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

["Eric Schulte" <schulte.eric@gmail.com>]

Hi Rainer,

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.

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.

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...

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

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
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"))

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.

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

> 
> *** 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

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

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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