Re: Re: [ANN] Org-babel integrated into Org-mode

[Rainer M Krug <r.m.krug@gmail.com>]

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On Fri, Jun 25, 2010 at 5:37 PM, Eric Schulte <schulte.eric@gmail.com>wrote:

> Hi Rainer,
>

Hi Eric


>
> First I'll give some expanded instructions in the hopes of helping out
> anyone else affected by my lack of good instructions in the announcement
> email.  Then I'll provide a re-write of your config below as an example.
>

Sounds perfect.


>
> Babel took the integration into Org-mode as an opportunity to do some
> much needed house cleaning.  Most importantly we have cleared out
> unnecessary configuration variables -- which is great unless you already
> have these variables set.
>
> We have eliminated the two main internal lists of languages, namely
> - org-babel-interpreters and
> - org-babel-tangle-langs
> so any config lines which mention those variables, can/should be
> stripped out in their entirety.  This includes any calls to the
> `org-babl-add-interpreter' function, whose sole purpose was to add
> languages to the org-babel-interpreters variable.
>

OK - I understand that and it makes perfect sense.


> alright, so with those calls stripped out, we may still in some cases
> want to associate a file name extension with certain languages, for
> example we want all of our emacs-lisp files to end in a ".el", we can do
> this will the `org-babel-tangle-lang-exts' variable.  In general you
> shouldn't need to touch this as it already has defaults for most common
> languages, and if a language is not present in org-babel-tangle-langs,
> then babel will just use the language name, so for example a file of c
> code will have a ".c" extension by default, sh code will have a ".sh"
> extension ect...
>

Perfect.


>
> You also mentioned shebang lines.  This configuration now lives in
> header arguments.  So the shebang for a single file can be set at the
> code block level, e.g.
>
> #+begin_src clojure :shebang #!/usr/bin/env clj
>  (println "with a shebang line, I can be run as a script!")
> #+end_src
>

That's perfect - it adds much flexibility, and to do it via header arguments
is absolutely perfect for me.


>
> note that whenever a file is tangled which includes a shebang line,
> org-babel will make the file executable, so there is good reason to only
>

Wow - even better!


> add shebangs at the source-code level.  However if you're sure that you
> want all of your code in some language (say shell scripts) to tangle out
> with shebang lines, then you can customize the default header arguments
> for that language, e.g.
>
> ;; ensure this variable is defined defined
> (unless (boundp 'org-babel-default-header-args:sh)
>  (setq org-babel-default-header-args:sh '()))
>
> ;; add a default shebang header argument
> (add-to-list 'org-babel-default-header-args:sh
>             '(:shebang . "#!/bin/bash"))
>

Good to know, but in general I am perfectly happy without shebang lines. But
there are cases, where they are necessary.


>
> The final change, is that to conform to Emacs guidelines, the prefix
> org-babel-* in all require lines, has been changed to ob-*, also, since
> Babel now loads by default with Org-mode you can remove any
>  (require 'org-babel)
> or
>  (require 'org-babel-init)
> that may by lying around your configuration.
>

OK - understood.


>
> Whew! that was alot of writing for a /simplification/ of configuration.
>

Well - but it made many things much clearer for me. It is often more
difficult to explain the changes which need to be made then to explain to a
new user how it should be done.


> Hopefully the example of your configuration below will be a more
> succinct demonstration of the needed transformations.
>
> Rainer M Krug <r.m.krug@gmail.com> writes:
>
> > Hi
> >
> > First of all thanks for integrating Org-babel into Org-mode.
> >
> > But for the less fluent elisp and org-mode users, I am slightly confused
> in
> > the changes necessary on my side.
> >
> > I have the following in my emacs.org file:
> >
> >
> > #+begin_src emacs-lisp
> >   (require 'org-babel-R)         ;; requires R and ess-mode
> >   ;; (require 'org-babel-ruby)      ;; requires ruby, irb, ruby-mode, and
> > inf-ruby
> >   (require 'org-babel-python)    ;; requires python, and python-mode
> >   ;; (require 'org-babel-clojure)   ;; requires clojure, clojure-mode,
> > swank-clojure and slime
> > #+end_src
>
> the above becomes
>
> #+begin_src emacs-lisp
>  (require 'ob-R)
>  ;; (require 'ob-ruby)
>  (require 'ob-python)
>  ;; (require 'ob-clojure)
> #+end_src
>

OK - done.


>
> >
> > *** Start babel
> > #+begin_src emacs-lisp
> >   (org-babel-load-library-of-babel)
> > #+end_src
>
> the above becomes
>
> #+begin_src emacs-lisp
>  (org-babel-lob-ingest "~/path/to/org/contrib/babel/library-of-babel.org")
> #+end_src
>

I don't seem to need this line anymore -  it is working without. Also, I
don't remember why I put it in...


> >
> > *** Customization of sh
> >   set shebang for sh script to "#!/bin/bash" and exclude additional
> comments
> > (t)
> > #+begin_src emacs-lisp
> >   (setq org-babel-tangle-langs
> >   (cons
> >   '("sh" "sh" "#!/bin/bash" t)
> >   (remove-if (lambda (el) (string= (car el) "sh"))
> org-babel-tangle-langs)))
> > #+end_src
>
> #+begin_src emacs-lisp
>  ;; ensure this variable is defined defined
>  (unless (boundp 'org-babel-default-header-args:sh)
>    (setq org-babel-default-header-args:sh '()))
>
>  ;; add a default shebang header argument
>  (add-to-list 'org-babel-default-header-args:sh
>               '(:shebang . "#!/bin/bash"))
> #+end_src
>
> >
> > *** Customization of R
> >   set shebang for R script to "" and exclude additional comments (t)
> > #+begin_src emacs-lisp
> >   (setq org-babel-tangle-langs
> >   (cons
> >   '("R" "R")
> >   (remove-if (lambda (el) (string= (car el) "R"))
> org-babel-tangle-langs)))
> > #+end_src
> >
>
> the above can be omitted entirely
>
> If you've made it this far, then thanks for your patience,


I have to thank you for the patience to write such a clear description. I
must say I enjoyed reading it. I would actually suggest to put this up on
the WiKi for org-babel, as it can help change ones configuration, but also
to understand how to configure the integrated org-babel - Thanks a lot.


> and please let me know if you run into any problems with the above.
>

Thanks again - it is working.

 Just one additional question: When I go on the menu to Org -- Documentation
-- Info Documentation, I still get the info help from version 6.21b,
although I installed the version from git, and under Org -- Documentation --
Show Version it gives me "Org-mode version 6.36trans
(release_6.36.408.g7f21f)".

Can I change this somehow? It seems that the Info Documentation is the one
which is part of emacs.

Cheers,

Rainer


>
> Best -- Eric
>
> >
> > which custimizes the shebang creation and the comments in the tangled
> file.
> > Do I have to change any settings, and if yes, how? The previous
> conversation
> > seems to say "yes, it needs to be changed", but I don't understand what
> and
> > how.
> >
> >
> > Thanks,
> >
> > Rainer.
> > On Thu, Jun 24, 2010 at 6:27 PM, Eric Schulte <schulte.eric@gmail.com
> >wrote:
> >
> >> Hi Sébastien,
> >>
> >> Sébastien Vauban <wxhgmqzgwmuf@spammotel.com> writes:
> >>
> >> [...]
> >> >
> >> > For my own understanding, what's the status of `Org-babel-screen', for
> >> which
> >> > I've never been able to understand completely all the differences with
> >> `sh' in
> >> > `Org-babel'?
> >> >
> >>
> >> I believe screen has more of a focus on sustained interaction with an
> >> interactive terminal, although to be honest I haven't really used it and
> >> can't say for sure.  Benjamin Andresen, the author, may have a more
> >> satisfying answer for you.
> >>
> >> >
> >> > Second, a problem with the following code:
> >> >
> >> >       ;; Org-babel needs to be told to recognize awk source code
> blocks
> >> and
> >> >       ;; how they should be tangled, which can be accomplished with
> the
> >> >       ;; following:
> >> >       (org-babel-add-interpreter "awk")
> >> >       (add-to-list 'org-babel-tangle-langs '("awk" "awk"))
> >> >
> >> >       (org-babel-add-interpreter "fortran")
> >> >       (add-to-list 'org-babel-tangle-langs '("fortran" "f"))
> >> >
> >> >       ;; ;; org-babel panics when trying to evaluate ruby code blocks
> >> because
> >> >       ;; ;; you don't have the required ruby executables available on
> >> your
> >> >       ;; ;; system. Probably the best way to deal with this is to
> remove
> >> ruby
> >> >       ;; ;; from the list of languages supported by babel:
> >> >       ;; (setq org-babel-interpreters (delete "ruby"
> >> org-babel-interpreters))
> >> >
> >> >       ;; make pre-built helper functions (`lob') available
> >> >       ;; (org-babel-load-library-of-babel)
> >> >
> >> >       ;; mapping between languages (listings in LaTeX) and their major
> >> mode
> >> >       ;; (in Emacs)
> >> >       (setq org-src-lang-modes
> >> >             '(("ocaml" . tuareg)
> >> >               ("elisp" . emacs-lisp)
> >> >               ;; ("Delphi" . perl)
> >> >               ("ditaa" . artist)
> >> >               ("asymptote" . asy)
> >> >               ("dot" . fundamental)))
> >> >       ;; )
> >> >
> >> > Neither org-babel-add-interpreter, neither its shorter version do
> exist
> >> now?
> >> >
> >>
> >> Yes, thanks for bringing this up! I realized last night that I forgot to
> >> mention this in the announcement.
> >>
> >> We have simplified the handling of languages in Org-babel, in that the
> >> org-babel-interpreters and org-babel-tangle-langs variables have both
> >> been removed.
> >>
> >> Rather than keeping explicit lists of supported languages, Babel will
> >> now try to work with every language, and will only give up if it can't
> >> find a needed function (e.g. if there is no org-babel-execute:foo
> >> function defined then babel will give up on evaluating a foo code
> >> block).  The only remaining language list is
> >> `org-babel-tangle-lang-exts' which can optionally be used to associate
> >> file extensions with language names, but is *not* required for
> >> evaluation or tangling.
> >>
> >> Given this, your configuration from above could be rewritten as
> >>
> >> --8<---------------cut here---------------start------------->8---
> >>       ;; Org-babel now needs less hand-holding :) however it could be
> >>      ;; useful to know extensions for some languages
> >>      (add-to-list 'org-babel-tangle-lang-exts '("fortran" . "f"))
> >>
> >>      ;; mapping between languages (listings in LaTeX) and their major
> mode
> >>      ;; (in Emacs)
> >>      (setq org-src-lang-modes
> >>            '(("ocaml" . tuareg)
> >>              ("elisp" . emacs-lisp)
> >>              ;; ("Delphi" . perl)
> >>              ("ditaa" . artist)
> >>              ("asymptote" . asy)
> >>              ("dot" . fundamental)))
> >>      ;; )
> >> --8<---------------cut here---------------end--------------->8---
> >>
> >> Cheers -- Eric
> >>
> >> >
> >> > Best regards,
> >> >   Seb
> >>
> >> _______________________________________________
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> >> Emacs-orgmode@gnu.org
> >> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> >>
>



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Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
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