Re: [O] [ox, patch] Keywords what should go in ox?

2015-03-19 Thread Nicolas Goaziou
Rasmus ras...@gmx.us writes:

 Keywords are akin to small headings to identify the contents of a
 document.  I see no reason to restrict this to the reader of the
 electronic version of a document.

What are you talking about? I don't want to restrict anything: AFAIU,
the feature you propose already exists in another form.

Again, your proposal is to have KEYWORDS mix two different things, i.e.,
set meta-data in document's header and set contents in the document. My
opinion is that for a given topic, you probably don't always want the
same contents, e.g., in \\hyperref{pdfkeywords={...}} and at the
beginning of the document, if only for the limitations on the syntax
allowed in the former.

Therefore, we may consider keeping the two features separated.

Do you think that you /always/ want pdfkeywords to hold exactly the
same contents as what you could put in your document? Do you think that
a user who wants to fill pdfkeywords will always want to also add these
contents in the body of the document?


Regards,



Re: [O] [RFC] [PATCH] Changes to Tag groups - allow nesting and regexps

2015-03-19 Thread Nicolas Goaziou
Gustav Wikström gustav.e...@gmail.com writes:

 I don't mind. Wrote a few lines and the patch is attached!

Applied. Thank you.

Regards,



Re: [O] restarting an org-babel session?

2015-03-19 Thread John Kitchin
Here is my solution so far:

http://kitchingroup.cheme.cmu.edu/blog/2015/03/19/Restarting-org-babel-sessions-in-org-mode-more-effectively/

It is a few functions that can go through the code blocks and
selectively rerun only the blocks that are in the session of the block
you run the restart command from. It is not tested too heavily, just
enough for this proof of concept.

j

Andreas Leha writes:

 Hi John,

 t...@tsdye.com (Thomas S. Dye) writes:
 Aloha all,

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

 That is an interesting one I did not know of. I would not want to always
 run every block, some of them might not be part of a session, and it is
 possible to have multiple named sessions in a buffer. It might be good
 practice to not do that though ;)

 If org-babel-execute-buffer is too much, there is
 org-babel-execute-subtree:

 ,-
 | org-babel-execute-subtree is an interactive autoloaded compiled Lisp
 | function in `ob-core.el'.
 |
 | It is bound to C-c C-v s, C-c C-v C-s.
 |
 | (org-babel-execute-subtree optional ARG)
 |
 | Execute source code blocks in a subtree.
 | Call `org-babel-execute-src-block' on every source block in
 | the current subtree.
 `-

 For finer control, this might work:

 ,--
 | #+name: recreate-my-named-session
 | #+header: :session my-named-session
 | #+begin_src lang
 | source-code-block-1
 | source-code-block-2
 | #+end_src
 `--


 That's what I am doing.  But that is manual book-keeping.  It means
 ultimate control but also the book-keeping to be accurate.  But I agree
 with John, that org could be smart enough to execute the blocks of one
 session.

 hth,
 Tom


 I will share my way of doing this if nothing else comes up.

 Please do.  I would be interested in such a function, as well.

 Thanks,
 Andreas



 Thomas S. Dye writes:

 Ken Mankoff mank...@gmail.com writes:

 On 2015-03-19 at 10:26, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Is it possible to restart an org-babel session from the current point?
 What I mean is if you have a largish org-file with many session blocks,
 and you want to go the end and continue it, you need to run each session
 block before the end to recreate the session.

 I am surprised there is no easy way to have an Org file run every code
 block in order either on command or on export. It seems like this
 would be a key component of reproducible research and literate
 documents.

 Maybe there is a way, but it isn't mentioned in the Evaluating code
 blocks section of the manual.

   -k.

 Would org-babel-execute-buffer work?

 ,
 | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
 | function in `ob-core.el'.
 |
 | (org-babel-execute-buffer optional ARG)
 |
 | Execute source code blocks in a buffer.
 | Call `org-babel-execute-src-block' on every source block in
 | the current buffer.
 `

 hth,
 Tom

 --
 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

--
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] Config best practices?

2015-03-19 Thread Marcin Borkowski
Hello all,

I'm wondering what people do to keep the configuration of their Org
files in order.  I use a dedicated top-level headline, with a COMMENT
keyword, but I started to think that a :noexport: tag might be a better
idea.

Are there any advantages of one over the other, or other approaches
altogether?

The reason I'm asking is that I'm tweaking my org-one-to-many utility so
that it propagates the config to all the generated files.

Best,

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



Re: [O] Include HTML fragments in HTML export

2015-03-19 Thread Giuseppe Lipari
Hi,

I have a similar setting, and it works fine for me:

#+INCLUDE: ./all_pub.html html

(notice the absence of  around the file name)

I use org-8.3beta (taken from the git repo some weeks ago).

Best,

Giuseppe Lipari







2015-03-18 19:46 GMT+01:00 Rasmus ras...@gmx.us:

 Hi,

 Titus von der Malsburg malsb...@posteo.de writes:


  * My personal home page
  ** Articles
  #+INCLUDE file1.html html
 
  ** Posters
  #+INCLUDE file2.html html

 This works in Org 8.3.  Org 8.2 does not seem to insert blocks
 cf. org-export-expand-include-keyword.

 Hope it helps,
 Rasmus

 --
 Me gusta la noche, me gustas tú





-- 
Giuseppe Lipari
LIFL
Université de Lille 1
blogs: http://scacciamennule.blogspot.com  (Italian)
http://scacciamennule.blogspot.com
  http://okpanico,wordpress.com  (Italian)
  http://algoland.wordpress.com   (English)


Re: [O] [ox, patch] Keywords what should go in ox?

2015-03-19 Thread Rasmus
Nicolas Goaziou m...@nicolasgoaziou.fr writes:

 Do you think that you /always/ want pdfkeywords to hold exactly the
 same contents as what you could put in your document?

You as in me: yes most certainly.

 Do you think that a user who wants to fill pdfkeywords will always want
 to also add these contents in the body of the document?

Which is why the patch provided a switch in #+OPTIONS.

—Rasmus

-- 
It was you, Jezebel, it was you



Re: [O] superscript without base

2015-03-19 Thread John Kitchin

I suppose $^{foo}$ will do what you want. you may need some additional
\mathrm command if you do not want math fonts.

or maybe try \textsuperscript{foo}

(untested)


Andreas Leha writes:

 Hi all,

 quick question: What is the syntax of superscripts without a 'base
 character'?

 I tried to use ^{foo} and {}^{foo} which both do not produce what I
 expect in the latex export.

 \nbsp^{foo} comes close.

 Best,
 Andreas

--
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] superscript without base

2015-03-19 Thread Andreas Leha
Hi all,

quick question: What is the syntax of superscripts without a 'base
character'?

I tried to use ^{foo} and {}^{foo} which both do not produce what I
expect in the latex export.

\nbsp^{foo} comes close.

Best,
Andreas




Re: [O] [patch, koma-letter] Change of subject behavior

2015-03-19 Thread Rasmus
Hi Nicolas,

Excellent comments.  Thanks a lot!

Nicolas Goaziou m...@nicolasgoaziou.fr writes:

 In this case, I suggest to change `org-koma-letter--special-headline'
 into `org-koma-letter--special-tag'

I agree.

 Eventually, since you're only interested in the first special tag
 encountered, it may be cleaner to exit early, e.g.,

Good idea.  I did it slightly differently with a funcall, but perhaps it's
slower (I have no idea).

 +   (format \\opening{%s}\n\n
 +   (org-export-data
 +(or (org-string-nw-p (plist-get info :opening))
 +(when (plist-get info :with-headline-opening)
 +  (org-element-map (org-element-parse-buffer) 'headline
^
   (plist-get info :parse-tree)

Thanks.  I *knew* it was fishy.

—Rasmus

-- 
Hooray!
From 5f6832704d011b4b966b52c0dc1f6076f7af6ea7 Mon Sep 17 00:00:00 2001
From: Rasmus ras...@gmx.us
Date: Wed, 18 Mar 2015 13:33:42 +0100
Subject: [PATCH 3/3] ox-koma-letter: Interpret #+SUBJECT.

* ox-koma-letter.el (org-koma-letter-template): Interpret #+SUBJECT.
---
 contrib/lisp/ox-koma-letter.el | 6 +-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/contrib/lisp/ox-koma-letter.el b/contrib/lisp/ox-koma-letter.el
index 33c8a1b..796b917 100644
--- a/contrib/lisp/ox-koma-letter.el
+++ b/contrib/lisp/ox-koma-letter.el
@@ -630,7 +630,11 @@ holding export options.
 		(mapconcat #'symbol-name with-subject ,
 	(let* ((title-as-subject (plist-get info :with-title-as-subject))
 	   (subject* (org-string-nw-p
-			  (org-export-data (plist-get info :subject) info)))
+			  (org-export-data
+			   (org-element-parse-secondary-string
+			(plist-get info :subject)
+			(org-element-restriction 'keyword))
+			   info)))
 	   (title* (and (plist-get info :with-title)
 			(org-string-nw-p
 			 (org-export-data (plist-get info :title) info
-- 
2.3.3

From 6f042fd397e7f3f5b4844921800a68b3ba91c403 Mon Sep 17 00:00:00 2001
From: Rasmus ras...@gmx.us
Date: Thu, 19 Mar 2015 12:10:30 +0100
Subject: [PATCH 2/3] ox-koma-letter: Stricter subject inference

* ox-koma-letter.el (org-koma-letter--special-tag): New function.
  (org-koma-letter-headline): Use org-koma-letter--special-tag
  and do not guess opening.
  (org-koma-letter-template): Directly infer subject from first
  non-special headline.
---
 contrib/lisp/ox-koma-letter.el | 41 +++--
 1 file changed, 27 insertions(+), 14 deletions(-)

diff --git a/contrib/lisp/ox-koma-letter.el b/contrib/lisp/ox-koma-letter.el
index 23da930..33c8a1b 100644
--- a/contrib/lisp/ox-koma-letter.el
+++ b/contrib/lisp/ox-koma-letter.el
@@ -412,6 +412,7 @@ was not present.
 (:with-place nil place org-koma-letter-use-place)
 (:with-subject nil subject org-koma-letter-subject-format)
 (:with-title-as-subject nil title-subject org-koma-letter-prefer-subject)
+(:with-headline-opening nil nil org-koma-letter-headline-is-opening-maybe)
 ;; Special properties non-nil when a setting happened in buffer.
 ;; They are used to prioritize in-buffer settings over lco
 ;; files.  See `org-koma-letter-template'.
@@ -553,19 +554,21 @@ Note that if a headline is tagged with a tag from
 `org-koma-letter-special-tags' it will not be exported, but
 stored in `org-koma-letter-special-contents' and included at the
 appropriate place.
-  (unless (let ((tag (car (org-export-get-tags headline info
-	(and tag
-		 (member-ignore-case
-		  tag (mapcar #'symbol-name (plist-get info :special-tags)))
-		 ;; Store association for later use and bail out.
-		 (push (cons tag contents) org-koma-letter-special-contents)))
-;; Opening is not defined yet: use headline's title.
-(when (and org-koma-letter-headline-is-opening-maybe
-	   (not (org-string-nw-p (plist-get info :opening
-  (plist-put info :opening
-		 (org-export-data (org-element-property :title headline) info)))
-;; In any case, insert contents in letter's body.
-contents))
+  (let ((special-tag (org-koma-letter--special-tag headline info)))
+(if (not special-tag)
+	contents
+  (push (cons special-tag contents) org-koma-letter-special-contents)
+  )))
+
+(defun org-koma-letter--special-tag (headline info)
+  Non-nil if HEADLINE is a special headline.
+INFO is a plist holding contextual information.  Returns first
+special tag headline.
+  (let ((special-tags (plist-get info :special-tags)))
+(catch 'exit
+  (dolist (tag (org-export-get-tags headline info))
+	(funcall (lambda (tag) (when tag (throw 'exit tag)))
+		 (assoc-string tag special-tags))
 
  Template
 
@@ -641,7 +644,17 @@ holding export options.
(format \\begin{letter}{%%\n%s}\n\n
 	   (org-koma-letter--determine-to-and-from info 'to))
;; Opening.
-   (format \\opening{%s}\n\n (plist-get info :opening))
+   (format \\opening{%s}\n\n
+	   (org-export-data
+	(or 

Re: [O] [patch, koma-letter] Change of subject behavior

2015-03-19 Thread Nicolas Goaziou
Rasmus ras...@gmx.us writes:

 +(defun org-koma-letter--special-tag (headline info)
 +  Non-nil if HEADLINE is a special headline.
 +INFO is a plist holding contextual information.  Returns first
^^^
Return, per (info (elisp)Documentation Tips)
   
 +special tag headline.
 +  (let ((special-tags (plist-get info :special-tags)))
 +(catch 'exit
 +  (dolist (tag (org-export-get-tags headline info))
 + (funcall (lambda (tag) (when tag (throw 'exit tag)))
 +  (assoc-string tag special-tags))

This is the usual definition for (let ...), i.e., you just wrote

  (let ((tag (assoc-string tag special-tags)))
(when tag (throw 'exit tag)))

Please just use `let', as it is much more readable.

AFAIC, you can push the patches, when the above is fixed. Thank you.


Regards,



Re: [O] superscript without base

2015-03-19 Thread Andreas Leha
Hi Rasmus,

Thanks for your continuing help here.

Rasmus ras...@gmx.us writes:
 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Hi Rasmus,

 Rasmus ras...@gmx.us writes:
 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Thanks for the answer.  So, there is no easy way out.  I think I'll
 stick to the \nbsp version, then.  Although introducing some character
 that will be removed during export through a filter might be handy in
 other cases, too.  I'll think about it.

 Why not make a \zwsp that inserts a zero width space?

 Because I did not know about \zwsp.  But also, \zwsp is exported
 literally to html, as my first quick test shows.

 _You'd_ have to add it to org-entities-user.


I see.  This did not occur to me, as the LaTeX export seemed to work
(well, it produced an Undefined control sequence error that I did not
spot).

But it put me on the right (?) track: I now found that both \zwnj and
\shy seem to produce what I want without any need for customization.  I
do not know which one is the bigger hack...

 You can also use a
 macro like {{{script(^whatever)}}} that expands to your liking.

 I am not sure what you are suggesting here.

 E.g.

 #+MACRO: sub \nbsp$1
 {{{sub(^foo)}}}

Thanks for the clarification.  I like the meaningful name (although I'd
go for #+MACRO: sup \zwnj^{$1}).  That even makes up for the syntax
of macros and I'll use that.

Thanks!
Andreas




Re: [O] superscript without base

2015-03-19 Thread Andreas Leha
Hi Rasmus,

Rasmus ras...@gmx.us writes:
 John Kitchin jkitc...@andrew.cmu.edu writes:

 or maybe try \textsuperscript{foo}

 This would work in at least KOMA-Script.

 Check org-match-substring-regexp.  As you see at subscripts must start
 with something that's not a space.  So I guess you could use a filter to
 remove some otherwise unused character or the the like...  Or change the
 the syntax table changed so that zero width space is somehow not an \s,
 but that's probably asking for trouble.


Thanks for the answer.  So, there is no easy way out.  I think I'll
stick to the \nbsp version, then.  Although introducing some character
that will be removed during export through a filter might be handy in
other cases, too.  I'll think about it.

Thanks,
Andreas




Re: [O] superscript without base

2015-03-19 Thread Rasmus
John Kitchin jkitc...@andrew.cmu.edu writes:

 or maybe try \textsuperscript{foo}

This would work in at least KOMA-Script.

Check org-match-substring-regexp.  As you see at subscripts must start
with something that's not a space.  So I guess you could use a filter to
remove some otherwise unused character or the the like...  Or change the
the syntax table changed so that zero width space is somehow not an \s,
but that's probably asking for trouble.

—Rasmus


-- 
In theory, practice and theory are the same. In practice they are not




Re: [O] superscript without base

2015-03-19 Thread Rasmus
Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Thanks for the answer.  So, there is no easy way out.  I think I'll
 stick to the \nbsp version, then.  Although introducing some character
 that will be removed during export through a filter might be handy in
 other cases, too.  I'll think about it.

Why not make a \zwsp that inserts a zero width space?  You can also use a
macro like {{{script(^whatever)}}} that expands to your liking.

—Rasmus

-- 
Together we will make the possible totay impossible!




Re: [O] superscript without base

2015-03-19 Thread Andreas Leha
Hi Rasmus,

Rasmus ras...@gmx.us writes:
 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Thanks for the answer.  So, there is no easy way out.  I think I'll
 stick to the \nbsp version, then.  Although introducing some character
 that will be removed during export through a filter might be handy in
 other cases, too.  I'll think about it.

 Why not make a \zwsp that inserts a zero width space?

Because I did not know about \zwsp.  But also, \zwsp is exported
literally to html, as my first quick test shows.

 You can also use a
 macro like {{{script(^whatever)}}} that expands to your liking.


I am not sure what you are suggesting here.

Best,
Andreas




Re: [O] superscript without base

2015-03-19 Thread Andreas Leha
Hi John,

Thanks a lot for your answer.

John Kitchin jkitc...@andrew.cmu.edu writes:
 I suppose $^{foo}$ will do what you want. you may need some additional
 \mathrm command if you do not want math fonts.

 or maybe try \textsuperscript{foo}

 (untested)


These both work (you are right about the math font).  But obviously only
in LaTeX.

I did not say explicitly but I'd prefer a
more backend-agnostic solution.

Best,
Andreas



 Andreas Leha writes:

 Hi all,

 quick question: What is the syntax of superscripts without a 'base
 character'?

 I tried to use ^{foo} and {}^{foo} which both do not produce what I
 expect in the latex export.

 \nbsp^{foo} comes close.

 Best,
 Andreas

 --
 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] superscript without base

2015-03-19 Thread Rasmus
Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Hi Rasmus,

 Rasmus ras...@gmx.us writes:
 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Thanks for the answer.  So, there is no easy way out.  I think I'll
 stick to the \nbsp version, then.  Although introducing some character
 that will be removed during export through a filter might be handy in
 other cases, too.  I'll think about it.

 Why not make a \zwsp that inserts a zero width space?
   
 Because I did not know about \zwsp.  But also, \zwsp is exported
 literally to html, as my first quick test shows.

_You'd_ have to add it to org-entities-user.

 You can also use a
 macro like {{{script(^whatever)}}} that expands to your liking.

 I am not sure what you are suggesting here.

E.g.

#+MACRO: sub \nbsp$1
{{{sub(^foo)}}}


-- 
What will be next?




Re: [O] restarting an org-babel session?

2015-03-19 Thread Thomas S. Dye
Ken Mankoff mank...@gmail.com writes:

 On 2015-03-19 at 10:26, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Is it possible to restart an org-babel session from the current point?
 What I mean is if you have a largish org-file with many session blocks,
 and you want to go the end and continue it, you need to run each session
 block before the end to recreate the session.

 I am surprised there is no easy way to have an Org file run every code
 block in order either on command or on export. It seems like this
 would be a key component of reproducible research and literate
 documents.

 Maybe there is a way, but it isn't mentioned in the Evaluating code
 blocks section of the manual.

   -k.

Would org-babel-execute-buffer work?

,
| org-babel-execute-buffer is an interactive autoloaded compiled Lisp
| function in `ob-core.el'.  
|
| (org-babel-execute-buffer optional ARG)   
|
| Execute source code blocks in a buffer.
| Call `org-babel-execute-src-block' on every source block in
| the current buffer.
`

hth,
Tom

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



[O] bug#18870: \emsp and alignment in org clock report

2015-03-19 Thread Subhan Michael Tindall
Agendas can  do get exported.  Current agenda buffer can be exported using 
org-agenda-write to several formats. Custom agendas can be assigned file 
name(s) and automatically export to one or more file types. 

See: http://orgmode.org/manual/Exporting-Agenda-Views.html


 -Original Message-
 From: emacs-orgmode-bounces+subhant=familycareinc@gnu.org
 [mailto:emacs-orgmode-bounces+subhant=familycareinc@gnu.org] On
 Behalf Of Leo Ufimtsev
 Sent: Wednesday, March 18, 2015 2:10 PM
 To: Nicolas Goaziou
 Cc: Ben Finney; 18...@debbugs.gnu.org
 Subject: [O] bug#18870: bug#18870: \emsp and alignment in org clock report
 
 I can't speak for the technical details,
 
 but I get the sense that \emsp isn't the right thing to be displayed on an
 *agenda clock report* because agenda clock reports don't get exported
 (afaik).
 
 Even \__ is more preffered than an \emsp, as \emsp is not 'easy to read' per
 se.
 
 Since there are clearly difference in opinions, maybe a solution is to have a
 variable like 'org-clockreport-indentation-character' which defaults to \emsp
 for correct export, but could be changed to spaces or '\__' by the user. This
 would give people the choice between better export or better text-buffer
 display.
 
 Thoughts?
 
 Leo Ufimtsev | Intern Software Engineer @ Eclipse Team
 
 - Original Message -
 From: Nicolas Goaziou m...@nicolasgoaziou.fr
 To: Ben Finney ben+em...@benfinney.id.au
 Cc: 18...@debbugs.gnu.org
 Sent: Tuesday, March 17, 2015 6:07:03 PM
 Subject: [O] bug#18870: \emsp and alignment in org clock report
 
 Ben Finney ben+em...@benfinney.id.au writes:
 
  The behaviour described – displaying “\emsp” instead of space
  characters – is a regression. That's what is being reported in this
  bug.
 
 There wasn't space characters in the first place, but \___ constructs.
 See commit bacfe5b4f7244eaf151f4e26a1d94dd8f66c1d19.
 
 Also, the bug is about table alignment when `org-pretty-entities' is used.
 
  Having some space character is not desirable as it would just move
  the problem the other way around (i.e., indentation would not appear
  during export)
 
  So the U+2003 EM SPACE character should be translated *during export*,
  and not be literally in the displayed text.
 
 No, because it means this character should be treated specially by Org (e.g.,
 LaTeX just ignores it so it needs to be turned into a space there).
 
 This is not a good idea, especially considering it is an invisible character.
 
  IS the above suggestion an acceptable solution?
 
 No, it isn't.
 
 An acceptable solution would be a character or a string that looks decent
 both in the buffer and in an exported document, without further processing.
 
  Note that this is not LaTeX-specific markup. This is called an
  entity, and is correctly exported in various back-ends.
 
  But not for display, which is the bug to be fixed here.
 
 Actually, it works more or less correctly for display on GUI with a non-nil 
 `org-
 pretty-entities', or calling `org-toggle-pretty-entities'.
 
 Regards,
 
 
 
 
 


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Re: [O] restarting an org-babel session?

2015-03-19 Thread Ken Mankoff

On 2015-03-19 at 10:26, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Is it possible to restart an org-babel session from the current point?
 What I mean is if you have a largish org-file with many session blocks,
 and you want to go the end and continue it, you need to run each session
 block before the end to recreate the session.

I am surprised there is no easy way to have an Org file run every code block in 
order either on command or on export. It seems like this would be a key 
component of reproducible research and literate documents.

Maybe there is a way, but it isn't mentioned in the Evaluating code blocks 
section of the manual.

  -k.
  



[O] restarting an org-babel session?

2015-03-19 Thread John Kitchin
Hi all,

Is it possible to restart an org-babel session from the current point?
What I mean is if you have a largish org-file with many session blocks,
and you want to go the end and continue it, you need to run each session
block before the end to recreate the session.

I have a little function that does that more or less, but it seemed like
a common enough need that it might already exist.

thanks,
--
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] restarting an org-babel session?

2015-03-19 Thread Thomas S. Dye
Aloha all,

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

 That is an interesting one I did not know of. I would not want to always
 run every block, some of them might not be part of a session, and it is
 possible to have multiple named sessions in a buffer. It might be good
 practice to not do that though ;)

If org-babel-execute-buffer is too much, there is
org-babel-execute-subtree:

,-
| org-babel-execute-subtree is an interactive autoloaded compiled Lisp
| function in `ob-core.el'.   
| 
| It is bound to C-c C-v s, C-c C-v C-s.  
| 
| (org-babel-execute-subtree optional ARG)   
| 
| Execute source code blocks in a subtree.
| Call `org-babel-execute-src-block' on every source block in 
| the current subtree.
`-

For finer control, this might work:

,--
| #+name: recreate-my-named-session
| #+header: :session my-named-session
| #+begin_src lang 
| source-code-block-1  
| source-code-block-2  
| #+end_src
`--

hth,
Tom


 I will share my way of doing this if nothing else comes up.

 Thomas S. Dye writes:

 Ken Mankoff mank...@gmail.com writes:

 On 2015-03-19 at 10:26, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Is it possible to restart an org-babel session from the current point?
 What I mean is if you have a largish org-file with many session blocks,
 and you want to go the end and continue it, you need to run each session
 block before the end to recreate the session.

 I am surprised there is no easy way to have an Org file run every code
 block in order either on command or on export. It seems like this
 would be a key component of reproducible research and literate
 documents.

 Maybe there is a way, but it isn't mentioned in the Evaluating code
 blocks section of the manual.

   -k.

 Would org-babel-execute-buffer work?

 ,
 | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
 | function in `ob-core.el'.
 |
 | (org-babel-execute-buffer optional ARG)
 |
 | Execute source code blocks in a buffer.
 | Call `org-babel-execute-src-block' on every source block in
 | the current buffer.
 `

 hth,
 Tom

 --
 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

-- 
T.S. Dye  Colleagues, Archaeologists
735 Bishop St, Suite 315, Honolulu, HI 96813
Tel: 808-529-0866, Fax: 808-529-0884
http://www.tsdye.com



Re: [O] restarting an org-babel session?

2015-03-19 Thread Ken Mankoff

On 2015-03-19 at 13:47, Thomas S. Dye t...@tsdye.com wrote:
 Ken Mankoff mank...@gmail.com writes:

 On 2015-03-19 at 10:26, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Is it possible to restart an org-babel session from the current point?
 What I mean is if you have a largish org-file with many session blocks,
 and you want to go the end and continue it, you need to run each session
 block before the end to recreate the session.

 I am surprised there is no easy way to have an Org file run every code
 block in order either on command or on export. It seems like this
 would be a key component of reproducible research and literate
 documents.

 Maybe there is a way, but it isn't mentioned in the Evaluating code
 blocks section of the manual.

   -k.

 Would org-babel-execute-buffer work?


Yes that works perfectly.

Thanks,

  -k.



Re: [O] restarting an org-babel session?

2015-03-19 Thread John Kitchin
That is an interesting one I did not know of. I would not want to always
run every block, some of them might not be part of a session, and it is
possible to have multiple named sessions in a buffer. It might be good
practice to not do that though ;)

I will share my way of doing this if nothing else comes up.

Thomas S. Dye writes:

 Ken Mankoff mank...@gmail.com writes:

 On 2015-03-19 at 10:26, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Is it possible to restart an org-babel session from the current point?
 What I mean is if you have a largish org-file with many session blocks,
 and you want to go the end and continue it, you need to run each session
 block before the end to recreate the session.

 I am surprised there is no easy way to have an Org file run every code
 block in order either on command or on export. It seems like this
 would be a key component of reproducible research and literate
 documents.

 Maybe there is a way, but it isn't mentioned in the Evaluating code
 blocks section of the manual.

   -k.

 Would org-babel-execute-buffer work?

 ,
 | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
 | function in `ob-core.el'.
 |
 | (org-babel-execute-buffer optional ARG)
 |
 | Execute source code blocks in a buffer.
 | Call `org-babel-execute-src-block' on every source block in
 | the current buffer.
 `

 hth,
 Tom

--
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] restarting an org-babel session?

2015-03-19 Thread Andreas Leha
Hi John,

t...@tsdye.com (Thomas S. Dye) writes:
 Aloha all,

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

 That is an interesting one I did not know of. I would not want to always
 run every block, some of them might not be part of a session, and it is
 possible to have multiple named sessions in a buffer. It might be good
 practice to not do that though ;)

 If org-babel-execute-buffer is too much, there is
 org-babel-execute-subtree:

 ,-
 | org-babel-execute-subtree is an interactive autoloaded compiled Lisp
 | function in `ob-core.el'.   
 | 
 | It is bound to C-c C-v s, C-c C-v C-s.  
 | 
 | (org-babel-execute-subtree optional ARG)   
 | 
 | Execute source code blocks in a subtree.
 | Call `org-babel-execute-src-block' on every source block in 
 | the current subtree.
 `-

 For finer control, this might work:

 ,--
 | #+name: recreate-my-named-session
 | #+header: :session my-named-session
 | #+begin_src lang 
 | source-code-block-1  
 | source-code-block-2  
 | #+end_src
 `--


That's what I am doing.  But that is manual book-keeping.  It means
ultimate control but also the book-keeping to be accurate.  But I agree
with John, that org could be smart enough to execute the blocks of one
session.

 hth,
 Tom


 I will share my way of doing this if nothing else comes up.

Please do.  I would be interested in such a function, as well.

Thanks,
Andreas



 Thomas S. Dye writes:

 Ken Mankoff mank...@gmail.com writes:

 On 2015-03-19 at 10:26, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Is it possible to restart an org-babel session from the current point?
 What I mean is if you have a largish org-file with many session blocks,
 and you want to go the end and continue it, you need to run each session
 block before the end to recreate the session.

 I am surprised there is no easy way to have an Org file run every code
 block in order either on command or on export. It seems like this
 would be a key component of reproducible research and literate
 documents.

 Maybe there is a way, but it isn't mentioned in the Evaluating code
 blocks section of the manual.

   -k.

 Would org-babel-execute-buffer work?

 ,
 | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
 | function in `ob-core.el'.
 |
 | (org-babel-execute-buffer optional ARG)
 |
 | Execute source code blocks in a buffer.
 | Call `org-babel-execute-src-block' on every source block in
 | the current buffer.
 `

 hth,
 Tom

 --
 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] [RFC] [PATCH] Changes to Tag groups - allow nesting and regexps

2015-03-19 Thread Gustav Wikström
Nicolas Goaziou m...@nicolasgoaziou.fr wrote:

 As a final step, would you mind preparing an entry in ORG-NEWS? I think
 most of it can be extracted from your commit messages.

I don't mind. Wrote a few lines and the patch is attached!

Best regards
Gustav


0001-ORG-NEWS-Mention-change-in-grouptags-functionality.patch
Description: Binary data


[O] bug#18870: bug#18870: \emsp and alignment in org clock report

2015-03-19 Thread Leo Ufimtsev
Interesting, I didn't know that. Thank you for pointing it out.

Maybe then just go along with the variable that would give people the choice, 
(I wouldn't mind '\emsp' being the default, so long as it can be changed to 
something else).

Thoughts?

Leo Ufimtsev | Intern Software Engineer @ Eclipse Team

- Original Message -
From: Subhan Michael Tindall subh...@familycareinc.org
To: Leo Ufimtsev lufim...@redhat.com, Nicolas Goaziou 
m...@nicolasgoaziou.fr
Cc: Ben Finney ben+em...@benfinney.id.au, 18...@debbugs.gnu.org
Sent: Thursday, March 19, 2015 12:48:40 PM
Subject: [O] bug#18870: \emsp and alignment in org clock report

Agendas can  do get exported.  Current agenda buffer can be exported using 
org-agenda-write to several formats. Custom agendas can be assigned file 
name(s) and automatically export to one or more file types. 

See: http://orgmode.org/manual/Exporting-Agenda-Views.html


 -Original Message-
 From: emacs-orgmode-bounces+subhant=familycareinc@gnu.org
 [mailto:emacs-orgmode-bounces+subhant=familycareinc@gnu.org] On
 Behalf Of Leo Ufimtsev
 Sent: Wednesday, March 18, 2015 2:10 PM
 To: Nicolas Goaziou
 Cc: Ben Finney; 18...@debbugs.gnu.org
 Subject: [O] bug#18870: bug#18870: \emsp and alignment in org clock report
 
 I can't speak for the technical details,
 
 but I get the sense that \emsp isn't the right thing to be displayed on an
 *agenda clock report* because agenda clock reports don't get exported
 (afaik).
 
 Even \__ is more preffered than an \emsp, as \emsp is not 'easy to read' per
 se.
 
 Since there are clearly difference in opinions, maybe a solution is to have a
 variable like 'org-clockreport-indentation-character' which defaults to \emsp
 for correct export, but could be changed to spaces or '\__' by the user. This
 would give people the choice between better export or better text-buffer
 display.
 
 Thoughts?
 
 Leo Ufimtsev | Intern Software Engineer @ Eclipse Team
 
 - Original Message -
 From: Nicolas Goaziou m...@nicolasgoaziou.fr
 To: Ben Finney ben+em...@benfinney.id.au
 Cc: 18...@debbugs.gnu.org
 Sent: Tuesday, March 17, 2015 6:07:03 PM
 Subject: [O] bug#18870: \emsp and alignment in org clock report
 
 Ben Finney ben+em...@benfinney.id.au writes:
 
  The behaviour described – displaying “\emsp” instead of space
  characters – is a regression. That's what is being reported in this
  bug.
 
 There wasn't space characters in the first place, but \___ constructs.
 See commit bacfe5b4f7244eaf151f4e26a1d94dd8f66c1d19.
 
 Also, the bug is about table alignment when `org-pretty-entities' is used.
 
  Having some space character is not desirable as it would just move
  the problem the other way around (i.e., indentation would not appear
  during export)
 
  So the U+2003 EM SPACE character should be translated *during export*,
  and not be literally in the displayed text.
 
 No, because it means this character should be treated specially by Org (e.g.,
 LaTeX just ignores it so it needs to be turned into a space there).
 
 This is not a good idea, especially considering it is an invisible character.
 
  IS the above suggestion an acceptable solution?
 
 No, it isn't.
 
 An acceptable solution would be a character or a string that looks decent
 both in the buffer and in an exported document, without further processing.
 
  Note that this is not LaTeX-specific markup. This is called an
  entity, and is correctly exported in various back-ends.
 
  But not for display, which is the bug to be fixed here.
 
 Actually, it works more or less correctly for display on GUI with a non-nil 
 `org-
 pretty-entities', or calling `org-toggle-pretty-entities'.
 
 Regards,
 
 
 
 
 


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[O] emac org literal examples

2015-03-19 Thread Francis J. Monari, Esquire
Literal Examples seem to begin with the following pattern: #+BEGIN_*.
 The * is often replaced by SRC EXAMPLE VERBATIM, etc..

Org Mode also recognizes Literal Examples with 'nonstandard' endings,
e.g. #+BEGIN_LANGUAGE.  Should users rely on these 'nonstandard'
Literal Examples being recognized in the future?

The SRC and EXAMPLE 'endings' receive special treatment, e.g. using
SRC the user can edit the Literal Example in a specific environment,
e.g. fundamental mode, enriched mode, or - of course - a mode designed
to work with a specific programing language.  How are the endings that
receive special treatment identified or registered?  Is is possible to
expand the set of endings that receive special treatment?

The ability to collapse specific lines of text with a title that can be
edited in a specific environment is a very powerful feature.  I do not,
however, want to misuse the feature or overload the SRC ending.  (The
SRC ending seems best reserved for programming languages or emacs modes.)

examples of the proposal:

1. The HTML ending could allow syntax highlighting.  The SRC ending
provides this for code.

2.
#+BEGIN_LANGUAGE Spanish
#+END_LANGUAGE
The literal example might then be edited in an environment convenient
for Spanish.

Thank you,

Frank.



Re: [O] How to represent Emacs keystrokes in Org?

2015-03-19 Thread Marcin Borkowski
Hi there,

it seems that reviving old threads is my new hobby;-).

On 2014-11-29, at 22:58, Marcin Borkowski mb...@wmi.amu.edu.pl wrote:

 On 2014-11-29, at 22:53, Marcin Borkowski wrote:

 On 2014-11-24, at 19:38, Rasmus wrote:

 Marcin Borkowski mb...@wmi.amu.edu.pl writes:

 Hello,

 I'm writing (in Org) a text on Emacs usage.  How to
 correctly/canonically represent keystrokes, like C-x RET f?
 Currently, I use =C-x RET f=; are there any alternatives?

 That's what I'd do.  Or ~C-x RET f~.  You could also use a macro, if you
 want it to me be more semantic (I hope I use this word correctly).

This might seem a good idea, but how do I do it?  (See below for
a concrete problem statement.)

 Houston, we've got a problem.  What about =M-,=?  Somehow it seems not
 to be interpreted in the right way: it does not get fontified correctly,
 nor does export in the right way.  What can I do about it?  I found
 about org-emphasis-regexp-components, is it the only way?  Also, how do
 I reload Org without restarting Emacs?  (I am an Emacs geek and I try to
 beat my record of emacs-uptime, you know. ;-) )

 Wow, I got an idea, and it worked.  Here's an excerpt from `C-u C-x ='
 at my solution;-):

  position: 11859 of 16051 (74%), column: 253
 character: ‍ (displayed as ‍) (codepoint 8205, #o20015, #x200d)
 preferred charset: unicode (Unicode (ISO10646))
 code point in charset: 0x200D
syntax: .  which means: punctuation
  to input: type C-x 8 RET HEX-CODEPOINT or C-x 8 RET NAME
   buffer code: #xE2 #x80 #x8D
 file code: #xE2 #x80 #x8D (encoded by coding system utf-8-unix)
   display: by this font (glyph code)
 xft:-unknown-Phetsarath OT-normal-normal-normal-*-17-*-*-*-*-0-iso10646-1 
 (#x120)

 Character code properties: customize what to show
   name: ZERO WIDTH JOINER

 A bit ugly trick, but works.  What are the opinions?

After a while I have to say that my opinion is strongly negative: this
breaks LaTeX export.  (LaTeX doesn’t like some unicode characters, it
turns out.)  Also, this was really an ugly hack...

So, here is my problem: how to represent a key like M-, or
e.g. a sequence \, (important in regexps) as “code” or “verbatim stuff”
in org-mode?  Neither =\,= nor ~\,~ work, of course.  Also, I’d like
this to be backend-agnostic, so \texttt{M-,} doesn’t really work.

What is the rationale behind forbidding the comma as the “border”
character in org-emphasis-regexp-components?  Should I change this
variable in my setup or is there a more general way to convince Org that
I really want verbatim/code snippets like =\,=?

Best,

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



[O] emac org diary entries

2015-03-19 Thread Francis J. Monari, Esquire
Emacs Org Mode recognizes diary entries both inside and outside angle
brackets (less than and greater than signs), e.g.:
%%(diary-date 2015 03 19), and
%%(diary-date 2015 03 19).
Should users rely on both forms being recognized in the future?

Emacs Org Mode also fully parses / recognizes diary entries not enclosed
in angle brackets that extend over multiple lines.  I believe that the
documentation indicates that entries on one line will be recognized.
Should users rely on expressions extending over multiple lines being
recognized in the future?

It would seem like both answers should be yes since the Emacs diary
program accepts both types of expressions.

Thank you,

Frank.



Re: [O] Include HTML fragments in HTML export

2015-03-19 Thread Titus von der Malsburg

Thanks Ramus and Giuseppe, as you say it works as expected in
v8.3beta.

  Titus


On 2015-03-19 Thu 01:28, Giuseppe Lipari wrote:
 Hi,

 I have a similar setting, and it works fine for me:

 #+INCLUDE: ./all_pub.html html

 (notice the absence of  around the file name)

 I use org-8.3beta (taken from the git repo some weeks ago).

 Best,

 Giuseppe Lipari







 2015-03-18 19:46 GMT+01:00 Rasmus ras...@gmx.us:

 Hi,

 Titus von der Malsburg malsb...@posteo.de writes:


  * My personal home page
  ** Articles
  #+INCLUDE file1.html html
 
  ** Posters
  #+INCLUDE file2.html html

 This works in Org 8.3.  Org 8.2 does not seem to insert blocks
 cf. org-export-expand-include-keyword.

 Hope it helps,
 Rasmus

 --
 Me gusta la noche, me gustas tú






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