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

[Carsten Dominik <carsten.dominik@gmail.com>]

Hi Eric,

On Jul 6, 2010, at 3:09 AM, Eric Schulte wrote:

> Hi Tom,
>
> Thanks for finding this error, the problem is that org-table is not
> being required before the source-code block is run.  As a temporary  
> fix
> you can put
>
>  (require 'org-table)
>
> somewhere in your configuration.
>
> As a long term solution I would want to talk to Carsten about how best
> to ensure that org-table is required when org-babel has been  
> required as
> I believe it may require some change in the org require tree.
>
> Carsten, do you have any suggestion?  I've tried a couple of  
> approaches
> but most result in a recursive require error.

You are using only a few entry points from org-table, and I have
just added these to the autoloads.  This fixes the current issue.

The require tree of Org could be better, but this is too complex
an issue for the moment.

- Carsten

>
> Thanks -- Eric
>
> "Thomas S. Dye" <tsd@tsdye.com> writes:
>
>> 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.
>>>
>>> _______________________________________________
>>> Emacs-orgmode mailing list
>>> Please use `Reply All' to send replies to the list.
>>> Emacs-orgmode@gnu.org
>>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>
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- Carsten