date:20140501

On Wednesday, 30 Apr 2014 at 16:59, John Kitchin wrote:
 Greetings,

 All the talk about citations in org-mode inspired me to finish and polish
 some code I have been working on for my group for a while on
 bibtex/reftex/org-mode integration. I packaged it up in a literate
 programming org-file here:
 https://github.com/jkitchin/jmax/blob/master/org-ref.org.

Hi John,

Thanks for this.  I'll play with it as it looks like a really nice
collection of utilities for links and I must admit that I still find I
under-use org links.  I'll post any feedback here in due course.

One quick comment: I think it's bad practice to define global bindings
for Fxx keys in a package.  Let the user define these keys outside the
package maybe?  I have F10 and F12 defined to some very common actions
for me (recentf and org-clock).

Thanks again,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

[O] [PATCH] Make the point visible when jumping to the mark

From 9191e4a364e251119cf8b7c72e41f6c0d09583f2 Mon Sep 17 00:00:00 2001
Message-ID: 87ha5aqa93@treetowl.lan
MIME-Version: 1.0
Content-Type: text/plain

*lisp/org.el: Advise commands which jump to the mark
---

There are several non-org commands that jump to a location and would be
unwieldy if the location remained hidden, (isearch, bookmark-jump,
save-place), but org-mode has code to fix them. In this patch, I
followed their example.

I have an emacs fsf copyright assignment completed  on file with fsf, I can
send gpg signed copy if you need it.

- Ian Kelling


 lisp/org.el |   21 +
 1 file changed, 21 insertions(+)

diff --git a/lisp/org.el b/lisp/org.el
index 44a4e44..9365059 100644
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -24326,6 +24326,27 @@ To get rid of the restriction, use 
\\[org-agenda-remove-restriction-lock].
   (outline-invisible-p)))
(org-show-context 'bookmark-jump)))
 
+(eval-after-load simple
+  '(defadvice set-mark-command (after org-make-visible activate)
+ Make the point visible with `org-show-context'.
+ (org-mark-jump-unhide)))
+
+(eval-after-load simple
+  '(defadvice exchange-point-and-mark (after org-make-visible activate)
+ Make the point visible with `org-show-context'.
+ (org-mark-jump-unhide)))
+
+(eval-after-load simple
+  '(defadvice pop-global-mark (after org-make-visible activate)
+ Make the point visible with `org-show-context'.
+ (org-mark-jump-unhide)))
+
+(defun org-mark-jump-unhide ()
+  Make the point visible with `org-show-context' after jumping to the mark.
+  (when (and (derived-mode-p 'org-mode)
+(outline-invisible-p))
+(org-show-context 'mark-goto)))
+
 ;; Make session.el ignore our circular variable
 (defvar session-globals-exclude)
 (eval-after-load session
-- 
1.7.10.4

[O] [PATCH] Fix error prone babel table output format detection

From dc0b727328266785528fe160046ae1aa8df8a993 Mon Sep 17 00:00:00 2001
Message-ID: 87zjj2ous9@treetowl.lan
MIME-Version: 1.0
Content-Type: text/plain

* lisp/ob-core.el: Test that all elements are in a list are lists
instead of just the first.

org-babel table output uses different formatting for a list of lists,
but detects it incorrectly causing an error, as in this example:
#+begin_src emacs-lisp 
'((1) 2)
#+end_src
---
 lisp/ob-core.el |3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 1348f04..5872b68 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2185,8 +2185,7 @@ code  the results are extracted in the syntax of the 
source
  (goto-char beg)
  (insert (concat (orgtbl-to-orgtbl
   (if (or (eq 'hline (car result))
-  (and (listp (car result))
-   (listp (cdr (car result)
+  (cl-every 'listp result))
   result (list result))
   '(:fmt (lambda (cell) (format %s cell 
\n))
  (goto-char beg) (when (org-at-table-p) (org-table-align)))
-- 
1.7.10.4

Re: [O] [PATCH] Fix error prone babel table output format detection

2014-05-01 Thread Achim Gratz

Ian Kelling writes:
 org-babel table output uses different formatting for a list of lists,
 but detects it incorrectly causing an error, as in this example:
 #+begin_src emacs-lisp 
 '((1) 2)
 #+end_src

So this isn't a proper table, what do you expect to happen?

 -(and (listp (car result))
 - (listp (cdr (car result)
 +(cl-every 'listp result))

This is wrong, because a table can come with any number of 'hline
symbols, so ostensibly not every element will be a listp.  Besides, you
can't use cl-every unless Org drops backwards compatibility with older
Emacsen or mandates cl-lib to be present.  Even then, you'd also need to
require cl-extra.


Regards,
Achim.
-- 
+[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]+

SD adaptations for Waldorf Q V3.00R3 and Q+ V3.54R2:
http://Synth.Stromeko.net/Downloads.html#WaldorfSDada

Re: [O] [PATCH] Fix error prone babel table output format detection

Achim Gratz strom...@nexgo.de writes:

 Ian Kelling writes:
 org-babel table output uses different formatting for a list of lists,
 but detects it incorrectly causing an error, as in this example:
 #+begin_src emacs-lisp 
 '((1) 2)
 #+end_src

 So this isn't a proper table, what do you expect to happen?

I expect to be able to emacs -q, make an org mode buffer containing 
that block, do ctrl-c c on it, and not have an error message pop up and
fail to have any output. What is improper about it? Would it be better
if org did not try to format it as a table?


 -   (and (listp (car result))
 -(listp (cdr (car result)
 +   (cl-every 'listp result))

 This is wrong, because a table can come with any number of 'hline
 symbols, so ostensibly not every element will be a listp.

Yes, I agree. It will have to test if elements are listp or hline. 


 Besides, you
 can't use cl-every unless Org drops backwards compatibility with older
 Emacsen or mandates cl-lib to be present.  Even then, you'd also need to
 require cl-extra.

I forgot about the multiple parts of cl. I originally wrote it without,
and can change it.

Re: [O] [babel][PATCHES] ob-R patches for review

2014-05-01 Thread Rainer M Krug

Charles C. Berry ccbe...@ucsd.edu writes:

 On Wed, 30 Apr 2014, Rainer M Krug wrote:

 Charles Berry ccbe...@ucsd.edu writes:

 Rainer M Krug Rainer at krugs.de writes:


 Hi

 Attached please find seven patches for review to implement the storing
 of org variables in their own environment and to make the org-issued R
 code look nicer in the R session.


 Rainer,


 I have suggestions and a concern.

 I suggest [...]


 That is effectively what I am doing as well, only that I am not using a
 package but an environment and add it to the search path.


 [...]

 OK. I did not study your patches closely enough. Sorry.

No problem.





 I also suggest that you introduce a customization variable to
 allow a user to turn off the functionality you have created.

 I don't think this is necessary as the behavior for the user does not
 change at all, only that it becomes safer to use org variables in R (see
 above).


 All you have to do is add this:

 (defvar org-babel-R-assign-elisp-function 'org-babel-R-assign-elisp
   Name or definition of function to handle `:var name=value'
 header args.
   )

 and change one line in org-babel-variable-assignments:R from

 (org-babel-R-assign-elisp to

(funcall org-babel-R-assign-elisp-function

 and the user can provide her own elisp assignment function.

 This gives users who want special behavior like creating something
 other than a data.frame the option of providing their own function.

This assumes, that the user knows elisp. For many customizations this is
necessary, but I would prefer a system where the user only has to
provide an R function which will be used. This offers less
customizability, but this would make it possible to use R to do the
customization. To write a new org-babel-R-assign-elisp-function would be
quite a challenge for an R programmer (like me...).

Thanks,

Rainer





 Best,


 Chuck

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

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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

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

email:  rai...@krugs.de

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Re: [O] [PATCH] Fix error prone babel table output format detection

Ian Kelling i...@iankelling.org writes:

 Achim Gratz strom...@nexgo.de writes:

 Ian Kelling writes:
 org-babel table output uses different formatting for a list of lists,
 but detects it incorrectly causing an error, as in this example:
 #+begin_src emacs-lisp 
 '((1) 2)
 #+end_src

 So this isn't a proper table, what do you expect to happen?

 I expect to be able to emacs -q, make an org mode buffer containing 
 that block, do ctrl-c c on it, and not have an error message pop up and
 fail to have any output. What is improper about it? Would it be better
 if org did not try to format it as a table?

Actually, I see what you mean by improper.



 -  (and (listp (car result))
 -   (listp (cdr (car result)
 +  (cl-every 'listp result))

 This is wrong, because a table can come with any number of 'hline
 symbols, so ostensibly not every element will be a listp.

 Yes, I agree. It will have to test if elements are listp or hline. 


 Besides, you
 can't use cl-every unless Org drops backwards compatibility with older
 Emacsen or mandates cl-lib to be present.  Even then, you'd also need to
 require cl-extra.

 I forgot about the multiple parts of cl. I originally wrote it without,
 and can change it.

Below is a patch that addresses the 2 previously mentioned
problems. 

-- 8 --
Subject: [PATCH] Fix error prone babel table output format detection

* lisp/ob-core.el: Test that all elements are in a list are lists or
'hline instead of just the first.

org-babel table output uses different formatting for a list of lists,
but detects it incorrectly causing an error, as in this example:
#+begin_src emacs-lisp 
'((1) 2)
#+end_src
---
 lisp/ob-core.el |   13 ++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 1348f04..b5b0bc7 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2184,9 +2184,16 @@ code  the results are extracted in the syntax of the 
source
 ((funcall proper-list-p result)
  (goto-char beg)
  (insert (concat (orgtbl-to-orgtbl
-  (if (or (eq 'hline (car result))
-  (and (listp (car result))
-   (listp (cdr (car result)
+(if (let ((len (length result))
+  (proper t)
+  (i 0)
+  elem)
+  (while (and proper ( i len ))
+(setq elem (nth i result))
+(unless (or (listp elem) (eq elem 
'hline))
+  (setq proper nil))
+(setq i (1+ i)))
+  proper)
   result (list result))
   '(:fmt (lambda (cell) (format %s cell 
\n))
  (goto-char beg) (when (org-at-table-p) (org-table-align)))
-- 
1.7.10.4

Re: [O] [PATCH] Fix error prone babel table output format detection

Ian Kelling i...@iankelling.org writes:
 Below is a patch that addresses the 2 previously mentioned
 problems. 

It's a bit late.  here is the same patch with correct indentation.

 -- 8 --
Subject: [PATCH] Fix error prone babel table output format detection

* lisp/ob-core.el: Test that all elements are in a list are lists or
'hline instead of just the first.

org-babel table output uses different formatting for a list of lists,
but detects it incorrectly causing an error. An example of a block
causing an error is an emacs lisp source block containing just 1 line:
'((1) 2)
---
 lisp/ob-core.el |   13 ++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 1348f04..9eb2c7a 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2184,9 +2184,16 @@ code  the results are extracted in the syntax of the 
source
 ((funcall proper-list-p result)
  (goto-char beg)
  (insert (concat (orgtbl-to-orgtbl
-  (if (or (eq 'hline (car result))
-  (and (listp (car result))
-   (listp (cdr (car result)
+  (if (let ((len (length result))
+(proper t)
+(i 0)
+elem)
+(while (and proper ( i len ))
+  (setq elem (nth i result))
+  (unless (or (listp elem) (eq elem 
'hline))
+(setq proper nil))
+  (setq i (1+ i)))
+proper)
   result (list result))
   '(:fmt (lambda (cell) (format %s cell 
\n))
  (goto-char beg) (when (org-at-table-p) (org-table-align)))
-- 
1.7.10.4

Re: [O] [PATCH] Fix error prone babel table output format detection

Ian Kelling i...@iankelling.org writes:
 It's a bit late.  here is the same patch with correct indentation.

That patch went out of it's way not to check more of the list than was
necessary, but after sending it, I kept thinking that it does extra
things which possibly negate any performance benefit of not checking the
whole list. So here is a simpler patch does the same thing, but goes
over the whole list. I'd love to hear a more experienced emacs lisper
weigh in on which is better.

-- 8 --
Subject: [PATCH] Fix error prone babel table output format detection

* lisp/ob-core.el: Test that all elements are in a list are lists or
'hline instead of just the first.

org-babel table output uses different formatting for a list of lists,
but detects it incorrectly causing an error. An example of a block
causing an error is an emacs lisp source block containing just 1 line:
'((1) 2)
---
 lisp/ob-core.el |7 ---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 1348f04..05ccb00 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2184,9 +2184,10 @@ code  the results are extracted in the syntax of the 
source
 ((funcall proper-list-p result)
  (goto-char beg)
  (insert (concat (orgtbl-to-orgtbl
-  (if (or (eq 'hline (car result))
-  (and (listp (car result))
-   (listp (cdr (car result)
+  (if (let ((proper t))
+(dolist (elem result proper)
+  (unless (or (listp elem) (eq elem 
'hline))
+(setq proper nil
   result (list result))
   '(:fmt (lambda (cell) (format %s cell 
\n))
  (goto-char beg) (when (org-at-table-p) (org-table-align)))
-- 
1.7.10.4

Re: [O] org-ref code

John,

I've been playing with the package although, so far, only for
citations.  A few points:

1. Do you have any support for choosing the type of citation entry
 (i.e. \cite versus \autocite versus ...) when inserting a
 citation in the text?
 
2. You define org-link-types.  Unfortunately, this overwrites my own
 definitions, especially for cite.  I wonder whether this type
 of customisation belongs in org-ref itself.  This is similar to
 my earlier comment about key bindings, I guess. 

3. I sometimes use biblatex instead of bibtex.  As a result, I do not
 use \bibliography and use \addbibresource instead.  I have
 defined my bibliography files in org-ref-default-bibliography but
 this is only picked up on initialisation.  It is difficult to
 update this for a document in progress (I had to locally set
 reftex-default-bibliography manually).

4. The customisation interface for org-ref-default-bibliography should be
 list aware...

Otherwise, seems to working just fine.

Thanks,
eric

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

[O] Title of org files in github not recognized

2014-05-01 Thread Julian Gehring


Hi,

How I can convince github to recognize the '#+TITLE:' field of an 
org-file?  This should be a 'h1' heading, while it is currently treated 
as normal text (for example, see 
https://github.com/julian-gehring/vignettes/blob/master/README.org).  I 
know that this is a problem of the parsing on github's site, but is 
anyone aware of a good solution?


Best wishes
Julian

Re: [O] Title of org files in github not recognized

Julian Gehring julian.gehr...@gmail.com writes:

 Hi,

 How I can convince github to recognize the '#+TITLE:' field of an org-file?  
 This should be a 'h1' heading, while it is
 currently treated as normal text (for example, see 
 https://github.com/julian-gehring/vignettes/blob/master/README.org).
 I know that this is a problem of the parsing on github's site, but is anyone 
 aware of a good solution?

 Best wishes
 Julian

Use free software, then you can fix it. One example,
https://gitlab.com/gitlab-org/gitlab-ce/blob/master/README.md

Re: [O] Contacts/Resources/People

2014-05-01 Thread Alexander Baier

Hello Shin,

On 2014-04-30 20:17 Shin Sungmin wrote:
 But, how does it make it easier to assign a person to a task in my
 todo.org? Is there any type of auto complete functionality?

You have the function org-contacts which helps you search through your
contacts. From there you can quickly jump to the contact you want to
link, store a link to that heading `org-store-link' and insert that link
in your todo.org with `C-c C-l' and then `M-p'.

 Do I have to make a manual link to the people.org file instance to be
 able to easily access that persons contact information?

In essence this is just a plain old manual org link to the right
headline in person.org. The procedure described above is not very
automatic.

You may want to take a look at helm. Its a completion and narrowing
framework, something a bit like ido, but way more powerful. There is a
plugin for helm that lets you search/complete/narrow over the headline
of an org-file. It might even offer to execute certain actions on said
headlines such as creating and inserting a link to them.

I just heard of said plugin, but never used it. If it does indeed have
described functionality it would make linking to a contact as simple as
pressing a key binding (launching helm on people.org) typing a few
characters to narrow to the contact you want to insert and press enter
to insert said link.

HTH,
--
Alexander Baier

Re: [O] Title of org files in github not recognized

Julian Gehring wrote:
 How I can convince github to recognize the '#+TITLE:' field of an org-file?
 This should be a 'h1' heading, while it is currently treated as normal text
 (for example, see
 https://github.com/julian-gehring/vignettes/blob/master/README.org).  I know
 that this is a problem of the parsing on github's site, but is anyone aware of
 a good solution?

That was supposed to be solved.

See https://github.com/wallyqs/org-ruby/issues/3

Best regards,
  Seb

-- 
Sebastien Vauban

Re: [O] org-ref code

2014-05-01 Thread Seb Frank

Hi Eric,

Now that you have mentioned it, do you have a good web resource / manual
for your set up, or would you mind sharing bits of it? It looks eminently
useful. I have a set up largely following this

http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/

but I wouldn't know how to get some of the things you mention (type of
citation entry, biblatex vs latex etc.) to work.

Thanks,
Seb

On Thu, May 1, 2014 at 6:01 AM, Eric S Fraga e.fr...@ucl.ac.uk wrote:

John,

I've been playing with the package although, so far, only for
citations. A few points:

1. Do you have any support for choosing the type of citation entry
(i.e. \cite versus \autocite versus ...) when inserting a
citation in the text?

2. You define org-link-types. Unfortunately, this overwrites my own
definitions, especially for cite. I wonder whether this type
of customisation belongs in org-ref itself. This is similar to
my earlier comment about key bindings, I guess.

3. I sometimes use biblatex instead of bibtex. As a result, I do not
use \bibliography and use \addbibresource instead. I have
defined my bibliography files in org-ref-default-bibliography but
this is only picked up on initialisation. It is difficult to
update this for a document in progress (I had to locally set
reftex-default-bibliography manually).

4. The customisation interface for org-ref-default-bibliography should be
list aware...

Otherwise, seems to working just fine.

Thanks,
eric

--
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: [O] org-ref code

2014-05-01 Thread John Kitchin

Thanks for the feedback. I moved the key-bindings for f10-12 out of org-ref.


On Thu, May 1, 2014 at 6:01 AM, Eric S Fraga e.fr...@ucl.ac.uk wrote:

 John,

 I've been playing with the package although, so far, only for
 citations.  A few points:

 1. Do you have any support for choosing the type of citation entry
  (i.e. \cite versus \autocite versus ...) when inserting a
  citation in the text?


Not at the moment. There are a few ways I can see doing this. With the
existing code, you can do M-x reftex-citation, select the format you want
and select the references. We could easily enough define additional formats
for other citation types. I found this way of inserting citations annoying,
because 99.99% of the time I want a simple cite link, and pressing  C-c ]
return regexp marking return was too much for me (




 2. You define org-link-types.  Unfortunately, this overwrites my own
  definitions, especially for cite.  I wonder whether this type
  of customisation belongs in org-ref itself.  This is similar to
  my earlier comment about key bindings, I guess.

 3. I sometimes use biblatex instead of bibtex.  As a result, I do not
  use \bibliography and use \addbibresource instead.  I have
  defined my bibliography files in org-ref-default-bibliography but
  this is only picked up on initialisation.  It is difficult to
  update this for a document in progress (I had to locally set
  reftex-default-bibliography manually).

 4. The customisation interface for org-ref-default-bibliography should be
  list aware...

 Otherwise, seems to working just fine.

 Thanks,
 eric

 --
 : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: [O] org-ref code

2014-05-01 Thread John Kitchin

sorry, premature send!


On Thu, May 1, 2014 at 8:36 AM, John Kitchin jkitc...@andrew.cmu.eduwrote:

 Thanks for the feedback. I moved the key-bindings for f10-12 out of
 org-ref.


 On Thu, May 1, 2014 at 6:01 AM, Eric S Fraga e.fr...@ucl.ac.uk wrote:

 John,

 I've been playing with the package although, so far, only for
 citations.  A few points:

 1. Do you have any support for choosing the type of citation entry
  (i.e. \cite versus \autocite versus ...) when inserting a
  citation in the text?


 Not at the moment. There are a few ways I can see doing this. With the
 existing code, you can do M-x reftex-citation, select the format you want
 and select the references. We could easily enough define additional formats
 for other citation types. I found this way of inserting citations annoying,
 because 99.99% of the time I want a simple cite link, and pressing  C-c ]
 return regexp marking return was too much for me (I cite a lot). I also
 found this method was not flexible, in the sense that it was not easy to
 add citations to an existing citation. That is why there is an ?a option to
 append citations in the code.


an alternative would be to use a prefix command that gave you an option to
change the cite format, similar to the minibuffer menu for cite links. I
have not written much prefix code before, but I will try that out.





 2. You define org-link-types.  Unfortunately, this overwrites my own
  definitions, especially for cite.  I wonder whether this type
  of customisation belongs in org-ref itself.  This is similar to
  my earlier comment about key bindings, I guess.


In the end, the link definitions can be as short as this:

#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(org-add-link-type
 cite
 'org-ref-cite-onclick-minibuffer-menu
 'org-ref-cite-link-format)
#+END_SRC

I wrote this for my research group to use, and eventually the links have to
be defined somewhere. I am not sure what the best place would be. It is an
interesting issue of reproducibility though. Two people with different link
definitions would get different results.


 3. I sometimes use biblatex instead of bibtex.  As a result, I do not
  use \bibliography and use \addbibresource instead.  I have
  defined my bibliography files in org-ref-default-bibliography but
  this is only picked up on initialisation.  It is difficult to
  update this for a document in progress (I had to locally set
  reftex-default-bibliography manually).


It should be easy enough to make an addbibresource link that does the same
thing as the bibliography link. And maybe to modify the find-bibliography
code to check for that too. I have never used biblatex though, so I dont
have any experience with it.



 4. The customisation interface for org-ref-default-bibliography should be
  list aware...


I think I fixed this.



 Otherwise, seems to working just fine.

 Thanks,
 eric

 --
 : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
 release_8.2.6-923-g233c11

Re: [O] Title of org files in github not recognized

2014-05-01 Thread Julian Gehring


Hi Seb,

Nice. So it seems that github is using an older version of org-ruby.  Is 
it clear what the update policy/cycle of github for softwares like 
org-ruby is?


Best wishes
Julian


On 01.05.2014 14:17, Sebastien Vauban wrote:

Julian Gehring wrote:

How I can convince github to recognize the '#+TITLE:' field of an org-file?
This should be a 'h1' heading, while it is currently treated as normal text
(for example, see
https://github.com/julian-gehring/vignettes/blob/master/README.org).  I know
that this is a problem of the parsing on github's site, but is anyone aware of
a good solution?


That was supposed to be solved.

See https://github.com/wallyqs/org-ruby/issues/3

Best regards,
   Seb

Re: [O] org-ref code

On Thursday,  1 May 2014 at 08:47, John Kitchin wrote:

[...]

Hi John,

thanks for your quick response!

 an alternative would be to use a prefix command that gave you an option to
 change the cite format, similar to the minibuffer menu for cite links. I
 have not written much prefix code before, but I will try that out.

This would be good, with many a way of stating the default one would
like?  For instance, for grant proposals, I often use autocite in
biblatex for generating citations as footnotes whereas for research
papers I use cite most often.  

 In the end, the link definitions can be as short as this:

 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (org-add-link-type
  cite
  'org-ref-cite-onclick-minibuffer-menu
  'org-ref-cite-link-format)
 #+END_SRC

My comment was not so much the definitions you used but that you were
overwriting those that I had already defined.  Your definitions were
arguably better than mine so maybe I was being a bit picky here... :)

 I wrote this for my research group to use, and eventually the links have to
 be defined somewhere. I am not sure what the best place would be. It is an
 interesting issue of reproducibility though. Two people with different link
 definitions would get different results.

Yes, this is true but there is so much that can be customised in org
that you will never have reproducibility at this level (e.g. handling of
latex snippets, code listings, even latex classes).  I would leave
something like this to a separate set of code that is not part of
org-ref.

 It should be easy enough to make an addbibresource link that does the same
 thing as the bibliography link. And maybe to modify the find-bibliography
 code to check for that too. I have never used biblatex though, so I dont
 have any experience with it.

I have only started using biblatex recently, and that was because I
wanted to use autocite.  The only change I had to make was \bibliography
to \addbibresource.  I still use the same bibtex files.  Of course,
others may be making more effective use of biblatex...

 4. The customisation interface for org-ref-default-bibliography should be
  list aware...

 I think I fixed this.

Thanks!
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: [O] org-ref code

On Thursday, 1 May 2014 at 08:21, Seb Frank wrote:
Hi Eric,

Now that you have mentioned it, do you have a good web resource / manual
for your set up, or would you mind sharing bits of it? It looks eminently
useful. I have a set up largely following this

http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/

but I wouldn't know how to get some of the things you mention (type of
citation entry, biblatex vs latex etc.) to work.

Hi Seb,

I don't have much of a setup, actually. You already do much more than I
do!

I tend to do things manually until somebody else posts something useful
already configured (like John has just done). For instance, I simply
use C-c C-l to store a link manually, typing in the type of link (cite
vs autocite) and the bibtex key directly. I used to use reftex with org
but found it got in the way although I cannot now remember how or why!

When in doubt, I resort to LaTeX. I have been using LaTeX for 30 years
or so. The beauty of org is that it allows me to fall back to LaTeX
without any hassle for most things.

I suffer (or have suffered badly in the past) from RSI so my main
concern is having things that are easy to type but paradoxically I don't
have a problem with typing normal text and I do touch type quickly. I
use evil mode which means I can avoid most chorded commands. To use
org, I have bound many org commands to keys in the normal state mode map
in evil. For instance, I have org-export-dispatch assigned to , e so
I can export to pdf and view it in emacs by typing , e l o. I have
similar key bindings for many org commands. For instance, t on a
headline will invoke org-todo. , n and , p move to next and
previous headlines, to org-metaleft, etc. The aim is to avoid all
or most M- and especially M-S- key bindings which kill my hands. C- is
not so bad but I avoid even these if possible.

I use a few yasnippets and make significant use of abbrev mode in Emacs
to help with typing. I also make use of org's own snippet system.

Sorry I cannot be more helpful and thanks for the link to your setup.

eric
--
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

[O] Heading vs Headline

Hello,

Particularly in the Org Beamer documentation, headlines seems the most
used term while there is a tag ignoreheading...

I have the impression that both terms (heading and headline) are
synonyms. Though, is this true, or is there some subtle nuance?

Best regards,
  Seb

-- 
Sebastien Vauban

[O] Agenda view in Fortnight mode

2014-05-01 Thread J. David Boyd


I've searched the docs, and looked through my .emacs and custom.el files, but
I don't see anywhere that lets me set the default view for the Agenda.

I would like it to come up in Fortnight mode as a default.  Is this possible?

Thanks.

Dave in New Port Richey, FL

Re: [O] Title of org files in github not recognized

Julian Gehring wrote:
 On 01.05.2014 14:17, Sebastien Vauban wrote:
 Julian Gehring wrote:
 How I can convince github to recognize the '#+TITLE:' field of an
 org-file?  This should be a 'h1' heading, while it is currently
 treated as normal text (for example, see
 https://github.com/julian-gehring/vignettes/blob/master/README.org).
 I know that this is a problem of the parsing on github's site, but
 is anyone aware of a good solution?

 That was supposed to be solved.

 See https://github.com/wallyqs/org-ruby/issues/3

 Nice. So it seems that github is using an older version of org-ruby.  Is it
 clear what the update policy/cycle of github for softwares like org-ruby is?

Unfortunately, not to me... ;-)

Best regards,
  Seb

-- 
Sebastien Vauban

Re: [O] Agenda view in Fortnight mode