6d3 100755
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -13478,23 +13478,26 @@ (defun org-add-planning-info (what optional time rest remove)
 	  (skip-chars-forward  \t)
 	  ;; Check if we have to remove something.
 	  (dolist (type (if what (cons what remove) remove))
-		(when (save-excursion
-			(re-search-forward
-			 (case type
-			   (closed org-closed-time-regexp)
-			   (deadline org-deadline-time-regexp)
-			   (scheduled org-scheduled-time-regexp)
-			   (otherwise (error Invalid planning type: %s type)))
-			 (line-end-position) t))
-		  (replace-match )
-		  (when (looking-at --+[^]+) (replace-match ))
-		  (when (and (not what) (eq type 'closed))
-		(save-excursion
-		  (beginning-of-line)
-		  (if (looking-at [ \t]*$)
-			  (delete-region (point) (1+ (point-at-eol)))
+		(save-excursion
+		  (when (re-search-forward
+			 (concat
+			   *
+			  (case type
+			(closed org-closed-time-regexp)
+			(deadline org-deadline-time-regexp)
+			(scheduled org-scheduled-time-regexp)
+			(otherwise
+			 (error Invalid planning type: %s type
+			 (line-end-position) t)
+		(replace-match )
+		(when (looking-at --+[^]+) (replace-match ))
+		(when (and (not what) (eq type 'closed))
+		  (save-excursion
+			(beginning-of-line)
+			(if (looking-at [ \t]*$)
+			(delete-region (point) (1+ (point-at-eol
 		;; Remove leading white spaces.
-		(when (and (not (bolp)) (looking-at [ \t]+)) (replace-match 
+		(when (looking-at [ \t]+) (replace-match 
 	 ((not what) (throw 'exit nil)) ; Nothing to do.
 	 (t (insert-before-markers \n)
 		(backward-char 1)
diff --git a/testing/lisp/test-org.el b/testing/lisp/test-org.el
index 35905d3..437b594 100644
--- a/testing/lisp/test-org.el
+++ b/testing/lisp/test-org.el
@@ -2858,6 +2858,165 @@ (ert-deftest test-org/at-planning-p ()
 	 * Headline\n*** Inlinetask\n*** END\npointDEADLINE: 2014-03-04 tue.
(let ((org-inlinetask-min-level 3)) (org-at-planning-p))
 
+(ert-deftest test-org/add-planning-info ()
+  Test `org-add-planning-info'.
+  ;; Create deadline when `org-adapt-indentation' is non-nil.
+  (should
+   (equal * H\n  DEADLINE: 2015-06-25\nParagraph
+	  (org-test-with-temp-text * H\nParagraphpoint
+	(let ((org-adapt-indentation t))
+	  (org-add-planning-info 'deadline 2015-06-25 Thu))
+	(replace-regexp-in-string
+	 \\( [.A-Za-z]+\\)  (buffer-string)
+	 nil nil 1
+  ;; Create deadline when `org-adapt-indentation' is nil.
+  (should
+   (equal * H\nDEADLINE: 2015-06-25\nParagraph
+	  (org-test-with-temp-text * H\nParagraphpoint
+	(let ((org-adapt-indentation nil))
+	  (org-add-planning-info 'deadline 2015-06-25 Thu))
+	(replace-regexp-in-string
+	 \\( [.A-Za-z]+\\)  (buffer-string)
+	 nil nil 1
+  ;; Update deadline when `org-adapt-indentation' is non-nil.
+  (should
+

Re: [O] HTML/images zipped?

2015-06-26 Thread Nick Dokos

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

 hm... maybe it has been a while since I ran that ;) I pushed some
 changes that seem to have it working on a small test file.


Yes, it does not fail any longer. Thanks!

 This code is somewhat on the border of a filter/custom export. There are
 probably links that will now work with it, I have not tested it super
 thoroughly.

 Notably, it does not preserve relative paths, but rather renames files
 and images and replaces the links in the org-file with the new
 names. It was too hard to figure out how to preserve the paths when I
 wrote this originally.


OK. I'm just kicking the tires for now.

 Nick Dokos writes:

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

 I did something like this for org-files:
 https://github.com/jkitchin/jmax/blob/master/ox-archive.el


 I tried this on some arbitrary org file (not containing any references) and 
 I got an error:


-- 
Nick

[O] ox-odt roundtrip editing?

2015-06-26 Thread joakim

I'm writing a manuscript for a publisher. The process looks like:

- I write a chapter in org mode, export it to odt

- I apply the styles the publisher wants to use with a libreoffice
  macro. This isn't particularily efficient, but I failed at modifying
  ox-odt to use custom templates.

- I get back comments on the chapter from the publisher, that use the
  libreoffice annotation feature. Here I basically can't use org-mode
  anymore.

Has someone attempted doing roundtrip editing ith libreoffice and org?
That is, convert the odt file back to org, including the annotations,
and edit fro there?

-- 
Joakim Verona

Re: [O] Bug: org-mode breaks flyspell [8.2.10 (release_8.2.10 @ /usr/share/emacs/24.4/lisp/org/)]

Hello,

Reuben Thomas r...@sc3d.org writes:

 Tested using “emacs -Q”, so you can ignore the details of my setup:

 Start up Emacs, M-x flyspell-mode datSPACE

 The mis-spelled (I’m using English, not Latin as my default language)
 “dat” is underwiggled.

 Type Backspace a SPACE

 The word is now “data”, and (in English or Latin!) is now correct, so not 
 underwiggled.

 M-x org-mode and repeat the exercise: the underwiggle on the letters of
 “dat” remains after I have typed the “a”.

Thank you.

Apparently, this issue cannot be reproduced on latest development
version of Org. You may want to switch to development version of Org or
wait for 8.3 to be released.

Regards,

-- 
Nicolas Goaziou

Re: [O] HTML/images zipped?

2015-06-26 Thread Rasmus

Peter Davis p...@pfdstudio.com writes:

 Is there any way to export HTML with all references images,
 etc. packaged in a ZIP file?

My guess is that at the moment your best bet is hacking some together with
ox-publish.  See org-publish-project-alist.

Hope it helps,
Rasmus

PS: On the list, we have talked about a .borg format that might serve for
similar situation but it's at an idea stage at the moment.

-- 
This message is brought to you by the department of redundant departments

[O] Bug: org-mode breaks flyspell [8.2.10 (release_8.2.10 @ /usr/share/emacs/24.4/lisp/org/)]

2015-06-26 Thread Reuben Thomas



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

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

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


Tested using “emacs -Q”, so you can ignore the details of my setup:

Start up Emacs, M-x flyspell-mode datSPACE

The mis-spelled (I’m using English, not Latin as my default language)
“dat” is underwiggled.

Type Backspace a SPACE

The word is now “data”, and (in English or Latin!) is now correct, so not 
underwiggled.

M-x org-mode and repeat the exercise: the underwiggle on the letters of
“dat” remains after I have typed the “a”.

Emacs  : GNU Emacs 24.4.1 (x86_64-pc-linux-gnu, GTK+ Version 3.10.8)
 of 2014-11-21 on skwd, modified by Debian
Package: Org-mode version 8.2.10 (release_8.2.10 @ 
/usr/share/emacs/24.4/lisp/org/)

current state:
==
(setq
 org-export-backends '(ascii html icalendar latex odt)
 org-tab-first-hook '(org-hide-block-toggle-maybe 
org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe 
org-babel-header-arg-expand)
 org-latex-classes '((article \\documentclass[11pt]{article} 
(\\section{%s} . \\section*{%s}) (\\subsection{%s} . \\subsection*{%s})
  (\\subsubsection{%s} . \\subsubsection*{%s}) 
(\\paragraph{%s} . \\paragraph*{%s})
  (\\subparagraph{%s} . \\subparagraph*{%s}))
 (report \\documentclass[11pt]{report} (\\part{%s} . 
\\part*{%s}) (\\chapter{%s} . \\chapter*{%s})
  (\\section{%s} . \\section*{%s}) (\\subsection{%s} 
. \\subsection*{%s}) (\\subsubsection{%s} . \\subsubsection*{%s}))
 (book \\documentclass[11pt]{book} (\\part{%s} . 
\\part*{%s}) (\\chapter{%s} . \\chapter*{%s})
  (\\section{%s} . \\section*{%s}) (\\subsection{%s} 
. \\subsection*{%s}) (\\subsubsection{%s} . \\subsubsection*{%s}))
 (scrartcl \\documentclass{scrartcl} (\\section{%s} . 
\\section*{%s}) (\\subsection{%s} . \\subsection*{%s})
  (\\subsubsection{%s} . \\subsubsection*{%s}) 
(\\paragraph{%s} . \\paragraph*{%s})
  (\\subparagraph{%s} . \\subparagraph*{%s}))
 )
 org-latex-default-packages-alist '((postscript ucs nil) ( pifont nil) 
(utf8x inputenc t) (T1 fontenc t) ( fixltx2e nil)
( graphicx t) ( longtable nil) ( 
float nil) ( wrapfig nil) ( rotating nil) (normalem ulem t)
( amsmath t) ( textcomp t) ( 
marvosym t) ( wasysym t) ( amssymb t) ( hyperref nil)
\\tolerance=1000 ( palatino nil))
 org-speed-command-hook '(org-speed-command-default-hook 
org-babel-speed-command-hook)
 org-occur-hook '(org-first-headline-recenter)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-html-format-drawer-function '(lambda (name contents) contents)
 org-latex-format-inlinetask-function 'ignore
 org-confirm-shell-link-function 'yes-or-no-p
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-export-with-section-numbers nil
 org-file-apps '((auto-mode . emacs) (\\.mm\\' . default) (\\.x?html?\\' . 
default) (\\.pdf\\' . default) (t . xdg-open %s)
 (system . xdg-open %s))
 org-export-with-toc nil
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-default-notes-file ~/Notes/Notes.org
 org-startup-indented t
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-latex-format-drawer-function '(lambda (name contents) contents)
 org-odt-format-headline-function 'ignore
 org-from-is-user-regexp \\Reuben Thomas\\
 org-src-mode-hook '(org-src-babel-configure-edit-buffer 
org-src-mode-configure-edit-buffer)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-babel-pre-tangle-hook '(save-buffer)
 org-mode-hook '((lambda nil (local-set-key \351 (quote 
org-toggle-iimage-in-org))) window-margin-mode
 #[nil \300\301\302\303\304$\207 [org-add-hook 
change-major-mode-hook org-show-block-all append local] 5]
 #[nil \300\301\302\303\304$\207 [org-add-hook 
change-major-mode-hook org-babel-show-result-all append local] 5]
 org-babel-result-hide-spec org-babel-hide-all-hashes 
turn-on-eldoc-mode)
 org-ascii-format-drawer-function '(lambda (name contents width) contents)
 org-odt-format-inlinetask-function 'ignore
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point 
org-babel-execute-safely-maybe)
 org-directory ~/Notes
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers 
org-cycle-hide-inline-tasks org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-footnote-define-inline t
 org-confirm-elisp-link-function 'yes-or-no-p
 org-metadown-hook

[O] can't assign to hline relative reference:

2015-06-26 Thread Marijn Schouten (hkBst)

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear list,

Consider the following small org table:

|   | grade | weight | weighed grade |
|---+---++---|
|   | 5 | 10 |50 |
|---+---++---|
| total |   || 0 |
#+TBLFM: @II$2=vsum(@I$2..@II-1$2)::$4=$2*$3

In the version of org (8.2.10) distributed with emacs 24.5, evaluating this 
table does not produces the expected result of column 2 being summed to a total 
of 5. Instead depending on point both the second and first columns will get an 
additional 5.

Through irc I found someone who tested this with the latest development version 
as of now and it instead produces the error: can't assign to hline relative 
reference. That also does not seem like the right behavior to me.

Could someone shed some light on the situation?

Marijn 

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[O] HTML/images zipped?