Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

I already tried three version: macports, build from sources and the bundled
version. All have this problem. So, I guess it has to do with the way emacs
interacts with my Python, but I don't know how to debug it.

Is there no one here that is a python/orgmode ninja that can give me a hand
here?

Thanks.
Dror

On Tue, Jun 2, 2015 at 2:21 PM, Ken Mankoff mank...@gmail.com wrote:


 Switch to an emacs that doesn't have this bug on your system. Try
 Homebrew-installed versions (although I know you aren't supposed to mix
 brew and macports, and I think you use macports).

   -k.

 On 2015-06-02 at 01:49, Dror Atariah dror...@gmail.com wrote:
  No ideas? Please, I really don't know how to tackle this. Thanks.




-- 
Dror Atariah, Ph.D.
de.linkedin.com/in/atariah

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

No ideas? Please, I really don't know how to tackle this. Thanks.

--
Dror Atariah,  PhD
Sent from mobile; excuse my brevity.
On May 26, 2015 8:39 PM, Dror Atariah dror...@gmail.com wrote:



 On Tue, May 26, 2015 at 4:02 PM, Ken Mankoff mank...@gmail.com wrote:



 Where you see everything printed twice. I notice that in addition, you
 have

  r/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/py6499_X0''', 'exec'));

 at the top of your buffer, and I do not. I think the exec might be
 causing everything to echo as it runs, so everything is printed 2x, and
 that confuses Org, and it is not able to capture your filename.


 It is the most promising suspect so far, but still I don't understand
 where is it coming from? BTW, I noticed that it is not the same directory
 as the one where the generated temp files are stored.

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

On Mon, May 25, 2015 at 8:30 PM, John Kitchin jkitc...@andrew.cmu.edu
wrote:

 With emacs -Q, and this org file:

 #+BEGIN_SRC emacs-lisp
 (org-babel-do-load-languages
  'org-babel-load-languages
  '((emacs-lisp . t)
(python . t)))
 #+END_SRC

 #+RESULTS:

 #+BEGIN_SRC python :session with_matplotlib :results file :exports both
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 fig=plt.figure(figsize=(3,2))
 plt.plot([1,3,2])
 plt.savefig('myfig.png')
 'myfig.png'
 #+END_SRC

 #+RESULTS:
 [[file:myfig.png]]

 I get what you expect to happen. In my customized emacs, I get something
 else that is more like you see.

I use emacs that come from MacPorts, so for -Q option I start it using:
/Applications/MacPorts/Emacs.app/Contents/MacOS/Emacs -Q

Your minimal example doesn't work for me, and in the results block I get:

#+RESULTS:
[[file:]]

This is basically, the same problematic result that I get when using my
regular initialized emacs.




 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 Mon, May 25, 2015 at 2:22 PM, Dror Atariah dror...@gmail.com wrote:

 On Mon, May 25, 2015 at 7:29 PM, Ken Mankoff mank...@gmail.com wrote:


 On 2015-05-25 at 13:25, Dror Atariah dror...@gmail.com wrote:
  I am sorry for reposting, but I'm still in the dark. Am I the only one
 who
  experience this kind of issue?

 Don't know.

  Did someone managed to reproduce the problem?

 I could not reproduce it.

  Does anyone see this message? :)

 Yes.


 Thanks for your reply :)



 I'm on Mac too, which is where your problem is. Are you starting with
 emacs -Q? I haven't seen you post a full MWE with both =init.el= and =
 test.org=. You did provide a test Org file but it wasn't clear to me if
 that was being used with emacs -Q.

 I tried to evaluate the problematic file using =emacs -Q= and the
 problem is the same.

 Following is the section of my =init.el= that deals with org-mode (if you
 need more, let me know):


 --8--8--8--8--8--8--8--8--8--8--8--8--8--8--
 ;;;
 ;; Org Mode related
 ;;;

 (setq org-directory ~/Dropbox/org)

 ;; Set a location for the list of agena files
 (setq org-agenda-files ~/.emacs.d/agenda_files)

 ;; Assigns org-mode to .org files
 (add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
 (define-key global-map \C-cl 'org-store-link)
 (define-key global-map \C-ca 'org-agenda)
 (setq org-log-done t)
 (when window-system (require 'org-mouse))

 ;; Auto enable flyspell-mode
 (add-hook 'org-mode-hook 'turn-on-flyspell)

 ;; Auto fill minor mode in org files
 (add-hook 'org-mode-hook 'turn-on-auto-fill)

 ;; Enable org-indent-mode for org buffers
 (add-hook 'org-mode-hook
   (lambda ()(org-indent-mode t)) t)

 ;; Use text-mode abbrev table in org-mode
 (add-hook 'org-mode-hook '(lambda () (setq local-abbrev-table
 text-mode-abbrev-table)))

 ;; Enables selection using SHIFT, while maintaining useful actions
 ;; related to SHITF in org
 (setq org-support-shift-select 't)

 ;; Enable smart qoutes (http://stackoverflow.com/q/15097114/671013)
 (setq org-export-with-smart-quotes t)

 ;; Customize the TODO-like keywords
 (setq org-use-fast-todo-selection t)
 (setq org-todo-keywords
   '((sequence TODO(t) PROCESS(p@/!) | DONE(d!) CANCELED(c@
 /!
 (setq org-todo-keyword-faces
   (quote ((TODO :foreground red :weight bold)
   (PROCESS :foreground blue :weight bold)
   (DONE :foreground forest green :weight bold)
   (CANCELLED :foreground forest green :weight bold
 (setq org-log-into-drawer t)

 ;; Capture-org
 (setq org-default-notes-file (concat org-directory /notes.org))
 (define-key global-map \C-cc 'org-capture)

 (setq org-capture-templates
   (quote ((t todo entry (file (concat org-directory /gtd.org))
* TODO %?\n%U\n%a\n :clock-in t :clock-resume t)
   (n note entry (file (concat org-directory /gtd.org))
* %? :NOTE:\n%U\n%a\n :clock-in t :clock-resume t)
   (j Journal entry (file+datetree (concat org-directory /
 diary.org))
* %?\n%U\n :clock-in t :clock-resume t)
   (v Vocabulary entry
(file+headline (concat org-directory /vocab.org)
   Vocabulary)
* %^{The word} :drill:\n:PROPERTIES:\n:Part-of-speech:
 %^{Part of speech|verb|noun|adj|adv}\n:END:\n %t\n %^{Extended word (may be
 empty)} \n** Answer \n%^{The definition})
   )))

 ;; Make use of refTeX in org-mode
 (defun org-mode-reftex-setup ()
   Setups RefTeX to be used with a org file. Code is based on
 http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

On Tue, May 26, 2015 at 3:49 AM, Ken Mankoff mank...@gmail.com wrote:


 Nick Dokos removed from Cc.

 On 2015-05-25 at 14:22, Dror Atariah dror...@gmail.com wrote:
  I tried to evaluate the problematic file using =emacs -Q= and the problem
  is the same.

 Sorry I can't help much. It works on my system.

 The only difference I see is my python version:

 #+BEGIN_SRC python :session background :results raw
 import sys
 sys.version
 #+END_SRC

 #+RESULTS:
 2.7.9 |Anaconda 2.2.0 (x86_64)| (default, Dec 15 2014, 10:37:34)
 [GCC 4.2.1 (Apple Inc. build 5577)]

I doesn't work also when I try to use the 2.7 version of Python.


  Following is the section of my =init.el= that deals with org-mode (if you
  need more, let me know):

 If the bug exists with emacs -Q, then sending a large init file is just
 noise and not helpful. A minimum working example would be similar to your
 previous email, but include the necessary Org setup code to execute Python,
 and nothing else.

I believe this is the example that John provided; which doesn't work for
me...

How can I make sure that my emacs -Q is really clean?


   -k.




-- 
Dror Atariah, Ph.D.
de.linkedin.com/in/atariah

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

On Tue, May 26, 2015 at 3:15 PM, Ken Mankoff mank...@gmail.com wrote:


 On 2015-05-26 at 09:11, Dror Atariah dror...@gmail.com wrote:
  I use emacs that come from MacPorts, so for -Q option I start it using:
  /Applications/MacPorts/Emacs.app/Contents/MacOS/Emacs -Q

 Consider using different compilation options, and/or a different Emacs.app
 package. It seems like that might be the easiest way to solve this problem.

This problem also happens when I use the standard OS X Emacs.app

I really don't understand what's going on here. Most likely it has to to
with my settings, but how and how to debug is beyond my reach.


   -k.




-- 
Dror Atariah, Ph.D.
de.linkedin.com/in/atariah

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

On Mon, May 25, 2015 at 8:30 PM, John Kitchin jkitc...@andrew.cmu.edu
wrote:

 With emacs -Q, and this org file:

 #+BEGIN_SRC emacs-lisp
 (org-babel-do-load-languages
  'org-babel-load-languages
  '((emacs-lisp . t)
(python . t)))
 #+END_SRC

 #+RESULTS:

 #+BEGIN_SRC python :session with_matplotlib :results file :exports both
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 fig=plt.figure(figsize=(3,2))# 4
 plt.plot([1,3,2])  # 3
 plt.savefig('myfig.png')  # 2
 'myfig.png' # 1
 #+END_SRC

 #+RESULTS:
 [[file:myfig.png]]


As I mentioned before, if I evaluate the second block as-is I get the
error. However, if I comment out all the lines except #1 then the code
returns the correct results block. Then, I started to add the numbered
lines. Adding #2 and #3 still doesn't break the behavior. Once adding line
#4 the behavior breaks. Maybe this observation can be helpful? This happens
both when starting Emacs -Q or without -Q.

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

On Tue, May 26, 2015 at 4:02 PM, Ken Mankoff mank...@gmail.com wrote:



 Where you see everything printed twice. I notice that in addition, you have

  r/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/py6499_X0''', 'exec'));

 at the top of your buffer, and I do not. I think the exec might be
 causing everything to echo as it runs, so everything is printed 2x, and
 that confuses Org, and it is not able to capture your filename.


It is the most promising suspect so far, but still I don't understand where
is it coming from? BTW, I noticed that it is not the same directory as the
one where the generated temp files are stored.

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

On Tue, May 26, 2015 at 4:02 PM, Ken Mankoff mank...@gmail.com wrote:


 On 2015-05-26 at 09:26, Dror Atariah dror...@gmail.com wrote:
  #+BEGIN_SRC python :session with_matplotlib :results file :exports both
  import matplotlib
  matplotlib.use('Agg')
  import matplotlib.pyplot as plt
  fig=plt.figure(figsize=(3,2))# 4
  plt.plot([1,3,2])  # 3
  plt.savefig('myfig.png')  # 2
  'myfig.png' # 1
  #+END_SRC
 
  #+RESULTS:
  [[file:myfig.png]]
 
 
  As I mentioned before, if I evaluate the second block as-is I get the
  error. However, if I comment out all the lines except #1 then the code
  returns the correct results block. Then, I started to add the numbered
  lines. Adding #2 and #3 still doesn't break the behavior. Once adding
 line
  #4 the behavior breaks. Maybe this observation can be helpful? This
 happens
  both when starting Emacs -Q or without -Q.


 Still no solution but a few comments:

 1) What you write here and on SE are not the same. Please cut-and-paste
 because details matter. For example, the SE code has import
 matplotlib.pyplot and then plt.figure but that code crashes because you
 did not import as plt like you do here...

I see. Let's focus on the code posted in this thread and assume that the
problem is not related to python mistakes.



 2) It seems to be an echo issue. In my *with_matplotlib* buffer in Emacs,
 I see:

 #+BEGIN_EXAMPLE
 Python 2.7.9 |Anaconda 2.2.0 (x86_64)| (default, Dec 15 2014, 10:37:34)
 [GCC 4.2.1 (Apple Inc. build 5577)] on darwin
 Type help, copyright, credits or license for more information.
 Anaconda is brought to you by Continuum Analytics.
 Please check out: http://continuum.io/thanks and https://binstar.org
  import matplotlib
  matplotlib.use('Agg')
  import matplotlib.pyplot as plt
 fig=plt.figure(figsize=(3,2))
 plt.plot([1,3,2])

 plt.savefig('myfig.png')
 'myfig.png'

 open('/var/folders/bl/trcxdptd1_q4k6q5fdhvp2m0gn/T/babel-52565cmH/python-525659vF',
 'w').write(str(_))
 'org_babel_python_eoe'
  [matplotlib.lines.Line2D object at 0x10454dd10]
  'myfig.png'
  'org_babel_python_eoe'
 
 #+END_EXAMPLE

 Where you see everything printed twice. I notice that in addition, you have

  r/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/py6499_X0''', 'exec'));

 at the top of your buffer, and I do not. I think the exec might be
 causing everything to echo as it runs, so everything is printed 2x, and
 that confuses Org, and it is not able to capture your filename.

This sounds like a promising hint. Where is this first line coming from?
How can I disable this double printing or figure out why is happening?




   -k.




-- 
Dror Atariah, Ph.D.
de.linkedin.com/in/atariah

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

I am sorry for reposting, but I'm still in the dark. Am I the only one who
experience this kind of issue? Did someone managed to reproduce the
problem? Does anyone see this message? :)

On Sat, May 23, 2015 at 8:49 PM, Dror Atariah dror...@gmail.com wrote:

 I am still helpless here. Any idea how to debug the problem? I would be
 happy to provide any kind of help, but I just cannot do it myself.

 Further findings:
 1) I don't think that matplotlib changes Python's '_', since the tmp file
 that contains the content of '_' is correct.
 2) Somehow, emacs/orgmode fails to extract the filename.
 3) It doesn't work also when using emacs 24.5 and orgmode 8.2.10.


 Following is an org file that tries to summarize the issue:

 #+TITLE: Integrate matplotlib figures in an org mode buffer
 * Goal
 The ultimate goal is to use org-babel as a replacement of IPython. The
 first motivation is to enable an easier version controling of the
 document. The first challenge I faced is integration of plots returned
 by ~matplotlib~ in the org buffer.
 * Capturing filename

 I would like to use (babel) orgmode as an interactive python
 notebook. Therefore, in order to allow the various code blocks to
 know each other, it is important to use the ~:session~
 option. However, once ~:session~ is used, together with ~matplotlib~
 the desired behavior is no longer in place.

 * Clean testing, no Matplotlib
 For the sake of testing, the following merely suppose to return the
 filename

 #+BEGIN_SRC python :session no_matplotlib :results file :exports both
 x = 'hello '
 y = 'world'
 z = x + y
 'foo.bar'
 #+END_SRC

 #+RESULTS:
 [[file:foo.bar]]

 *Passed* Indeed, the ~RESULTS~ block contains a link to the filename
 indicated by the last string.

 * Importing Matplotlib

 The following minimal example should generate a simple figure,
 ~myfig.png~, and orgmode should capture it and interpret it as a
 filename to be used by the following ~RESULTS~ block.

 #+BEGIN_SRC python :session with_matplotlib :results file :exports both
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 fig=plt.figure(figsize=(3,2))
 plt.plot([1,3,2])
 plt.savefig('myfig.png')
 'myfig.png'
 #+END_SRC

 #+RESULTS:
 [[file:]]

 *Failed!* This time, it doesn't work anymore. The file ~myfig.png~ is
  properly generated, but the last string is not captured by
  ~matplotlib~. Following is the content of the corresponding
  interactive python session:

 #+BEGIN_SRC
 Process with_matplotlib finished
 Python 3.4.3 (default, Mar 10 2015, 14:53:35)
 [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
 Type help, copyright, credits or license for more information.
,
 '''/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/py32771xVI''', 'exec'));
 import matplotlib
  import matplotlib
 matplotlib.use('Agg')
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import matplotlib.pyplot as plt
 fig=plt.figure(figsize=(3,2))
 fig=plt.figure(figsize=(3,2))
 plt.plot([1,3,2])
 plt.plot([1,3,2])
 plt.savefig('myfig.png')
 plt.savefig('myfig.png')
 'myfig.png'
 'myfig.png'


 open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-32771x4j/python-32771-fO',
 'w').write(str(_))
 open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-32771x4j/python-32771-fO',
 'w').write(str(_))




 'org_babel_python_eoe'
 'org_babel_python_eoe'
  [matplotlib.lines.Line2D object at 0x108e01828]
  'myfig.png'
   9
'org_babel_python_eoe'
 
 #+END_SRC

 * Some background

 ** Python Version
 #+BEGIN_SRC python :session background :results raw
 import sys
 sys.version
 #+END_SRC

 #+RESULTS:
 3.4.3 (default, Mar 10 2015, 14:53:35)
 [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)]

 ** Matplotlib version
 #+BEGIN_SRC python :session background :results raw
 import matplotlib
 matplotlib.__version__
 #+END_SRC

 #+RESULTS:
 1.4.3

 ** System
 I am running Emacs version ~GNU Emacs 24.5.1 (x86_64-apple-darwin14.1.0,
 NS apple-appkit-1344.72) of 2015-04-19 on tenten-slave.macports.org~

 The orgmode version is: ~Org-mode version 8.2.10
 (8.2.10-40-gc763fa-elpaplus @
 /Users/drorata/.emacs.d/elpa/org-plus-contrib-20150518/)~

 ** Stackoverflow reference
 I also posted a question in the SE network:
 [[
 http://emacs.stackexchange.com/questions/11075/org-mode-python-session-does-not-return-a-file-name
 ]]

 * Question
 So, my question is how to tackle/debug this issue? Can someone give me
 a hand here? That would be really great! Thanks!




-- 
Dror Atariah, Ph.D.
de.linkedin.com/in/atariah

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

On Mon, May 25, 2015 at 7:29 PM, Ken Mankoff mank...@gmail.com wrote:


 On 2015-05-25 at 13:25, Dror Atariah dror...@gmail.com wrote:
  I am sorry for reposting, but I'm still in the dark. Am I the only one
 who
  experience this kind of issue?

 Don't know.

  Did someone managed to reproduce the problem?

 I could not reproduce it.

  Does anyone see this message? :)

 Yes.


Thanks for your reply :)



 I'm on Mac too, which is where your problem is. Are you starting with
 emacs -Q? I haven't seen you post a full MWE with both =init.el= and =
 test.org=. You did provide a test Org file but it wasn't clear to me if
 that was being used with emacs -Q.

 I tried to evaluate the problematic file using =emacs -Q= and the problem
is the same.

Following is the section of my =init.el= that deals with org-mode (if you
need more, let me know):

--8--8--8--8--8--8--8--8--8--8--8--8--8--8--
;;;
;; Org Mode related
;;;

(setq org-directory ~/Dropbox/org)

;; Set a location for the list of agena files
(setq org-agenda-files ~/.emacs.d/agenda_files)

;; Assigns org-mode to .org files
(add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
(define-key global-map \C-cl 'org-store-link)
(define-key global-map \C-ca 'org-agenda)
(setq org-log-done t)
(when window-system (require 'org-mouse))

;; Auto enable flyspell-mode
(add-hook 'org-mode-hook 'turn-on-flyspell)

;; Auto fill minor mode in org files
(add-hook 'org-mode-hook 'turn-on-auto-fill)

;; Enable org-indent-mode for org buffers
(add-hook 'org-mode-hook
  (lambda ()(org-indent-mode t)) t)

;; Use text-mode abbrev table in org-mode
(add-hook 'org-mode-hook '(lambda () (setq local-abbrev-table
text-mode-abbrev-table)))

;; Enables selection using SHIFT, while maintaining useful actions
;; related to SHITF in org
(setq org-support-shift-select 't)

;; Enable smart qoutes (http://stackoverflow.com/q/15097114/671013)
(setq org-export-with-smart-quotes t)

;; Customize the TODO-like keywords
(setq org-use-fast-todo-selection t)
(setq org-todo-keywords
  '((sequence TODO(t) PROCESS(p@/!) | DONE(d!) CANCELED(c@
/!
(setq org-todo-keyword-faces
  (quote ((TODO :foreground red :weight bold)
  (PROCESS :foreground blue :weight bold)
  (DONE :foreground forest green :weight bold)
  (CANCELLED :foreground forest green :weight bold
(setq org-log-into-drawer t)

;; Capture-org
(setq org-default-notes-file (concat org-directory /notes.org))
(define-key global-map \C-cc 'org-capture)

(setq org-capture-templates
  (quote ((t todo entry (file (concat org-directory /gtd.org))
   * TODO %?\n%U\n%a\n :clock-in t :clock-resume t)
  (n note entry (file (concat org-directory /gtd.org))
   * %? :NOTE:\n%U\n%a\n :clock-in t :clock-resume t)
  (j Journal entry (file+datetree (concat org-directory /
diary.org))
   * %?\n%U\n :clock-in t :clock-resume t)
  (v Vocabulary entry
   (file+headline (concat org-directory /vocab.org)
  Vocabulary)
   * %^{The word} :drill:\n:PROPERTIES:\n:Part-of-speech:
%^{Part of speech|verb|noun|adj|adv}\n:END:\n %t\n %^{Extended word (may be
empty)} \n** Answer \n%^{The definition})
  )))

;; Make use of refTeX in org-mode
(defun org-mode-reftex-setup ()
  Setups RefTeX to be used with a org file. Code is based on
http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/.

Once you run this, you will be asked to set a master file of the org.
  (interactive)
  (load-library reftex)
  (and (buffer-file-name)
   (file-exists-p (buffer-file-name))
   (reftex-parse-all))
  (define-key org-mode-map (kbd C-c )) 'reftex-citation)
  )

;; Open indirect buffer in new frame
(setq org-indirect-buffer-display 'new-frame)

;; Set common TAGS
;; Check:
http://sachachua.com/blog/2008/01/tagging-in-org-plus-bonus-code-for-timeclocks-and-tags/
(setq org-tag-alist '(
  (PRIVATE . ?p)
  (:startgroup . nil)
  (WORK .?w)
  (:grouptags . nil)
  (WORK@mittagseminar . ?m)
  (WORK@open_questions . ?i)
  (WORK@diss . ?d)
  (WORK@CV . nil)
  (:endgroup . nil)
  (:startgroup . nil)
  (IT . ?I)
  (:grouptags . nil)
  (IT@emacs . nil)
  (IT@git . nil)
  (IT@TeX . nil)
  (:endgroup . nil)
  (:startgroup . nil)
  (PROG . ?p)
  (:grouptags . nil)
  (PROG@mathematica . nil)
  (PROG@cgal . nil

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

I am still helpless here. Any idea how to debug the problem? I would be
happy to provide any kind of help, but I just cannot do it myself.

Further findings:
1) I don't think that matplotlib changes Python's '_', since the tmp file
that contains the content of '_' is correct.
2) Somehow, emacs/orgmode fails to extract the filename.
3) It doesn't work also when using emacs 24.5 and orgmode 8.2.10.


Following is an org file that tries to summarize the issue:

#+TITLE: Integrate matplotlib figures in an org mode buffer
* Goal
The ultimate goal is to use org-babel as a replacement of IPython. The
first motivation is to enable an easier version controling of the
document. The first challenge I faced is integration of plots returned
by ~matplotlib~ in the org buffer.
* Capturing filename

I would like to use (babel) orgmode as an interactive python
notebook. Therefore, in order to allow the various code blocks to
know each other, it is important to use the ~:session~
option. However, once ~:session~ is used, together with ~matplotlib~
the desired behavior is no longer in place.

* Clean testing, no Matplotlib
For the sake of testing, the following merely suppose to return the filename

#+BEGIN_SRC python :session no_matplotlib :results file :exports both
x = 'hello '
y = 'world'
z = x + y
'foo.bar'
#+END_SRC

#+RESULTS:
[[file:foo.bar]]

*Passed* Indeed, the ~RESULTS~ block contains a link to the filename
indicated by the last string.

* Importing Matplotlib

The following minimal example should generate a simple figure,
~myfig.png~, and orgmode should capture it and interpret it as a
filename to be used by the following ~RESULTS~ block.

#+BEGIN_SRC python :session with_matplotlib :results file :exports both
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(3,2))
plt.plot([1,3,2])
plt.savefig('myfig.png')
'myfig.png'
#+END_SRC

#+RESULTS:
[[file:]]

*Failed!* This time, it doesn't work anymore. The file ~myfig.png~ is
 properly generated, but the last string is not captured by
 ~matplotlib~. Following is the content of the corresponding
 interactive python session:

#+BEGIN_SRC
Process with_matplotlib finished
Python 3.4.3 (default, Mar 10 2015, 14:53:35)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type help, copyright, credits or license for more information.
   ,
'''/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/py32771xVI''', 'exec'));
import matplotlib
 import matplotlib
matplotlib.use('Agg')
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(3,2))
fig=plt.figure(figsize=(3,2))
plt.plot([1,3,2])
plt.plot([1,3,2])
plt.savefig('myfig.png')
plt.savefig('myfig.png')
'myfig.png'
'myfig.png'


open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-32771x4j/python-32771-fO',
'w').write(str(_))
open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-32771x4j/python-32771-fO',
'w').write(str(_))




'org_babel_python_eoe'
'org_babel_python_eoe'
 [matplotlib.lines.Line2D object at 0x108e01828]
 'myfig.png'
  9
   'org_babel_python_eoe'

#+END_SRC

* Some background

** Python Version
#+BEGIN_SRC python :session background :results raw
import sys
sys.version
#+END_SRC

#+RESULTS:
3.4.3 (default, Mar 10 2015, 14:53:35)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)]

** Matplotlib version
#+BEGIN_SRC python :session background :results raw
import matplotlib
matplotlib.__version__
#+END_SRC

#+RESULTS:
1.4.3

** System
I am running Emacs version ~GNU Emacs 24.5.1 (x86_64-apple-darwin14.1.0, NS
apple-appkit-1344.72) of 2015-04-19 on tenten-slave.macports.org~

The orgmode version is: ~Org-mode version 8.2.10
(8.2.10-40-gc763fa-elpaplus @
/Users/drorata/.emacs.d/elpa/org-plus-contrib-20150518/)~

** Stackoverflow reference
I also posted a question in the SE network:
[[
http://emacs.stackexchange.com/questions/11075/org-mode-python-session-does-not-return-a-file-name
]]

* Question
So, my question is how to tackle/debug this issue? Can someone give me
a hand here? That would be really great! Thanks!

[O] Capturing file name from python session when using matplotlib

[Dror Atariah]

* Capturing filename

I would like to use (babel) orgmode as an interactive python
notebook. Therefore, in order to allow the various code blocks to
know each other, it is important to use the ~:session~
option. However, once ~:session~ is used, together with ~matplotlib~
the desired behavior is no longer in place.

* Clean testing, no Matplotlib
For the sake of testing, the following merely suppose to return the filename

#+BEGIN_SRC python :session no_matplotlib :results file :exports both
x = 'hello '
y = 'world'
z = x + y
'foo.bar'
#+END_SRC

#+RESULTS:
[[file:foo.bar]]

*Passed* Indeed, the ~RESULTS~ block contains a link to the filename
indicated by the last string.

* Importing Matplotlib

The following minimal example should generate a simple figure,
~myfig.png~, and orgmode should capture it and interpret it as a
filename to be used by the following ~RESULTS~ block.

#+BEGIN_SRC python :session with_matplotlib :results file
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(3,2))
plt.plot([1,3,2])
plt.savefig('myfig.png')
'myfig.png'
#+END_SRC

#+RESULTS:
[[file:]]

*Failed!* This time, it doesn't work anymore. The file ~myfig.png~ is
 properly generated, but the last string is not captured by
 ~matplotlib~. Following is the content of the corresponding
 interactive python session:

#+BEGIN_SRC
Python 3.4.3 (default, Feb 27 2015, 00:22:26)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type help, copyright, credits or license for more information.
   ,
'''/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/py27084Z6S''', 'exec'));
import matplotlib
import matplotlib
matplotlib.use('Agg')
 matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(3,2))
fig=plt.figure(figsize=(3,2))
plt.plot([1,3,2])
plt.plot([1,3,2])
plt.savefig('myfig.png')
plt.savefig('myfig.png')
'myfig.png'
'myfig.png'


open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-2708423D/python-27084mEZ',
'w').write(str(_))
open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-2708423D/python-27084mEZ',
'w').write(str(_))




'org_babel_python_eoe'
'org_babel_python_eoe'
[matplotlib.lines.Line2D object at 0x1071d3860]
 'myfig.png'
  9
   'org_babel_python_eoe'

#+END_SRC

* Some background

** Python Version
#+BEGIN_SRC python :session background :results output
import sys
sys.version
#+END_SRC

#+RESULTS:
: import sys
:  sys.version
: '3.4.3 (default, Feb 27 2015, 00:22:26) \n[GCC 4.2.1 Compatible Apple
LLVM 6.0 (clang-600.0.56)]'
: sys.executable
: '/Users/drorata/py-envs/generic3.4/bin/python'
:
:

** System
I am running Emacs version ~GNU Emacs 24.4.51.1 (x86_64-apple-darwin14.1.0,
NS apple-appkit-1344.72) of 2015-02-02 on boxname.local~

The orgmode version is: ~Org-mode version 8.2.10
(8.2.10-40-gc763fa-elpaplus @
/Users/username/.emacs.d/elpa/org-plus-contrib-20150504/)~

** Stackoverflow reference
I also posted a question in the SE network:
[[
http://emacs.stackexchange.com/questions/11075/org-mode-python-session-does-not-return-a-file-name
]]

* Question
So, my question is how to tackle/debug this issue? Can someone give me
a hand here? That would be really great! Thanks!

-- 
Dror Atariah, Ph.D.
de.linkedin.com/in/atariah

Re: [O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

Obviously, I have the directory in place, and the file is actually saved
properly in it. The version is use is:
Org-mode version 8.2.10 (8.2.10-40-gc763fa-elpaplus @
/Users/drorata/.emacs.d/elpa/org-plus-contrib-20150504/)

Finally, here is the output that I have in the python interactive session:

---8---8---8---8---8---8---8---8---8---8---8---8---
 import matplotlib
import matplotlib
 matplotlib.use('Agg')
matplotlib.use('Agg')
import matplotlib.pyplot as plt
 import matplotlib.pyplot as plt
fig=plt.figure(figsize=(3,2))
 fig=plt.figure(figsize=(3,2))
plt.plot([1,3,2])
 plt.plot([1,3,2])
fig.tight_layout()
fig.tight_layout()
plt.savefig('images/myfig.png')
plt.savefig('images/myfig.png')
'images/myfig.png' # return this to org-mode
'images/myfig.png' # return this to org-mode


open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-22151hFS/python-22151B4O',
'w').write(str(_))
open('/var/folders/kz/1c2cxn1x60n_t5p2j1p02b18gn/T/babel-22151hFS/python-22151B4O',
'w').write(str(_))




'org_babel_python_eoe'
'org_babel_python_eoe'
[matplotlib.lines.Line2D object at 0x10ebb6eb8]
 'images/myfig.png'
  16
   'org_babel_python_eoe'

---8---8---8---8---8---8---8---8---8---8---8---8---

From this it seems like the right thing happens, but still org doesn't
manage to capture it. I'm still in the dark. At work I manage to get the
images inserted properly and it is simply fabulous! I want it also on my
mac!!! :)

Thanks in advance,
Dror



On Sat, May 2, 2015 at 7:11 PM, Nick Dokos ndo...@gmail.com wrote:

 Dror Atariah dror...@gmail.com writes:

  How can I solve this problem?

 I should have added: ... after I create the images directory.
 I don't think the savefig() can do that.

[O] [Orgmode] Unable to capture the file name generated using matplotlib

[Dror Atariah]

Consider the following example (from the documentation):

---8---8---8---8---8---8---8---8---8---
#+begin_src python :session :results file
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(3,2))
plt.plot([1,3,2])
fig.tight_layout()
plt.savefig('images/myfig.pdf')
'images/myfig.pdf' # return this to org-mode
#+end_src
---8---8---8---8---8---8---8---8---8---

It should return something like

---8---8---8---8---8---8---8---8---8---
#+RESULTS:
[[file:images/myfig.pdf]]
---8---8---8---8---8---8---8---8---8---

But for me it returns merely

---8---8---8---8---8---8---8---8---8---
#+RESULTS:
[[file:]]
---8---8---8---8---8---8---8---8---8---

That is, it doesn't capture the file name that should be the last
evaluation.

How can I solve this problem?

Re: [O] org-mode and python pandas

[Dror Atariah]

Using the tabulate python module it is possible to have the following
inline workaround:

8888888
#+BEGIN_SRC python :results raw
import pandas as pd
import numpy as np
from tabulate import tabulate

df = pd.DataFrame(np.random.random((4,3)), columns=['A','B','C'])
print(foo)
return(tabulate(df, headers=keys, tablefmt=orgtbl))
#+END_SRC

#+RESULTS:
|   |A |B |C |
|---+--+--+--|
| 0 | 0.754799 | 0.492722 | 0.144595 |
| 1 | 0.198475 | 0.417721 | 0.083459 |
| 2 | 0.645011 | 0.444857 | 0.278874 |
| 3 | 0.314883 |   0.7521 | 0.789418 |
8888888

However, this is not optimal, mainly because it pollutes the code block.
Note, that the :results is set to `raw`.

A brief discussion with Dov, yielded the following better workaround:
8888
888
(setq org-babel-python-wrapper-method 
def main():
%s

res = main()
if 'pandas.core.frame.DataFrame' in str(type(res)):
from tabulate import tabulate
out = tabulate(res, headers='keys', tablefmt='orgtbl')
else:
out = str(res)

open('%s', 'w').write(out))
8888
888

This allows a nice output of pandas.DataFrame (again when using :results
raw). Unfortunately, this wrapper has no influence in the case when
:session is used. To that end, it is possible to hack

8888
888
(defun org-babel-python-evaluate-session
(session body optional result-type result-params)
  Pass BODY to the Python process in SESSION.
If RESULT-TYPE equals 'output then return standard output as a
string.  If RESULT-TYPE equals 'value then return the value of the
last statement in BODY, as elisp.
  (let* ((send-wait (lambda () (comint-send-input nil t) (sleep-for 0 5)))
 (dump-last-value
  (lambda
(tmp-file pp)
(mapc
 (lambda (statement) (insert statement) (funcall send-wait))
 (if pp
 (list
  import pprint
  (format open('%s', 'w').write(pprint.pformat(_))
  (org-babel-process-file-name tmp-file 'noquote)))
   (list (format _org_tmp = _;

if 'pandas.core.frame.DataFrame' in str(type(_org_tmp)):
from tabulate import tabulate
_org_out = tabulate(_org_tmp, headers='keys', tablefmt='orgtbl')
else:
_org_out = _org_tmp

open('%s', 'w').write(str(_org_out))
 (org-babel-process-file-name tmp-file
  'noquote)))
 (input-body (lambda (body)
   (mapc (lambda (line) (insert line) (funcall send-wait))
 (split-string body [\r\n]))
   (funcall send-wait)))
 (results
  (case result-type
(output
 (mapconcat
  #'org-babel-trim
  (butlast
   (org-babel-comint-with-output
   (session org-babel-python-eoe-indicator t body)
 (funcall input-body body)
 (funcall send-wait) (funcall send-wait)
 (insert org-babel-python-eoe-indicator)
 (funcall send-wait))
   2) \n))
(value
 (let ((tmp-file (org-babel-temp-file python-)))
   (org-babel-comint-with-output
   (session org-babel-python-eoe-indicator nil body)
 (let ((comint-process-echoes nil))
   (funcall input-body body)
   (funcall dump-last-value tmp-file
(member pp result-params))
   (funcall send-wait) (funcall send-wait)
   (insert org-babel-python-eoe-indicator)
   (funcall send-wait)))
   (org-babel-eval-read-file tmp-file))
(unless (string= (substring org-babel-python-eoe-indicator 1 -1)
results)
  (org-babel-result-cond result-params
results
(org-babel-python-table-or-string results)
8888
888

This works, but I would be surprised if this hack meets org-mode's
standards. Nevertheless, maybe someone would find it useful.

What do you think? How can it be improved?

Best,
Dror

[O] Scope of properties as variables for babel blocks

[Dror Atariah]

#+title: Scope of properties as variables for babel blocks
* Overview

I have the following scenario in mind: =func1= and =func2= are two
functions that can be executed in two modes: =foo= and =bar=. Each
mode yields a different set of results, that have to be discussed,
separately, in two different subtrees.

The goal is to have one subtree where they are executed in one mode
and a second subtree for the other mode.

The functions are defined in a dedicated [[Code][subtree]].

* Bar setting

Now, I want to execute the function in =bar= mode:
#+PROPERTY:  var mode=bar

#+CALL: func1()

#+RESULTS:
: default

#+CALL: func2()

#+RESULTS:
: default

* Foo setting

In this node I want to execute  the functions in =foo= mode:
#+PROPERTY:  var mode=foo

#+CALL: func1()

#+RESULTS:
: default

#+CALL: func2()

#+RESULTS:
: default

* Code
#+name: func1
#+begin_src python
return mode
#+end_src

#+RESULTS: func1
: foo

#+name: func2
#+begin_src python
return mode
#+end_src

#+RESULTS: func2
: default-val

* Question:

How can I implement this kind of workflow in a reproducible org mode
document?

[O] [babel][table] Passing argument to Python code block using org-sbe

[Dror Atariah]

Consider the following code:

-8--
#+NAME: test
#+BEGIN_SRC python :var x=foobar
return len(x)
#+END_SRC
-8--

It is possible to call this, as follows:

-8--
#+CALL: test(x=fb)
-8--

However, I fail to call this function and pass an argument to it when using
org-sbe:
-8--
| 6 | #ERROR |
#+TBLFM: @1$1='(org-sbe test)::@1$2='(org-sbe test (x (fb)))
-8--

I tried several possibilities, but nothing worked. Is it at all possible?

Thanks in advance,
Dror

PS: I posted also a SE question: http://stackoverflow.com/q/25789183/671013

Re: [O] specifying the coding language resulting from a a :results code source block

[Dror Atariah]

Indeed, this seems to do the trick!
Thanks!

On Thu, Sep 11, 2014 at 8:19 PM, Ista Zahn istaz...@gmail.com wrote:

 Can't you just do

 #+begin_src foo :wrap src bar
hello world
 #+end_src

 ?

 Best,
 Ista


 On Thu, Sep 11, 2014 at 5:11 AM, Dror Atariah dror...@gmail.com wrote:
  Is there some change in the status of this issue? Can one now specify the
  language of the result?
 
  Cheers,
  Dror
 
  --
  Mahalo Tom,
 
  It looks like that's what I'll be doing for the ruby block.  That said,
 it
  would be great if the :results code argument would allow a language
  specification.
 
  Greg
 
 
  On Jun 27, 2012, at 10:22 AM, Thomas S. Dye wrote:
 
  Greg Tucker-Kellogg address@hidden writes:
 
  I have a Ruby block that creates some dot code.  I'd like to be able
  to have the #+RESULTS block enclosed
  in a src block that starts #+BEGIN_SRC dot.  Using :results value
  code generates the enclosing SRC block,
  but using the same language (Ruby) used to generate the code.  Is
  there a way to specify the coding language
  of a generated #+RESULTS  src block?
 
  Thanks,
 
  Greg
 
  Aloha Greg,
 
  This works for me with an emacs-lisp code block named harris-matrix that
  generates dot code.
 
  #+header: :var input=harris-matrix
  #+header: :file temp.pdf
  #+header: :cmdline -Tpdf
  #+header: :results output
  #+BEGIN_SRC dot
  $input
  #+END_SRC
 
  It's not quite what you were after, but it might help?
 
  All the best,
  Tom
 
  --
  Thomas S. Dye
  http://www.tsdye.com

[O] Unable to use org-sbe

[Dror Atariah]

I'm trying to use org-sbe but keep failing... I'm trying to use the example
that can be found in the documentation of ob-table.el and the second column
is filled with #ERROR.

Here is the related output piped to *Messages*:

Re-applying formulas to full table...(line 10)
Re-applying formulas to 10 lines...done
Re-applying formulas...done [2 times]


I would be happy to provide further information, if only I'd know where to
look for it.

Org version:
Org-mode version 8.2.7c (8.2.7c-61-g4b9146-elpaplus @
/my/path/.emacs.d/elpa/org-plus-contrib-20140908/)

Thanks in advance,
Dror

Re: [O] specifying the coding language resulting from a a :results code source block

[Dror Atariah]

Is there some change in the status of this issue? Can one now specify the
language of the result?

Cheers,
Dror

--
Mahalo Tom,

It looks like that's what I'll be doing for the ruby block.  That said, it
would be great if the :results code argument would allow a language
specification.

Greg


On Jun 27, 2012, at 10:22 AM, Thomas S. Dye wrote:

 Greg Tucker-Kellogg address@hidden writes:

 I have a Ruby block that creates some dot code.  I'd like to be able
 to have the #+RESULTS block enclosed
 in a src block that starts #+BEGIN_SRC dot.  Using :results value
 code generates the enclosing SRC block,
 but using the same language (Ruby) used to generate the code.  Is
 there a way to specify the coding language
 of a generated #+RESULTS  src block?

 Thanks,

 Greg

 Aloha Greg,

 This works for me with an emacs-lisp code block named harris-matrix that
 generates dot code.

 #+header: :var input=harris-matrix
 #+header: :file temp.pdf
 #+header: :cmdline -Tpdf
 #+header: :results output
 #+BEGIN_SRC dot
 $input
 #+END_SRC

 It's not quite what you were after, but it might help?

 All the best,
 Tom

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

Re: [O] Google + org-mode agenda? can it be done?

[Dror Atariah]

It seems like the function org-export-icalendar-combine-agenda-files (as 
discussed in the first link provided by @Matt) has to be replace with 
org-icalendar-combine-agenda-files when working with a new version of org. Am 
I right?

Cheers,
Dror
On Mar 5, 2014, at 22:50 PM, Matt Lundin wrote:

 Sharon Kimble boudic...@talktalk.net writes:
 
 Can the google calendar work with org-mode agenda please? I haven't
 seen any indication that it can be done when I've been googling around.
 But I thought that I would ask anyway. 
 
 Synchronization is not seamless, but it can be accomplished with some
 setup. See:
 
 http://orgmode.org/worg/org-tutorials/org-google-sync.html
 
 And on the same tack, can google tasks work with org-modes TODO lists
 please?
 
 This tool does bi-directional synchronization (org-files - google
 tasks). Note: it synchronizes files, not the agenda's todo list.
 
 https://bitbucket.org/edgimar/michel-orgmode
 
 Matt

[O] [BUG] Problem with org-mobile.el

[Dror Atariah]

In the past (http://article.gmane.org/gmane.emacs.orgmode/79803/) I had a 
problem with pushing using org-mobile, and it was solved as detailed in 
(http://thread.gmane.org/gmane.emacs.orgmode/79856/focus=79876). Indeed now the 
patch can be found in ELPA, but it still introduces the same problem as 
reported above. 

My setting is:
Emacs  : GNU Emacs 24.3.1 (x86_64-apple-darwin, NS apple-appkit-1038.36)
 of 2013-03-13 on bob.porkrind.org
Package: Org-mode version 8.2.4 (8.2.4-3-g7fe99a-elpa @ 
/Users/drorata/.emacs.d/elpa/org-plus-contrib-20140217/)

Line #463 in org-mobile.el is:
((eq (car x) :grouptags) nil)

which should be the fix. I could fix the issue by moving this line after the 
following one, have:

((eq (car x) :newline) nil)
((eq (car x) :grouptags) nil)

for lines #463-464 instead of 

((eq (car x) :grouptags) nil)
((eq (car x) :newline) nil)

which is the current state.

Can someone verify this?

Best,
Dror

Re: [O] Unable to push to org-mobile

[Dror Atariah]

I'm sorry I keep bugging with this... ;)

On Dec 14, 2013, at 22:06 PM, Nick Dokos wrote:

 Nick Dokos ndo...@gmail.com writes:
 
 Dror Atariah dror...@gmail.com writes:
 
 2. What's next? I believe this is a bug... How can I report it?
 
 Consider it reported - thanks for checking it. I'll push the proposed fix 
 later
 on today. If it is wrong, we can revert it later, but at least for now
 it seems to fix the bug.
 
 
 I pushed the patch.

I believe that the patch is wrong. The line
((eq (car x) :grouptags) nil) is currently (as per the version of ELPA) #463, 
but it yields the same error as the one I reported initially. I moved it to 
line #464 (right after the one with :newline) and it solved the issue. 

1. Does it make sense?
2. If it does, then why?
3. Maybe you want to correct this?

All the best and cheers,
Dror

Re: [O] Unable to push to org-mobile

[Dror Atariah]

On Dec 15, 2013, at 15:17 PM, Nick Dokos wrote:

 Dror Atariah dror...@gmail.com writes:
 
 On Dec 14, 2013, at 22:06 PM, Nick Dokos wrote:
 
 Nick Dokos ndo...@gmail.com writes:
 
 Dror Atariah dror...@gmail.com writes:
 
 2. What's next? I believe this is a bug... How can I report it?
 
 Consider it reported - thanks for checking it. I'll push the proposed fix 
 later
 on today. If it is wrong, we can revert it later, but at least for now
 it seems to fix the bug.
 
 
 I pushed the patch.
 
 Does it mean that I could update the installation through ELPA tomorrow and 
 the patch will be there?
 
 I don't think so - I pushed the patch to the master branch of the git
 repo. But I'm not clear on what happens next, so somebody else will have
 to answer your question.
Update: I have just updated from ELPA, and the patch is not there... I had to 
re-patch the missing line.

Best,
Dror

Re: [O] Unable to push to org-mobile

[Dror Atariah]

On Jan 12, 2014, at 13:53 PM, Bastien wrote:

 Dror Atariah dror...@gmail.com writes:
 
 Update: I have just updated from ELPA, and the patch is not
 there... I had to re-patch the missing line.
 
 The ELPA packages are built from the maint branch, from the
 master branch, so patches in the master branch do not show up
 there, that's why you had to re-patch this.
So what's the point of the daily updates of the ELPA packages?

Best,
Dror

Re: [O] Unable to push to org-mobile

[Dror Atariah]

On Jan 12, 2014, at 14:26 PM, Bastien wrote:

 Hi Dror,
 
 Dror Atariah dror...@gmail.com writes:
 
 So what's the point of the daily updates of the ELPA packages?
 
 To get bug fixed when you use ELPA.

Wasn't the issue discussed originally in this thread a bug (and its fix)? Why 
it is not reflected in the ELPA? I just want to understand what's going on... 
No criticism or anything like that :)

Best,
Dror

Re: [O] Unable to push to org-mobile

[Dror Atariah]

On Dec 13, 2013, at 23:08 PM, Nick Dokos wrote:

 Dror Atariah dror...@gmail.com writes:
 
 Managed to get [backtrace] output... 
 
 You can find it here: https://gist.github.com/drorata/7950857
 
 I could not find my way in this output... :(
 
 
 If you look at the top of the backtrace it shows this:
 
 ,
 | Debugger entered--Lisp error: (wrong-type-argument sequencep :grouptags)
 | mapconcat(identity (PRIVATE { WORK :grouptags WORK@mittagseminar 
 WORK@open_questions WORK@diss WORK@CV } { IT :grouptags 
 IT@emacs IT@git IT@TeX } { PROG :grouptags PROG@mathematica 
 PROG@cgal } } 4freeTime bms_friday emacs interesting_questions 
 mittagseminar Mittagsseminar NOTE private results work Yvinec 
 Ziegler)  )
 | (insert #+TAGS:  (mapconcat (quote identity) tags  ) \n)
 | ...
 | org-mobile-create-index-file()
 `
 
 The mapconcat line can be evaluated on its own - it does not depend on
 anything else. If you cut and paste it into your *scratch* buffer and
 modify it slightly like this:
 
 --8---cut here---start-8---
 (mapconcat 'identity '(PRIVATE { WORK :grouptags WORK@mittagseminar 
 WORK@open_questions WORK@diss WORK@CV } { IT :grouptags 
 IT@emacs IT@git IT@TeX } { PROG :grouptags PROG@mathematica 
 PROG@cgal } } 4freeTime bms_friday emacs interesting_questions 
 mittagseminar Mittagsseminar NOTE private results work Yvinec 
 Ziegler)  )
 --8---cut here---end---8---
 
 and evaluate it with C-j, you get the exact error. Now look in
 org-mobile-create-index-file for the call
 
 
 (insert #+TAGS:  (mapconcat 'identity tags  ) \n)
 
 You'll find it on line 470 (at least in the version I'm using).
 Before this line there is this code:
 
 ...
 (setq def-tags (mapcar
 (lambda (x)
   (cond ((null x) nil)
 ((stringp x) x)
 ((eq (car x) :startgroup) {)
 ((eq (car x) :endgroup) })
 ((eq (car x) :newline) nil)
 ((listp x) (car x
 def-tags))
 (setq def-tags (delq nil def-tags))
 (setq tags (org-delete-all def-tags tags))
 (setq tags (sort tags (lambda (a b) (string (downcase a) (downcase b)
 (setq tags (append def-tags tags nil))
 (insert #+TAGS:  (mapconcat 'identity tags  ) \n)
 ...
 
 You'll notice that :startgroup is replaced by { , :endgroup is
 replaced by } and :newline is deleted - but there is no mention of
 :grouptags which leads me to suspect that there should be an extra
 line in there, perhaps
 
 ((eq (car x) :grouptags) nil)
 
 Maybe you can try it - better yet, maybe somebody who has some idea of
 how org-mobile works should take a look. I note that if I delete the
 :grouptags instances in the mapconcat call above, it completes without
 error.
Bingo! Adding this line allowed me to complete org-mobile-push successfully! 
Amazing. I have three closing questions:

1. What made you look into lines #460-464? Now when you pointed, it is somehow 
straightforward to check line #470, but there seems to be no indication 
regarding the broken code.
2. What's next? I believe this is a bug... How can I report it?
3. Finally, in the meanwhile, till the bug-fix is out, what is the best 
practice to maintain this patch locally?

Thanks a lot for your hand It was great having it!
Dror
 
 Nick

Re: [O] Unable to push to org-mobile

[Dror Atariah]

On Dec 14, 2013, at 22:06 PM, Nick Dokos wrote:

 Nick Dokos ndo...@gmail.com writes:
 
 Dror Atariah dror...@gmail.com writes:
 
 2. What's next? I believe this is a bug... How can I report it?
 
 Consider it reported - thanks for checking it. I'll push the proposed fix 
 later
 on today. If it is wrong, we can revert it later, but at least for now
 it seems to fix the bug.
 
 
 I pushed the patch.

Does it mean that I could update the installation through ELPA tomorrow and the 
patch will be there?

Thanks for your help!
Dror

[O] Unable to push to org-mobile

[Dror Atariah]

Today I realized that I cannot execute successfully 'org-mobile-push'. In 
particular here is the output from '*Messages*':

Creating agendas...
Agenda written to Org file /Users/drorata/Dropbox/MobileOrg/agendas.org
Creating agendas...done
Saving all Org-mode buffers...
(No files need saving)
Saving all Org-mode buffers... done
Copying files...
Writing index file...
org-mobile-create-index-file: Wrong type argument: sequencep, :grouptags

I first step I took was to update the package; now 'org-version' yields 
Org-mode version 8.2.4 (8.2.4-3-g7fe99a-elpa @ 
/Users/user/.emacs.d/elpa/org-plus-contrib-20131209/). However, problem is 
still here.

Next I don't really know what to do... I have all my emacs' settings in 
https://github.com/drorata/emacs_setup

How can I debug this problem and solve it?

Re: [O] Unable to push to org-mobile

[Dror Atariah]

On Dec 13, 2013, at 16:08 PM, Nick Dokos wrote:

 Dror Atariah dror...@gmail.com writes:
 
 Today I realized that I cannot execute successfully 'org-mobile-push'. In 
 particular here is the output from '*Messages*':
 
 Creating agendas...
 Agenda written to Org file /Users/drorata/Dropbox/MobileOrg/agendas.org
 Creating agendas...done
 Saving all Org-mode buffers...
 (No files need saving)
 Saving all Org-mode buffers... done
 Copying files...
 Writing index file...
 org-mobile-create-index-file: Wrong type argument: sequencep, :grouptags
 
 I first step I took was to update the package; now 'org-version' yields 
 Org-mode version 8.2.4 (8.2.4-3-g7fe99a-elpa @ 
 /Users/user/.emacs.d/elpa/org-plus-contrib-20131209/). However, problem is 
 still
 here.
 
 Next I don't really know what to do... I have all my emacs' settings in 
 https://github.com/drorata/emacs_setup
 
 How can I debug this problem and solve it?
 
 In the same way that you debug all such problems: toggle debug-on-error,
 try to do org-mobile-push again and look at the resulting backtrace (or
 post it so others can look at it).
I evaluated (setq debug-on-error t), and then executed org-mobile-push again. 
There was no output in the *Backtrace* buffer 

 A shot in the dark: what's the value of org-tag-alist?
The value of org-tag-alist is:

((PRIVATE . 112)
 (:startgroup)
 (WORK . 119)
 (:grouptags)
 (WORK@mittagseminar . 109)
 (WORK@open_questions . 105)
 (WORK@diss . 100)
 (WORK@CV)
 (:endgroup \.nil)
 (:startgroup)
 (IT . 73)
 (:grouptags)
 (IT@emacs)
 (IT@git)
 (IT@TeX)
 (:endgroup)
 (:startgroup)
 (PROG . 112)
 (:grouptags)
 (PROG@mathematica)
 (PROG@cgal)
 (:endgroup)
 (:endgroup)
 (4freeTime . 52))

What should be the next step?

Thanks in advance!
Dror

Re: [O] Unable to push to org-mobile

[Dror Atariah]

On Dec 13, 2013, at 20:51 PM, Nick Dokos wrote:

 Dror Atariah dror...@gmail.com writes:
 
 On Dec 13, 2013, at 16:08 PM, Nick Dokos wrote:
 
 Dror Atariah dror...@gmail.com writes:
 
 Today I realized that I cannot execute successfully 'org-mobile-push'. In 
 particular here is the output from '*Messages*':
 
 Creating agendas...
 Agenda written to Org file /Users/drorata/Dropbox/MobileOrg/agendas.org
 Creating agendas...done
 Saving all Org-mode buffers...
 (No files need saving)
 Saving all Org-mode buffers... done
 Copying files...
 Writing index file...
 org-mobile-create-index-file: Wrong type argument: sequencep, :grouptags
 
 I first step I took was to update the package; now 'org-version' yields 
 Org-mode version 8.2.4 (8.2.4-3-g7fe99a-elpa @
 /Users/user/.emacs.d/elpa/org-plus-contrib-20131209/). However,
 problem is still
 here.
 
 Next I don't really know what to do... I have all my emacs' settings in 
 https://github.com/drorata/emacs_setup
 
 How can I debug this problem and solve it?
 
 In the same way that you debug all such problems: toggle debug-on-error,
 try to do org-mobile-push again and look at the resulting backtrace (or
 post it so others can look at it).
 I evaluated (setq debug-on-error t), and then executed org-mobile-push 
 again. There was no output in the *Backtrace* buffer 
 
 
 Try deleting the org-mobile.elc file and reloading org-mobile.el. Then
 try evaluating
 
 (let ((debug-on-error t))
  (org-mobile-push))
 
 and see if that gives you a backtrace.

Managed to get output... 

You can find it here: https://gist.github.com/drorata/7950857

I could not find my way in this output... :(

 A shot in the dark: what's the value of org-tag-alist?
 The value of org-tag-alist is:
 
 ((PRIVATE . 112)
 (:startgroup)
 (WORK . 119)
 (:grouptags)
 (WORK@mittagseminar . 109)
 (WORK@open_questions . 105)
 (WORK@diss . 100)
 (WORK@CV)
 (:endgroup \.nil)
  ^
 This looks strange to me, although it's not clear it would cause the
 problem even if it is wrong (which it may or may not be).
Indeed strange, and probably a typo. There was a missing space. I corrected 
this before taking the measures you mentioned above.
 
 Nick
 

Best,
Dror

[O] Line breaks in org-mode having version control in mind

[Dror Atariah]

I am trying to extend my usage of org, and one of the things I want to 
integrate is version controlling of my org files. This is obviously straight 
forward, but I am wondering about the best line breaking approach to use. In my 
LaTeX docs I maintain one physical line per sentence [1]. This way, when I 
change one word in a paragraph, it affects only one line, and looking for 
differences between versions is easy. Otherwise, when using fill-paragraph for 
instance, one gets messy changes of the file, as the one word change can 
influence the whole paragraph.

Therefore, as I mentioned, in LaTeX I use visual-line-mode and I insert 
manually line breaks at the end of sentences (or where *I* find appropriate). 
What would be the best practice for org? I understand that visual-line-mode has 
some problems when it comes to tables... What other issues are there? What do 
you do when you keep your org file under VC? 

Thanks in advance,
Dror

[1] http://tex.stackexchange.com/a/4378/412

Re: [O] Markup (blod for instance) over line breaks

[Dror Atariah]

On Oct 13, 2013, at 22:22 PM, Marcin Borkowski wrote:

 Dnia 2013-10-13, o godz. 21:58:20
 Dror Atariah dror...@gmail.com napisał(a):
 
 
 On Oct 13, 2013, at 21:38 PM, Marcin Borkowski wrote:
 
 Dnia 2013-10-13, o godz. 20:49:30
 Dror Atariah dror...@gmail.com napisał(a):
 
 Dear org-moders,
 
 It might be terribly simple, but I failed to find a solution. How
 can I mark several words as bold (or emphasized or any similar
 markup), in particular if the words spans over *more then one
 line*?
 
 A similar problem can occur when one is pasting a long line into an
 org-mode buffer and then, after it is being broken into shorter
 lines, you try to make it bold.
 
 The documentation
 (http://orgmode.org/org.html#Emphasis-and-monospace) states that
 this kind of markup is aimed at words - so it might not support
 sentences and in particular long ones... Is it correct?
 
 Not really an answer, but does visual-line-mode help in your use
 case?
 It does help. Doesn't org-mode has some sort of dedicated
 line-breaking mechanism? How would you turn it into a complete
 solution?
 
 Not that I know of.  Basically, lines may be /visual/ (i.e., broken by
 the display engine at spaces etc., but the whole paragraph is one long
 line in the file) or /physical/ (i.e., with newline characters at the
 end of each line).  In Emacs, you an use M-q to fill a paragraph
 (more or less, convert from visual to physical lines), and something
 along the lines of C-u 9 9 9 9 9 C-x f M-q to unfill a paragraph.
 (There are also unfill functions (quod google), though they are not
 part of stock Emacs.)
 
 There is an ongoing discussion on which is better, too long to repeat
 any of the arguments here.  For a LaTeX-centric approach, see e.g.
 http://tex.stackexchange.com/questions/4376/good-strategy-for-line-breaks-with-paragraphs-of-latex-source
 (note that Emacs's longline-mode was a predecessor of visual-line-mode).
In this case I suppose I will revert to visual-line-mode, just like I have in 
my LaTeX buffers. 

 And indeed, bold/italic spanning more than a few words might not be a
 good idea.  And in cases it is, it's problably better to define a
 specialized environment (in LaTeX lingo) - like one for theorems
 (which are often typeset in italics).
What is the org-mode's equivalent of LaTeX's environment? That COULD be very 
helpful.

Thanks,
Dror

Re: [O] Markup (blod for instance) over line breaks

[Dror Atariah]

On Oct 14, 2013, at 07:11 AM, Eric Abrahamsen wrote:

 Dror Atariah dror...@gmail.com writes:
 
 Dear org-moders,
 
 It might be terribly simple, but I failed to find a solution. How can
 I mark several words as bold (or emphasized or any similar markup),
 in particular if the words spans over *more then one line*?
 
 A similar problem can occur when one is pasting a long line into an
 org-mode buffer and then, after it is being broken into shorter
 lines, you try to make it bold.
 
 The documentation (http://orgmode.org/org.html#Emphasis-and-monospace
 ) states that this kind of markup is aimed at words - so it might not
 support sentences and in particula r long ones... Is it correct?
 
 Thanks in advance,
 Dror
 
 I use autofill mode, and then change the value of
 `org-emphasis-regexp-components'. That variable is a list, the fifth
 element of which says how many newlines the emphasis markers will allow.
 I set it to three:
 
 (setf (nth 4 org-emphasis-regexp-components) 3)
Thanks for the tip. It somehow didn't help. I did M-x org-reload after 
setting this, but it didn't help spanning the italic in my case over several 
lines.


Cheers,
Dror

[O] Markup (blod for instance) over line breaks

[Dror Atariah]

Dear org-moders,

It might be terribly simple, but I failed to find a solution. How can I mark 
several words as bold (or emphasized or any similar markup), in particular if 
the words spans over *more then one line*?

A similar problem can occur when one is pasting a long line into an org-mode 
buffer and then, after it is being broken into shorter lines, you try to make 
it bold.

The documentation (http://orgmode.org/org.html#Emphasis-and-monospace) states 
that this kind of markup is aimed at words - so it might not support sentences 
and in particular long ones... Is it correct?

Thanks in advance,
Dror

Re: [O] Markup (blod for instance) over line breaks

[Dror Atariah]

On Oct 13, 2013, at 21:38 PM, Marcin Borkowski wrote:

 Dnia 2013-10-13, o godz. 20:49:30
 Dror Atariah dror...@gmail.com napisał(a):
 
 Dear org-moders,
 
 It might be terribly simple, but I failed to find a solution. How can
 I mark several words as bold (or emphasized or any similar markup),
 in particular if the words spans over *more then one line*?
 
 A similar problem can occur when one is pasting a long line into an
 org-mode buffer and then, after it is being broken into shorter
 lines, you try to make it bold.
 
 The documentation
 (http://orgmode.org/org.html#Emphasis-and-monospace) states that this
 kind of markup is aimed at words - so it might not support sentences
 and in particular long ones... Is it correct?
 
 Not really an answer, but does visual-line-mode help in your use case?
It does help. Doesn't org-mode has some sort of dedicated line-breaking 
mechanism? How would you turn it into a complete solution?

Best,
Dror

Re: [O] Unable to finalize capture

[Dror Atariah]

On Oct 4, 2013, at 23:04 PM, Nick Dokos wrote:

 Dror Atariah dror...@gmail.com writes:
 
 M-x locate-library RET org RET
 Returns:
 Library is file ~/.emacs.d/elpa/org-plus-contrib-20130930/org.elc
 
 N.B. Never used elpa, so take with appropriately sized grain of salt.
 
 Not sure whether this is a problem, but why is org.elc in the main
 directory and not under
 
 ~/.emacs.d/elpa/org-plus-contrib-20130930/org/lisp?
 
 Maybe you are using a left-over org.elc?

Probably, this is somehow the case... I think the directory structure that you 
can see is the default one of ELPA - I don't think I tweaked it.


 and
 
 M-x list-load-path-shadows RET
 Returns (I hope I collected only the relevant entries):
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
 /Users/user_name/.emacs.d/elpa/org-20130930/org
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
 /Users/user_name/.emacs.d/elpa/org-20130812/org
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
 /Users/user_name/.emacs.d/elpa/org-20130923/org
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130812/org
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130923/org
 /Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
 /Applications/Emacs.app/Contents/Resources/lisp/org/org
 
 I guess that the above output suggests that org-mode is properly installed 
 (via ELPA), isn't it? I'm afraid that I am not hinted by this output.
 
 
 Check that your org.el does include the definition  of the variable.
 Then load the uncompiled version using an explicit path:
The file ~/.emacs.d/elpa/org-plus-contrib-20130930/org.el contains the 
definition of the variable org-bookmark-names-plist

 M-x load-file RET /Users/user_name/.emacsd./elpa//org/lisp/org.el RET
 
 *Now* is the variable defined? If so, does capture work?
Indeed, loading it manually, solved the problem.

 I'd probably clean up the .elc files and compile anew. Then restart
 emacs.
I didn't know how to recompile the files, and what exactly do you mean by 
cleaning the .elc's; so I did something else. I removed the old directories of 
org-mode from the ELPA directory, restarted emacs and it  now seems to work 
fine.

Thanks and all the best,
Dror

[O] Unable to finalize capture

[Dror Atariah]

It seems like after the last update I've made to org-mode the capturing of 
notes does not work properly. Currently I have version 8.0.7 (20130930) from 
the ELPA. Hitting C-c c (i.e. org-capture) brings the list of capture templates 
and then I can choose one of them to open a buffer where I can actually entry 
the note. The problem is that once I'm done, hitting C-c C-c doesn't close the 
capturing buffer. The content is saved in the right place but I'm not returned 
to the place where I started the capturing. In the *Messages* buffer I get the 
following error: org-capture-finalize: Symbol's value as variable is void: 
org-bookmark-names-plist

I don't really know where to start debugging this problem. Any ideas?

I believe the following are all the related setting that I have:

;; Capture-org
(setq org-default-notes-file (concat org-directory /notes.org))
(define-key global-map \C-cc 'org-capture)

(setq org-capture-templates
  (quote ((t todo entry (file (concat org-directory /gtd.org))
   * TODO %?\n%U\n%a\n :clock-in t :clock-resume t)
  (n note entry (file (concat org-directory /gtd.org))
   * %? :NOTE:\n%U\n%a\n :clock-in t :clock-resume t)
  (j Journal entry (file+datetree (concat org-directory 
/diary.org))
   * %?\n%U\n :clock-in t :clock-resume t)
  (v Vocabulary entry
   (file+headline (concat org-directory /vocab.org)
  Vocabulary)
   * %^{The word} :drill:\n:PROPERTIES:\n:Part-of-speech: %^{Part 
of speech|verb|noun|adj|adv}\n:END:\n %t\n %^{Extended word (may be empty)} 
\n** Answer \n%^{The definition})
  )))

[O] Unable to finalize a capture

[Dror Atariah]

It seems like after the last update I've made to org-mode the capturing of 
notes does not work properly. Currently I have version 8.0.7 (20130930) from 
the ELPA. 

Hitting `C-c c` (i.e. org-capture) brings the list of capture templates and 
then I can choose one of them to open a buffer where I can actually entry the 
note. The problem is that once I'm done, hitting `C-c C-c` doesn't close the 
capturing buffer. The content is saved in the right place but I'm not returned 
to the place where I started the capturing. In the *Messages* buffer I get the 
following error: 
org-capture-finalize: Symbol's value as variable is void: 
org-bookmark-names-plist

I don't really know where to start debugging this problem. Any ideas?

I believe the following are all the related setting that I have:

;; Capture-org
(setq org-default-notes-file (concat org-directory /notes.org))
(define-key global-map \C-cc 'org-capture)

(setq org-capture-templates
 (quote ((t todo entry (file (concat org-directory /gtd.org))
  * TODO %?\n%U\n%a\n :clock-in t :clock-resume t)
 (n note entry (file (concat org-directory /gtd.org))
  * %? :NOTE:\n%U\n%a\n :clock-in t :clock-resume t)
 (j Journal entry (file+datetree (concat org-directory 
/diary.org))
  * %?\n%U\n :clock-in t :clock-resume t)
 (v Vocabulary entry
  (file+headline (concat org-directory /vocab.org)
 Vocabulary)
  * %^{The word} :drill:\n:PROPERTIES:\n:Part-of-speech: %^{Part 
of speech|verb|noun|adj|adv}\n:END:\n %t\n %^{Extended word (may be empty)} 
\n** Answer \n%^{The definition})
 )))

Re: [O] Unable to finalize capture

[Dror Atariah]

On Oct 4, 2013, at 14:56 PM, Nick Dokos wrote:

 Dror Atariah dror...@gmail.com writes:
 
 It seems like after the last update I've made to org-mode the
 capturing of notes does not work properly. Currently I have version
 8.0.7 (20130930) from the ELPA. Hitting C-c c (i.e. org-capture)
 brings the list of capture templates and then I can choose one of them
 to open a buffer where I can actually entry the note. The problem is
 that once I'm done, hitting C-c C-c doesn't close the capturing
 buffer. The content is saved in the right place but I'm not returned
 to the place where I started the capturing. In the *Messages* buffer I
 get the following error: org-capture-finalize: Symbol's value as
 variable is void: org-bookmark-names-plist
 
 
 org-bookmark-names-plist is defined in org.el. Try evaluating
 
 (require 'org)
This evaluation can be found in my init file. I can evaluate this manually 
without any problem. 

 and seeing if the variable is now defined:
 
 C-h v org-bookmark-names-plist RET
The variable is not defined. Thus, I guess I'm facing the following case in 
your answer:

 If the variable is not defined, check whether you have some old
 obsolete org.el lying around:
 
 M-x locate-library RET org RET
Returns:
Library is file ~/.emacs.d/elpa/org-plus-contrib-20130930/org.elc

 and
 
 M-x list-load-path-shadows RET
Returns (I hope I collected only the relevant entries):
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
/Users/user_name/.emacs.d/elpa/org-20130930/org
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
/Users/user_name/.emacs.d/elpa/org-20130812/org
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
/Users/user_name/.emacs.d/elpa/org-20130923/org
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130812/org
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130923/org
/Users/user_name/.emacs.d/elpa/org-plus-contrib-20130930/org hides 
/Applications/Emacs.app/Contents/Resources/lisp/org/org

I guess that the above output suggests that org-mode is properly installed (via 
ELPA), isn't it? I'm afraid that I am not hinted by this output.

What further steps can I take?

[O] Changing packages and their order in LaTeX export

[Dror Atariah]

I need to include 'amsmath' package in my LaTeX export. Using #+LATEX_HEADER: 
\usepackage{xyz} adds it at the end of the list, and then there are LaTeX 
related problems.

I tried to find where the default list is defined - it seems like it is in 
org.el. However, I have several copies of this file, and I don't know which one 
is the right one to change.

So, two questions:
1. Should I change the org.el or is it somewhere else?
2. If it is the org.el, then how can I tell which file is the one which is 
used? Should I restart emacs after each edit of this file for the changes to 
take effect?

Thanks!
Dror Atariah

Re: [O] Changing packages and their order in LaTeX export

[Dror Atariah]

 I need to include 'amsmath' package in my LaTeX export. Using
 #+LATEX_HEADER: \usepackage{xyz} adds it at the end of the list, and
 then there are LaTeX related problems.
 I tried to find where the default list is defined - it seems like it
 is in org.el. However, I have several copies of this file, and I don't
 know which one is the right one to change.
 
 Does M-x customize-group RET org-export-latex RET show something that
 could be of interest to you.
This worked for me! Where did you find it in the manual? I looked there. 
Sometimes the manual's instructions are too cryptic for me - in the sense that 
I find the variable name, but I don't know how to change it.
 
 As a user, in principle, you should refuse to look at elisp files. But
 it's a very good idea to look at the manuals though.
Thanks for the tip!

 2. If it is the org.el, then how can I tell which file is the one
 which is used? Should I restart emacs after each edit of this file for
 the changes to take effect?
Can you still answer this question? How can I ask emacs to tell me where is the 
file it is using and should I restart after each such change?

Thanks,
Dror

[O] Changing the font family in HTML export

[Dror Atariah]

Dear org mode users,

I'm trying to change the font used when exporting .org to .html. At the moment, 
I get 

style type=text/css
 !--/*--![CDATA[/*!--*/
  html { font-family: Times, serif; font-size: 12pt; }

In the generated .html file. I would like to control this part, namely, I would 
like to have for example:

style type=text/css
 !--/*--![CDATA[/*!--*/
  html { font-family: Helvatica, sans-serif; font-size: 12pt; }

Instead. I found several hints, but my emacs skill failed me, and I couldn't 
find a solution.

Can you help me? Thanks in advance,
Dror

Re: [O] Changing the font family in HTML export

[Dror Atariah]

This solved the problem. However, as you pointed out, in case I want to 
publish/share this generated html, I have to send as well another file, and it 
is not longer self contained. In the automatically, generated html, there is a 
section at the beginning:
--==--
style type=text/css
 !--/*--![CDATA[/*!--*/
  html { font-family: Times, serif; font-size: 12pt; }
  .title  { text-align: center; }
  .todo   { color: red; }
  .done   { color: green; }
  .tag{ background-color: #add8e6; font-weight:normal }
...
--==--

Isn't there a way to tell orgmode to change this part, and, for example, use a 
different font?

On Jun 28, 2011, at 10:42 AM, Manuel Giraud wrote:

 Dror Atariah dror...@gmail.com writes:
 
 Thanks for the quick answer!
 I think you could use an external css file for that. You can do so by
 setting the STYLE property in you org file like that:
 
 --8---cut here---start-8---
 #+TITLE: My page
 #+STYLE: link rel=stylesheet href=my_own.css type=text/css/
 
 * My first title
 --8---cut here---end---8---
 This means that I have to generate and put my_own.css file in the
 right place. 
 
 Yes. But I don't know how you publish things after having generated the
 html. You may just have to copy this file in the right place once.
 
 
 What should this file contain? 
 
 It's a css file it could contain many things (see
 http://www.w3schools.com/css/ for good tutorials and test). But in your
 case this will do the trick:
 
 --8---cut here---start-8---
 html { font-family: Helvetica, sans-serif; font-size: 12pt; }
 --8---cut here---end---8---
 
 
 I'm happy with the formatting of the exported html, I only want to
 change the font. Is this still the right approach?
 
 I still think it is the best option because one day you'd like to change
 the color of h1's title and this approach still stand (in fact that's
 what css are for).
 
 Best regards,
 -- 
 Manuel Giraud

Dror Atariah
---
Landline:+49-30-43024501
Mobile: +49-176-67116376
Mobile (in IL): +972 54 5912389
IM:   dror...@gmail.com
   dror...@hotmail.com

Re: [O] Changing the font family in HTML export

[Dror Atariah]

On Jun 28, 2011, at 14:10 PM, Christian Moe wrote:

 Hi,
 
 The tips you have received from others about customizing various variables 
 are likely to be what you want (will work for all your documents). But for 
 completeness' sake: to change things on a file-by-file basis, you can do it 
 Manuel's way, but without an external stylesheet, like this:
 
 #+STYLE:stylehtml { font-family: Helvetica, sans-serif; font-size: 12pt; 
 }/style
 
 Your custom CSS is included in the HEAD of the generated document, after the 
 default CSS, which it overrides.
This was most helpful actually! Thanks!
 
 Yours,
 Christian
 
 On 6/28/11 11:00 AM, Dror Atariah wrote:
 This solved the problem. However, as you pointed out, in case I want to 
 publish/share this generated html, I have to send as well another file, and 
 it is not longer self contained. In the automatically, generated html, there 
 is a section at the beginning:
 --==--
 style type=text/css
  !--/*--![CDATA[/*!--*/
   html { font-family: Times, serif; font-size: 12pt; }
   .title  { text-align: center; }
   .todo   { color: red; }
   .done   { color: green; }
   .tag{ background-color: #add8e6; font-weight:normal }
 ...
 --==--
 
 Isn't there a way to tell orgmode to change this part, and, for example, use 
 a different font?
 
 On Jun 28, 2011, at 10:42 AM, Manuel Giraud wrote:
 
 Dror Atariahdror...@gmail.com  writes:
 
 Thanks for the quick answer!
 I think you could use an external css file for that. You can do so by
 setting the STYLE property in you org file like that:
 
 --8---cut here---start-8---
 #+TITLE: My page
 #+STYLE:link rel=stylesheet href=my_own.css type=text/css/
 
 * My first title
 --8---cut here---end---8---
 This means that I have to generate and put my_own.css file in the
 right place.
 
 Yes. But I don't know how you publish things after having generated the
 html. You may just have to copy this file in the right place once.
 
 
 What should this file contain?
 
 It's a css file it could contain many things (see
 http://www.w3schools.com/css/ for good tutorials and test). But in your
 case this will do the trick:
 
 --8---cut here---start-8---
 html { font-family: Helvetica, sans-serif; font-size: 12pt; }
 --8---cut here---end---8---
 
 
 I'm happy with the formatting of the exported html, I only want to
 change the font. Is this still the right approach?
 
 I still think it is the best option because one day you'd like to change
 the color of h1's title and this approach still stand (in fact that's
 what css are for).
 
 Best regards,
 --
 Manuel Giraud

[O] Re: Update org-mode

[Dror Atariah]

Let me summarize the steps I carried out eventually, to use the package 
manager. Note, I am using emacs 23 based editor which was shipped with org-mode 
6.33.

* Updating
Follow the steps:
** Intsall the package manager
*** Download the =packages.el= file from
http://repo.or.cz/w/emacs.git/blob_plain/1a0a666f941c99882093d7bd08ced15033bc3f0c:/lisp/emacs-lisp/package.el.

Save in in =~/Library/elisp= for example.
*** Add the following code to the =.emacs=:
#+BEGIN_SRC elisp

(setq load-path (cons ~/Library/elisp load-path))
(require 'package)
(package-initialize)

#+END_SRC

*** Verify
To verify this part, in /emacs/ hit =M-x list-packages RET org=. Here
you should see a list of optional packages. /Note:/ you may ignore the
warning: =failed to download org-mode archive=.
** Updating org-mode
*** Enter the =list-packages=
Hit =M-x list-packages RET=.

In there mark for installation by =i= the org package and the =x= for
the actual installation.
*** Restart emacs
*** Verify
Hit =M-x locate-library RET org= to verify the installation. You should now
have org-mode up and running.

Thank you all!
Dror

On Apr 1, 2011, at 18:24 PM, Jambunathan K wrote:

 Dror Atariah dror...@gmail.com writes:
 
 I tried to follow the update process described here:
 http://orgmode.org/worg/org-faq.html under:
 How do I keep current with bleeding edge development?
 
 Search for ELPA in FAQ. Maybe that will work well for you ...
 

Re: [O] Update org-mode

[Dror Atariah]

@Christian: Here's my updated Makefile (at least the first part):

# Name of your emacs binary
EMACS=/Applications/Aquamacs.app/Contents/MacOS/Aquamacs

# Where local software is found
#prefix=/usr/local
prefix=~/Applications

# Where local lisp files go.
lispdir   = $(prefix)/Aquamacs.app/Contents/Resources/lisp

# Where info files go.
infodir = $(prefix)/Aquamacs.app/Contents/Resources/info

Running the make install finally (after make  make doc) yielded a rather 
long process with lots of output. However, when I reopened Aquamacs and and 
.org file, the version checked still showed 6.33x

Anything I should do otherwise?

Thnx!

On Apr 2, 2011, at 22:13 PM, Christian Moe wrote:

 In the Makefile, what settings do you have under these headings?
 
 # Name of your emacs binary
 # Where local software is found
 # Where local lisp files go.
 # Where info files go.
 
 I'm one of the oddballs who compile and install every new Org version, 
 because in the start I thought that was the right way, and it's become a 
 habit.
 
 The Makefile needs to point to the right paths for your Aquamacs application 
 and its site-lisp and info subdirectories. I don't use Aquamacs, but mutatis 
 mutandis it's probably similar to that for GNU Emacs on the Mac, namely:
 
 # Name of your emacs binary
 EMACS=/Applications/Emacs.app/Contents/MacOS/emacs
 
 # Where local software is found
 prefix=/Applications
 
 # Where local lisp files go.
 lispdir = $(prefix)/Emacs.app/Contents/Resources/site-lisp
 
 # Where info files go.
 infodir = $(prefix)/Emacs.app/Contents/Resources/info
 
 I quickly found that git pulls would overwrite my hand-edited Makefile, and a 
 hand-edited Makefile caused conflicts on the next pull, and I didn't 
 understand git at all.
 
 So I did a shell script that pulls org-mode, copies the Makefile, applies a 
 patch with the above changes to the Makefile, compiles and installs, and then 
 switches back the Makefile copy. Works for me.
 
 Yours,
 Christian
 
 
 
 On 4/1/11 5:20 PM, Dror Atariah wrote:
 I tried to follow the update process described here:
 http://orgmode.org/worg/org-faq.html under:
 How do I keep current with bleeding edge development?
 
 The only change I made was the place where I checked out the new version. 
 Instead of ~/elisp I have ~/Library/elisp.
 
 Everything went smooth, except that I had to add sudo before the make 
 install. Without the sudo, I got an access denied error. Anyway, at the 
 end, I got no warnings and it seems like the process was smooth. But when I 
 checked the version of org-mode in aquamacs it was still 6.33x
 
 I am using Emacs 23.3.1 (i386-apple-darwin9.8.0, NS apple-appkit-949.54)
  of 2011-03-19 on braeburn.aquamacs.org - Aquamacs Distribution 2.2 on a mac 
 OS 10.6.7.
 
 What should I do in order to fix it?
 
 Thanks in advance,
 Dror
 
 
 
 
 
 

Dror Atariah
---
Landline:+49-30-43024501
Mobile: +49-176-67116376
Mobile (in IL): +972 54 5912389
IM:   dror...@gmail.com
   dror...@hotmail.com

Re: [O] Re: Update org-mode

[Dror Atariah]

I have added the following:

 (setq load-path (cons
(expand-file-name ~/Library/elisp)
load-path))
 (require 'org-install)

No change in the way Aquamacs+org-mode behaves. In particular version still 
shows 6.33x... :(

[O] Re: Update org-mode

[Dror Atariah]

It seems like I have to install the package manager.

I followed the instructions in the org-mode FAQ. Added:

(setq load-path (cons ~/Library/elisp load-path))
(require 'package)
(package-initialize)

To my .emacs, where packages.el located in ~/Library/elisp.

Then, when I restart Aquamacs I get the following error:

Warning (initialization): An error occurred while loading 
`/Users/drorata/.emacs':

Symbol's value as variable is void: package-subdirectory-regexp

To ensure normal operation, you should investigate and remove the
cause of the error in your initialization file.  Start Emacs with
the `--debug-init' option to view a complete error backtrace.

What should I do?


Thanks for your time!!

Dror

On Apr 3, 2011, at 10:58 AM, Jambunathan K wrote:

 Dror Atariah dror...@gmail.com writes:
 
 Good morning Jambunathan,
 
 I did consider this, however, I couldn't make this work for me
 either. I think I'm running a too old version of Emacs/Aquamacs. If
 you could help me set this up that would be great!!
 
 I am using Emacs 23.3.1 (i386-apple-darwin9.8.0, NS
 apple-appkit-949.54) of 2011-03-19 on braeburn.aquamacs.org - Aquamacs
 Distribution 2.2 on a mac OS 10.6.7.
 
 I don't use Mac. But on my windows machine, I have installed
 ELPA/Orgmode on emacs-23.3.
 
 Follow instructions in
 http://orgmode.org/worg/org-faq.html#installing-via-elpa
 
 You have to install package manager first and then install new org-mode.
 
 I don't know where exactly failure heppaned. Tell me which step
 failed. I would be able to help better.
 
 Did Orgmode show up when you did M-x list-packages?
 
 Jambunathan K.
 

Dror Atariah
---
Landline:+49-30-43024501
Mobile: +49-176-67116376
Mobile (in IL): +972 54 5912389
IM:   dror...@gmail.com
   dror...@hotmail.com

Re: [O] Update org-mode

[Dror Atariah]

On Apr 3, 2011, at 11:55 AM, Christian Moe wrote:

 On 4/3/11 10:08 AM, Dror Atariah wrote:
 # Where local software is found
 #prefix=/usr/local
 prefix=~/Applications
 
 Hi,
 
 Try
 
 prefix=/Applications
 
 without the tilde.

That made the trick! I'll try to follow and solve also the package-manager path.

THANKS!!!

[O] Update org-mode

[Dror Atariah]

I tried to follow the update process described here:
http://orgmode.org/worg/org-faq.html under:
How do I keep current with bleeding edge development?

The only change I made was the place where I checked out the new version. 
Instead of ~/elisp I have ~/Library/elisp.

Everything went smooth, except that I had to add sudo before the make 
install. Without the sudo, I got an access denied error. Anyway, at the end, 
I got no warnings and it seems like the process was smooth. But when I checked 
the version of org-mode in aquamacs it was still 6.33x

I am using Emacs 23.3.1 (i386-apple-darwin9.8.0, NS apple-appkit-949.54)
 of 2011-03-19 on braeburn.aquamacs.org - Aquamacs Distribution 2.2 on a mac OS 
10.6.7.

What should I do in order to fix it?

Thanks in advance,
Dror

[O] Re: Update org-mode

[Dror Atariah]

 #+begin_src elisp
 (setq load-path (cons
 (expand-file-name ~/Library/elisp)
 load-path))
 (require 'org-install)
 #+end_src
 
@Yagnesh: where should I plug this code into?

[Orgmode] Using latexmk for LaTeX compilation

[Dror Atariah]

I want to use latexmk as the LaTeX exporting engine, I following this link's 
(http://orgmode.org/worg/org-faq.html#using-xelatex-for-pdf-export) 
instruction, but it didn't work.

Note, that exporting the .org to .tex file and then manually running latexmk 
-pdf works flawlessly.

I'm very new to emacs and I can't find what is wrong here.

I also posted a question here 
http://tex.stackexchange.com/questions/10562/emacs-org-mode-and-latexmk. You 
can find some more details there.

Thanks a lot!
Dror
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