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Re: [O] babel work flow
From: |
Eric Schulte |
Subject: |
Re: [O] babel work flow |
Date: |
Fri, 15 Jul 2011 09:36:55 -0600 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/24.0.50 (gnu/linux) |
address@hidden (Thomas S. Dye) writes:
> "Sebastien Vauban" <address@hidden> 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/