From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: babel work flow Date: Fri, 15 Jul 2011 09:36:55 -0600 Message-ID: <87mxgfk10q.fsf@gmail.com> References: <80oc0x9uyz.fsf@somewhere.org> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([140.186.70.92]:57559) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1QhkSv-0006Lb-5G for emacs-orgmode@gnu.org; Fri, 15 Jul 2011 11:38:13 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1QhkSn-0001mK-6W for emacs-orgmode@gnu.org; Fri, 15 Jul 2011 11:38:08 -0400 Received: from mail-iw0-f169.google.com ([209.85.214.169]:44733) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1QhkSm-0001jy-Tf for emacs-orgmode@gnu.org; Fri, 15 Jul 2011 11:38:01 -0400 Received: by mail-iw0-f169.google.com with SMTP id 8so1408124iwn.0 for ; Fri, 15 Jul 2011 08:38:00 -0700 (PDT) List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: "Thomas S. Dye" Cc: Sebastien Vauban , Org-mode tsd@tsdye.com (Thomas S. Dye) writes: > "Sebastien Vauban" 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/