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* babel work flow
@ 2011-07-13 23:09 Thomas S. Dye
  2011-07-14  7:34 ` Sebastien Vauban
  0 siblings, 1 reply; 5+ messages in thread
From: Thomas S. Dye @ 2011-07-13 23:09 UTC (permalink / raw)
  To: Org-mode

Aloha all,

I want to use one of the dot utilities, tred, in a way that preserves my
ability to distribute the Org-mode file as reproducible research, i.e.,
intermediate results should end up in the Org-mode file or be passed
along in a chain.

Right now I have a python routine that reads a couple of Org-mode tables
and outputs a valid dot graph.  I'm saving this to a file, dot-temp.gv,
and then running some shell commands, like this:

#+begin_src sh
  tred dot-temp.gv > test.gv
  dot -o test.pdf -Tpdf test.gv
  open test.pdf
#+end_src

The graph is just what I want, but I can't see how to automate the
process in Org-mode.  In particular, the tred step trips me up.  Do I
have to make babel, tred-aware?

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

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: babel work flow
  2011-07-13 23:09 babel work flow Thomas S. Dye
@ 2011-07-14  7:34 ` Sebastien Vauban
  2011-07-14 15:53   ` Thomas S. Dye
  0 siblings, 1 reply; 5+ messages in thread
From: Sebastien Vauban @ 2011-07-14  7:34 UTC (permalink / raw)
  To: emacs-orgmode-mXXj517/zsQ

Hi Thomas,

Thomas S. Dye wrote:
> I want to use one of the dot utilities, tred, in a way that preserves my
> ability to distribute the Org-mode file as reproducible research, i.e.,
> intermediate results should end up in the Org-mode file or be passed
> along in a chain.
>
> Right now I have a python routine that reads a couple of Org-mode tables
> and outputs a valid dot graph.  I'm saving this to a file, dot-temp.gv,
> and then running some shell commands, like this:
>
> #+begin_src sh
>   tred dot-temp.gv > test.gv
>   dot -o test.pdf -Tpdf test.gv
>   open test.pdf
> #+end_src
>
> The graph is just what I want, but I can't see how to automate the
> process in Org-mode.  In particular, the tred step trips me up.  Do I
> have to make babel, tred-aware?

Sorry if I misunderstand, but could you be more explicit (for me) on what the
problem is?  Why is it a problem for you to have that sh block inside your
Org. It is executed automagically upon exporting, no?  If yes, why is that not
good enough?

Best regards,
  Seb

-- 
Sebastien Vauban

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: babel work flow
  2011-07-14  7:34 ` Sebastien Vauban
@ 2011-07-14 15:53   ` Thomas S. Dye
  2011-07-15 15:36     ` Eric Schulte
  0 siblings, 1 reply; 5+ messages in thread
From: Thomas S. Dye @ 2011-07-14 15:53 UTC (permalink / raw)
  To: Sebastien Vauban; +Cc: Org-mode

"Sebastien Vauban" <wxhgmqzgwmuf@spammotel.com> writes:

> Hi Thomas,
>
> Thomas S. Dye wrote:
>> I want to use one of the dot utilities, tred, in a way that preserves my
>> ability to distribute the Org-mode file as reproducible research, i.e.,
>> intermediate results should end up in the Org-mode file or be passed
>> along in a chain.
>>
>> Right now I have a python routine that reads a couple of Org-mode tables
>> and outputs a valid dot graph.  I'm saving this to a file, dot-temp.gv,
>> and then running some shell commands, like this:
>>
>> #+begin_src sh
>>   tred dot-temp.gv > test.gv
>>   dot -o test.pdf -Tpdf test.gv
>>   open test.pdf
>> #+end_src
>>
>> The graph is just what I want, but I can't see how to automate the
>> process in Org-mode.  In particular, the tred step trips me up.  Do I
>> have to make babel, tred-aware?
>
> Sorry if I misunderstand, but could you be more explicit (for me) on what the
> problem is?  Why is it a problem for you to have that sh block inside your
> Org. It is executed automagically upon exporting, no?  If yes, why is that not
> good enough?
>
> Best regards,
>   Seb

Aloha Seb,

Yes, babel is working fine and the sh block does its job.

The problem is that I like to see intermediate results in the Org-mode
file and the sh block works instead with files that reside outside Org-mode.

In this particular case, I'd prefer to have dot-temp.gv in a results
block in the Org-mode file, and then pass this results block into a
source code block where tred can manipulate it, and which returns its
results to the Org-mode file.

That way, the skeptical inquirer need only consult the Org-mode file to
be convinced that tred removed the transitive relations from the
digraph.  It would be an easy matter to compare the two results blocks.

All the best,
Tom

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

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: babel work flow
  2011-07-14 15:53   ` Thomas S. Dye
@ 2011-07-15 15:36     ` Eric Schulte
  2011-07-15 16:58       ` Thomas S. Dye
  0 siblings, 1 reply; 5+ messages in thread
From: Eric Schulte @ 2011-07-15 15:36 UTC (permalink / raw)
  To: Thomas S. Dye; +Cc: Sebastien Vauban, Org-mode

tsd@tsdye.com (Thomas S. Dye) writes:

> "Sebastien Vauban" <wxhgmqzgwmuf@spammotel.com> writes:
>
>> Hi Thomas,
>>
>> Thomas S. Dye wrote:
>>> I want to use one of the dot utilities, tred, in a way that preserves my
>>> ability to distribute the Org-mode file as reproducible research, i.e.,
>>> intermediate results should end up in the Org-mode file or be passed
>>> along in a chain.
>>>
>>> Right now I have a python routine that reads a couple of Org-mode tables
>>> and outputs a valid dot graph.  I'm saving this to a file, dot-temp.gv,
>>> and then running some shell commands, like this:
>>>
>>> #+begin_src sh
>>>   tred dot-temp.gv > test.gv
>>>   dot -o test.pdf -Tpdf test.gv
>>>   open test.pdf
>>> #+end_src
>>>
>>> The graph is just what I want, but I can't see how to automate the
>>> process in Org-mode.  In particular, the tred step trips me up.  Do I
>>> have to make babel, tred-aware?
>>
>> Sorry if I misunderstand, but could you be more explicit (for me) on what the
>> problem is?  Why is it a problem for you to have that sh block inside your
>> Org. It is executed automagically upon exporting, no?  If yes, why is that not
>> good enough?
>>
>> Best regards,
>>   Seb
>
> Aloha Seb,
>
> Yes, babel is working fine and the sh block does its job.
>
> The problem is that I like to see intermediate results in the Org-mode
> file and the sh block works instead with files that reside outside Org-mode.
>
> In this particular case, I'd prefer to have dot-temp.gv in a results
> block in the Org-mode file, and then pass this results block into a
> source code block where tred can manipulate it, and which returns its
> results to the Org-mode file.
>
> That way, the skeptical inquirer need only consult the Org-mode file to
> be convinced that tred removed the transitive relations from the
> digraph.  It would be an easy matter to compare the two results blocks.
>
> All the best,
> Tom

Hi Tom,

Maybe rather than saving the output of your python block to an external
file you could save it into the Org-mode file, into a results block
named e.g., "dot-temp", and then you could do the following in your sh
code block...

#+begin_src sh :var body=dot-temp
  echo $dot-temp > dot-temp.gv 
  tred dot-temp.gv > test.gv
  dot -o test.pdf -Tpdf test.gv
  rm dot-temp.gv
  open test.pdf
#+end_src

Hope this helps -- Eric

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: babel work flow
  2011-07-15 15:36     ` Eric Schulte
@ 2011-07-15 16:58       ` Thomas S. Dye
  0 siblings, 0 replies; 5+ messages in thread
From: Thomas S. Dye @ 2011-07-15 16:58 UTC (permalink / raw)
  To: Eric Schulte; +Cc: Sebastien Vauban, Org-mode

Eric Schulte <schulte.eric@gmail.com> writes:

> tsd@tsdye.com (Thomas S. Dye) writes:
>
>> "Sebastien Vauban" <wxhgmqzgwmuf@spammotel.com> writes:
>>
>>> Hi Thomas,
>>>
>>> Thomas S. Dye wrote:
>>>> I want to use one of the dot utilities, tred, in a way that preserves my
>>>> ability to distribute the Org-mode file as reproducible research, i.e.,
>>>> intermediate results should end up in the Org-mode file or be passed
>>>> along in a chain.
>>>>
>>>> Right now I have a python routine that reads a couple of Org-mode tables
>>>> and outputs a valid dot graph.  I'm saving this to a file, dot-temp.gv,
>>>> and then running some shell commands, like this:
>>>>
>>>> #+begin_src sh
>>>>   tred dot-temp.gv > test.gv
>>>>   dot -o test.pdf -Tpdf test.gv
>>>>   open test.pdf
>>>> #+end_src
>>>>
>>>> The graph is just what I want, but I can't see how to automate the
>>>> process in Org-mode.  In particular, the tred step trips me up.  Do I
>>>> have to make babel, tred-aware?
>>>
>>> Sorry if I misunderstand, but could you be more explicit (for me) on what the
>>> problem is?  Why is it a problem for you to have that sh block inside your
>>> Org. It is executed automagically upon exporting, no?  If yes, why is that not
>>> good enough?
>>>
>>> Best regards,
>>>   Seb
>>
>> Aloha Seb,
>>
>> Yes, babel is working fine and the sh block does its job.
>>
>> The problem is that I like to see intermediate results in the Org-mode
>> file and the sh block works instead with files that reside outside Org-mode.
>>
>> In this particular case, I'd prefer to have dot-temp.gv in a results
>> block in the Org-mode file, and then pass this results block into a
>> source code block where tred can manipulate it, and which returns its
>> results to the Org-mode file.
>>
>> That way, the skeptical inquirer need only consult the Org-mode file to
>> be convinced that tred removed the transitive relations from the
>> digraph.  It would be an easy matter to compare the two results blocks.
>>
>> All the best,
>> Tom
>
> Hi Tom,
>
> Maybe rather than saving the output of your python block to an external
> file you could save it into the Org-mode file, into a results block
> named e.g., "dot-temp", and then you could do the following in your sh
> code block...
>
> #+begin_src sh :var body=dot-temp
>   echo $dot-temp > dot-temp.gv 
>   tred dot-temp.gv > test.gv
>   dot -o test.pdf -Tpdf test.gv
>   rm dot-temp.gv
>   open test.pdf
> #+end_src
>
> Hope this helps -- Eric

Aloha Eric,

With a few modifications I got exactly what I wanted.  Thanks!

This takes a valid dot digraph in a results block, runs it through tred
so transitive relations are removed, creates a pdf file, and then writes
the dot source produced by tred back to the Org-mode file.

 #+begin_src sh :var body=dot-digraph :results output raw
    echo $body > dot-temp.gv
    tred dot-temp.gv > dot-temp-tred.gv
    dot -o test.pdf -Tpdf dot-temp-tred.gv
    cat dot-temp-tred.gv
    rm dot-temp-tred.gv
  #+end_src

All the best,
Tom

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

^ permalink raw reply	[flat|nested] 5+ messages in thread

end of thread, other threads:[~2011-07-15 16:58 UTC | newest]

Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2011-07-13 23:09 babel work flow Thomas S. Dye
2011-07-14  7:34 ` Sebastien Vauban
2011-07-14 15:53   ` Thomas S. Dye
2011-07-15 15:36     ` Eric Schulte
2011-07-15 16:58       ` Thomas S. Dye

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