Re: [Orgmode] [Update Config] Babel changes -- security updates and final integration push

[Thomas S. Dye]

Hi Eric,

Thanks for all your work integrating Babel into Org-mode.

I've pulled the latest Org-mode and changed my initialization  
according to your message.  I also pulled the latest starter-kit, so I  
think I have all the latest code.

When I try to evaluate this code block I get an error that orgtbl-to- 
orgtbl is void.

#+begin_src emacs-lisp
  (list 1 (+ 2 3))
#+end_src

Here is a backtrace:

Debugger entered--Lisp error: (void-function orgtbl-to-orgtbl)
  (orgtbl-to-orgtbl (if (or ... ...) result (list result)) (quote  
(:fmt ...)))
  (concat (orgtbl-to-orgtbl (if ... result ...) (quote ...)) "\n")
  (insert (concat (orgtbl-to-orgtbl ... ...) "\n"))
  (cond ((not ...) (insert ...) (goto-char beg) (when ... ...))  
((member "file" result-params) (insert result)) ((member "html" result- 
params) (insert ...)) ((member "latex" result-params) (insert ...))  
((member "code" result-params) (insert ...)) ((or ... ...) (save- 
excursion ...) (if ... ...)) (t (org-babel-examplize-region ... ...  
results-switches)))
  (let ((existing-result ...) (results-switches ...) beg end) (when  
existing-result (goto-char existing-result) (save-excursion ... ...)  
(forward-line 1) (setq beg ...) (cond ... ... ...)) (setq results- 
switches (if results-switches ... "")) (cond (... ... ... ...)  
(... ...) (... ...) (... ...) (... ...) (... ... ...) (t ...)) (setq  
end (if ... ... ...)) (when (and indent ... ...) (indent-rigidly beg  
end indent)))
  (save-excursion (let (... ... beg end) (when existing- 
result ... ... ... ... ...) (setq results-switches ...)  
(cond ... ... ... ... ... ... ...) (setq end ...) (when ... ...)))
  (if (and result-params (member "silent" result-params)) (progn  
(message ...) result) (when (and ... ...) (setq result ...)) (save- 
excursion (let ... ... ... ... ... ...)) (message "finished"))
  (if (= (length result) 0) (if (member "value" result-params)  
(message "No result returned by source block") (message "Source block  
produced no output")) (if (and result-params ...) (progn ... result)  
(when ... ...) (save-excursion ...) (message "finished")))
  org-babel-insert-result((1 5) ("replace") ("emacs-lisp" "(list 1 (+  
2 3))\n" ((:cache . "no") (:colnames . "no") (:comments . "")  
(:exports . "code") (:hlines . "yes") (:noweb . "yes") (:results .  
"replace") (:session . "none") (:shebang . "") (:tangle . "")) "" nil  
nil 0) nil 0 "emacs-lisp")
  (if (and (not arg) new-hash (equal new-hash old-hash)) (save- 
excursion (goto-char ...) (end-of-line 1) (forward-char 1) (setq  
result ...) (message ...) result) (setq result (funcall cmd body  
params)) (if (eq result-type ...) (setq result ...)) (org-babel-insert- 
result result result-params info new-hash indent lang) (run-hooks  
(quote org-babel-after-execute-hook)) result)
  (progn (fset (quote call-process-region) (function* ...)) (unless  
(fboundp cmd) (error "No org-babel-execute function for %s!" lang))  
(if (and ... new-hash ...) (save-excursion ... ... ... ... ... result)  
(setq result ...) (if ... ...) (org-babel-insert-result result result- 
params info new-hash indent lang) (run-hooks ...) result))
  (unwind-protect (progn (fset ... ...) (unless ... ...)  
(if ... ... ... ... ... ... result)) (if --cl-letf-bound-- (fset ... -- 
cl-letf-save--) (fmakunbound ...)))
  (let* ((--cl-letf-bound-- ...) (--cl-letf-save-- ...)) (unwind- 
protect (progn ... ... ...) (if --cl-letf-bound-- ... ...)))
  (letf ((... ...)) (unless (fboundp cmd) (error "No org-babel- 
execute function for %s!" lang)) (if (and ... new-hash ...) (save- 
excursion ... ... ... ... ... result) (setq result ...) (if ... ...)  
(org-babel-insert-result result result-params info new-hash indent  
lang) (run-hooks ...) result))
  (letf* ((... ...)) (unless (fboundp cmd) (error "No org-babel- 
execute function for %s!" lang)) (if (and ... new-hash ...) (save- 
excursion ... ... ... ... ... result) (setq result ...) (if ... ...)  
(org-babel-insert-result result result-params info new-hash indent  
lang) (run-hooks ...) result))
  (flet ((call-process-region ... ...)) (unless (fboundp cmd) (error  
"No org-babel-execute function for %s!" lang)) (if (and ... new- 
hash ...) (save-excursion ... ... ... ... ... result) (setq  
result ...) (if ... ...) (org-babel-insert-result result result-params  
info new-hash indent lang) (run-hooks ...) result))
  (unwind-protect (flet (...) (unless ... ...)  
(if ... ... ... ... ... ... result)) (setq call-process-region (quote  
org-babel-call-process-region-original)))
  (let* ((info ...) (evaluation-confirmed ...) (lang ...)  
(params ...) (new-hash ...) (old-hash ...) (body ...) (result- 
params ...) (result-type ...) (cmd ...) (dir ...) (default- 
directory ...) (org-babel-call-process-region-original ...)  
(indent ...) result) (unwind-protect (flet ... ... ...) (setq call- 
process-region ...)))
  org-babel-execute-src-block(nil ("emacs-lisp" "(list 1 (+ 2 3)) 
\n" ((:cache . "no") (:colnames . "no") (:comments . "") (:exports .  
"code") (:hlines . "yes") (:noweb . "yes") (:results . "replace")  
(:session . "none") (:shebang . "") (:tangle . "")) "" nil nil 0))
  (progn (org-babel-execute-src-block current-prefix-arg info) t)
  (if info (progn (org-babel-execute-src-block current-prefix-arg  
info) t) nil)
  (let ((info ...)) (if info (progn ... t) nil))
  (if (not org-babel-no-eval-on-ctrl-c-ctrl-c) (let (...) (if  
info ... nil)) nil)
  org-babel-execute-src-block-maybe()
  run-hook-with-args-until-success(org-babel-execute-src-block-maybe)
  (cond ((or ... org-occur-highlights org-latex-fragment-image- 
overlays) (and ... ...) (org-remove-occur-highlights) (org-remove- 
latex-fragment-image-overlays) (message "Temporary highlights/overlays  
removed from current buffer")) ((and ... ...) (funcall org-finish- 
function)) ((run-hook-with-args-until-success ...)) ((or ... ...)  
(call-interactively ...)) ((org-on-target-p) (call-interactively ...))  
((and ... ...) (call-interactively ...)) ((org-on-heading-p) (call- 
interactively ...)) ((org-at-table\.el-p) (message "Use C-c ' to edit  
table.el tables")) ((org-at-table-p) (org-table-maybe-eval-formula)  
(if arg ... ...) (call-interactively ...)) ((or ... ...) (call- 
interactively ...)) ((org-at-item-checkbox-p) (call- 
interactively ...)) ((org-at-item-p) (if arg ... ...)) ((save- 
excursion ... ...) (beginning-of-line 1) (save-excursion ...)) ((save- 
excursion ... ...) (cond ... ...)) ((org-clock-update-time-maybe)) (t  
(error "C-c C-c can do nothing useful at this location")))
  (let ((org-enable-table-editor t)) (cond (... ... ... ... ...)  
(... ...) (...) (... ...) (... ...) (... ...) (... ...) (... ...)  
(... ... ... ...) (... ...) (... ...) (... ...) (... ... ...)  
(... ...) (...) (t ...)))
  org-ctrl-c-ctrl-c(nil)
  call-interactively(org-ctrl-c-ctrl-c nil nil)


All the best,
Tom
On Jul 5, 2010, at 8:31 AM, Eric Schulte wrote:

> Hi,
>
> I've just merged a large set of Babel related security measures and
> layout/initialization updates into the master branch of the git
> repository.
>
> These changes will require existing babel users to update their
> configuration, see the following instructions for details -- even if  
> you
> think you've read similar instructions before these are worth reading.
> http://eschulte.github.com/babel-dev/DONE-document-configuration-changes-for-Babel-integration.html
>
> From here on out Babel development in the master branch will settle  
> down
> along with the rest of the current Org-mode feature freeze.
>
> Thanks -- Eric
>
> please reply to this email with any question or problems you  
> encounter,
> a text export of the contents of the web page linked above is provided
> below.
>
> DONE document configuration changes for Babel integration
> ==========================================================
> Babel took the integration into Org-mode as an opportunity to do
> some much needed house cleaning.  Most importantly we have
> simplified the enabling of language support, and cleared out
> unnecessary configuration variables -- which is great unless you
> already have a working configuration under the old model.
>
> The most important changes regard the /location/ and /enabling/
> of Babel (both core functionality and language specific support).
>
> Babel: Babel is now part of the core of Org-mode, so it is
>     now loaded along with the rest of Org-mode.  That means that
>     there is /no configuration/ required to enable the main
>     Babel functionality.  For current users, this means that
>     statements like
>
>     (require 'org-babel)
>
>     or
>
>     (require 'org-babel-init)
>
>     that may by lying around in your configuration must now be
>     removed.
>
> load path: Babel (including all language specific files --
>     aside from those which are located in the =contrib/=
>     directory for reasons of licencing) now lives in the base of
>     the Org-mode lisp directory, so /no additional directories/
>     need to be added to your load path to use babel.  For Babel
>     users this means that statements adding babel-specific
>     directories to your load-path should now be removed from
>     your config.
>
> language support: It is no longer necessary to require
>     language specific support on a language-by-language basis.
>     Specific language support should now be managed through the
>     `org-babel-load-languages' variable.  This variable can be
>     customized using the Emacs customization interface, or
>     through the addition of something like the following to your
>     configuration (note: any language not mentioned will /not/
>     be enabled, aside from =emacs-lisp= which is enabled by
>     default)
>
>     (org-babel-do-load-languages
>      'org-babel-load-languages
>      '((R . t)
>        (ditaa . t)
>        (dot . t)
>        (emacs-lisp . t)
>        (gnuplot . t)
>        (haskell . nil)
>        (ocaml . nil)
>        (python . t)
>        (ruby . t)
>        (screen . nil)
>        (sh . t)
>        (sql . nil)
>        (sqlite . t)))
>
>     Despite this change it is still possible to add
>     language support through the use of =require=
>     statements, however to conform to Emacs file-name
>     regulations all Babel language files have changed
>     prefix from =org-babel-*= to =ob-*=, so the require
>     lines must also change e.g.
>
>     (require 'org-babel-R)
>
>     should be changed to
>
>     (require 'ob-R)
>
> We have eliminated the =org-babel-tangle-w-comments= variable as
> well as 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.
>
> 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, shell-scripts (identified with =sh=) will
> have a =.sh= extension etc...
>
> The configuration of /shebang/ lines 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, Babel will make the file executable, so there is good
> reason to only add /shebangs/ at the source-code block 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 important change included in this release is the
> addition of new security measures into Babel.  These measures are
> in place to protect users from the accidental or uninformed
> execution of code.  Along these lines /every/ execution of a code
> block will now require an explicit confirmation from the user.
> These confirmations can be stifled through customization of the
> `org-confirm-babel-evaluate' variable, e.g.
>
>  ;; I don't want to be prompted on every code block evaluation
>  (setq org-confirm-babel-evaluate nil)
>
> In addition, it is now possible to remove code block evaluation
> form the =C-c C-c= keybinding.  This can be done by setting the
> =org-babel-no-eval-on-ctrl-c-ctrl-c= variable to a non-nil value,
> e.g.
>
>  ;; I don't want to execute code blocks with C-c C-c
>  (setq org-babel-no-eval-on-ctrl-c-ctrl-c t)
>
> An additional keybinding has been added for code block
> evaluation, namely =C-c C-v e=.
>
> Whew! that seems like a lot of effort for a /simplification/ of
> configuration.
>
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