Commit Graph

623 Commits

Author SHA1 Message Date
Eric Schulte 93ab492464 babel: updating results in place and adding `prepend' and `append' :results options
Thanks to Graham Smith for pointing out the need for in-place
  results updates

* contrib/babel/lisp/org-babel.el (org-babel-merge-params): adding
  append and prepend as exclusive options to the :results header
  argument

  (org-babel-insert-result): now updating results in place, and
  honoring the `prepend' and `append' :results header arguments
2010-06-07 16:50:59 -07:00
Eric Schulte 8d7ab3a4b7 babel: adding :noeval header argument to inhibit execution of code blocks on export
* contrib/babel/lisp/org-babel.el (org-babel-header-arg-names): adding
  :noeval header argument which can be specified to inhibit the
  execution of a source block during export.

* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-do-export):
  adding :noeval header argument which can be specified to inhibit the
  execution of a source block during export.
2010-06-07 14:08:06 -07:00
Eric Schulte ac2e6fefee babel: more careful not to evaluate code blocks without sessions on export
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-do-export): now
  explicitly checking if session is equal to "none" on export
2010-06-07 13:35:28 -07:00
Eric Schulte aa794b50b9 babel: now removing existing results when exporting "code" or "none"
Thanks to Russell Adams for pointing this out

* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-do-export):
  Removing existing results on export.
2010-06-07 13:20:22 -07:00
Eric Schulte 134de59fd7 babel: cleaning up indentation
* contrib/babel/lisp/org-babel.el (org-babel-expand-src-block-maybe):
  Cleaning up indentation

* contrib/babel/lisp/org-babel.el (org-babel-load-in-session-maybe):
  Cleaning up indentation
2010-06-07 13:14:52 -07:00
Eric Schulte 9c02bf4946 babel: more robust newline regexp in `org-babel-comint-with-output'
* contrib/babel/lisp/org-babel-comint.el (org-babel-comint-with-output):
  Placing a more general regexp substitution for matching newlines
  returned by comint.  This new option should definitely cover all
  cases.
2010-06-07 12:58:38 -07:00
Eric Schulte 8318845f6d babel: stashing away text dangling after the process mark in comint buffers
* contrib/babel/lisp/org-babel-comint.el (org-babel-comint-with-output):
  If there is dangling text left after the process mark in a comint
  buffer, it will now be safely stored away during babel execution,
  and then replaced when babel is finished with the buffer.

  This commit also fixes some indentation issues.
2010-06-07 12:25:58 -07:00
Eric Schulte 909f375ba6 babel: fixing indentation in org-babel-ruby.el
* contrib/babel/lisp/langs/org-babel-ruby.el (org-babel-execute:ruby):
  fixing indentation

* contrib/babel/lisp/langs/org-babel-ruby.el (org-babel-ruby-evaluate):
  fixing indentation
2010-06-07 12:13:37 -07:00
Eric Schulte 6e34e75888 babel: small wait on new ruby sessions to allow process to start
* contrib/babel/lisp/langs/org-babel-ruby.el (org-babel-ruby-initiate-session):
   Adding a small wait after stating a new ruby session.  This avoids
   errors with `ansi-color-process-output' not being able to find the
   process mark.
2010-06-07 12:08:43 -07:00
Eric Schulte dc2baab09c babel: protecting restrictions on `org-babel-execute-subtree' 2010-06-07 11:52:04 -07:00
Eric Schulte ee94addaac babel: now strips protective commas from code blocks on tangling 2010-06-07 11:46:11 -07:00
Eric Schulte 4e43e7fea8 babel: adding library-of-babel functions for file I/O
* contrib/babel/lisp/org-babel.el (org-babel-insert-result): Replaced
  call to `org-cycle' with a call to the simpler and more appropriate
  `org-table-align'.

* contrib/babel/library-of-babel.org (Read/Write): adding
  library-of-babel functions for file I/O
2010-06-06 19:56:09 -07:00
Eric Schulte 367d81d9dc babel: all code blocks with sessions are now evaluated on export
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-do-export):

  This brings babel more inline with Sweave, by ensuring that any code
  block which could change the state in a persistent session is
  executed.  Prior to this change the following org-mode text like would
  not export as expected because the x variable would not be
  initialized.

  ** inline expressions
     :PROPERTIES:
     :session:  *R*
     :END:

  #+begin_src R :exports code :results silent
    x<-5
  #+end_src

  the sum of 1 and 4 is equal to src_R{x}
2010-06-06 19:13:14 -07:00
Carsten Dominik f70956ff5a Merge branch 'master' of git+ssh://repo.or.cz/srv/git/org-mode 2010-06-04 21:02:41 +02:00
Bernt Hansen dc602f3b2e Emacs 22 support - use org-string-match-p
* contrib/lisp/org-special-blocks.el (org-special-blocks-make-special-cookies):
Emacs 22 doesn't have string-match-p
* lisp/org-freemind.el (org-freemind-write-mm-buffer):
(org-freemind-get-node-style):
Emacs 22 doesn't have string-match-p
* lisp/org-html.el (org-html-make-link):
Use new org-string-match-p for compatibility
2010-06-04 21:01:29 +02:00
Eric Schulte 507e06f586 org-mime: now allows style customization based on class attributes 2010-06-04 10:56:56 -06:00
Nicolas Goaziou 359a86cda4 babel-asymptote: now accepts variables in a variety of types 2010-06-04 09:51:18 -06:00
Eric Schulte 198780f1ff babel: adding some newline padding around tangle code blocks 2010-06-02 14:07:20 -06:00
Eric Schulte c5e3660fa9 babel: tangle works when buffer name and file name differ
Thanks to "w t" from the mailing list for reporting this bug and
  providing reproduction information.
2010-06-02 09:07:23 -06:00
Eric Schulte 47a6c25df3 org-babel-tangle: fixing indentation 2010-06-02 09:07:22 -06:00
Eric Schulte afab7897a5 babel: fixed error resolving references on export
Thanks to Nicolas Goaziou for reporting this problem
2010-06-02 09:07:01 -06:00
Eric Schulte b7e273f25d babel-exp: minor documentation and indentation changes 2010-06-02 09:07:00 -06:00
Eric Schulte 8fac7aa38b Merge branch 'master' of git+ssh://repo.or.cz/srv/git/org-mode 2010-05-28 08:48:22 -06:00
Eric Schulte ff58dacc7c babel: `org-babel-tangle-w-comments' controls comment insertion in tangled code
* contrib/babel/lisp/org-babel-tangle.el (org-babel-spec-to-string):
  The insertion of automatically generated comments into tangled code
  is now customizable through the `org-babel-tangle-w-comments'
  variable.
2010-05-28 08:48:03 -06:00
Dan Davison e5d8764de6 babel: Declare R-specific header arguments
* babel/lisp/langs/org-babel-R.el
(org-babel-header-arg-names:R):
New variable to contain R-specific header args
2010-05-28 09:53:13 -04:00
Dan Davison 71cd358e21 babel: check properties for language-specific header arguments
* contrib/babel/lisp/org-babel.el
(org-babel-params-from-properties):
Check for language-specific header arguments
(org-babel-parse-src-block-match):
Pass lang parameter when checking properties for header args
(org-babel-parse-inline-src-block-match):
Pass lang parameter when checking properties for header args
2010-05-28 09:50:20 -04:00
Michael Sperber 6fc2ea3b9b Xemacs incompatibilities
Carsten Dominik <carsten.dominik@gmail.com> writes:

> On May 17, 2010, at 4:39 PM, Michael Sperber wrote:
>
>> In particular, fixing the require won't be enough: org-babel-python.el
>> uses `run-python' and interacts with the inferior Python, whereas
>> python-mode.el defines `py-shell'.
>>
>> Should I try to abstract over the differences?
>
> Yes, this would be much appreciated. (I think, Eric or Dan?)

OK, I've attached a patch that makes `org-babel-python' work on XEmacs.
Most of the issues are pure XEmacs issues.  Notes:

- XEmacs doesn't have [[:digit:]] - I hope to rectify this in the
  future, but it seems there's no downside in this particular case to
  replacing by [0-9].
- XEmacs doesn't have `move-end-of-line', but does have `end-of-line'.
  I don't understand the intent of having both of these, but the code
  seems fine with `end-of-line'.
- It seems there are way too few `require's throughout org-babel.  I
  don't know if it's OK to add the ones I needed.
- `org-babel-python-evaluate' looked broken as-is: It doesn't use the
  `body' argument properly, the result is (I think) processed in the
  wrong order and not properly split into lines.  I've fixed all these,
  but a review is probably in order.
2010-05-26 22:45:01 -06:00
Eric Schulte 5d52daab10 babel: org-babel-execute-buffer is no longer flummoxed by hidden subtrees 2010-05-26 19:44:04 -06:00
Eric Schulte 8d78778c89 babel: updated key bindings in refcard
and removed a binding which was shadowing the `keyboard-quit'
2010-05-26 16:55:48 -06:00
Eric Schulte 4f113630f8 org-babel-exp: no longer throws errors on empty bodies 2010-05-25 20:20:13 -06:00
Eric Schulte ceeb4681ef babel: tangled files which include shebang lines are now made executable 2010-05-25 20:01:20 -06:00
Eric Schulte 6151c88f10 babel: replaced `line-number-at-pos' with `count-lines' 2010-05-25 17:31:34 -06:00
Eric Schulte d84699459e babel: xemacs variable compatibility check -- thanks to Volker Zell 2010-05-25 17:29:41 -06:00
Carsten Dominik cdef6061bf Fix typo 2010-05-20 05:42:24 +02:00
Carsten Dominik 5eb7bf8a03 Add Anthony Lander's org-mac-link-grabber.el 2010-05-19 23:49:40 +02:00
Eric Schulte 2139651c0d babel: org-babel-clean-text-properties now checks for valid argument
thanks to Michael Sperber for pointing this out
2010-05-17 17:13:20 -06:00
Eric Schulte 236f209b25 babel: changes to org-babel key bindings 2010-05-17 17:08:32 -06:00
Carsten Dominik 38b4fcc90c XEmacs compatibility 2010-05-14 14:40:44 +02:00
Eric Schulte b7555ae433 babel: new keymap `org-babel-map' and new prefix keys "C-c C-v" 2010-05-12 23:51:41 -06:00
Carsten Dominik 4b1ee671b8 Merge branch 'master' of git+ssh://repo.or.cz/srv/git/org-mode 2010-05-11 23:31:38 +02:00
Carsten Dominik 7a0619cbe8 Fix bug in org-git-link.el 2010-05-11 23:31:30 +02:00
Eric Schulte 98af57cdbd babel: ob-sh.el now respects the :results "scalar" option 2010-05-07 17:18:38 -06:00
Eric Schulte 37f9639a43 Merge branch 'master' of git+ssh://repo.or.cz/srv/git/org-mode 2010-05-04 09:58:25 -06:00
Eric Schulte a16e887fff org-mime: now using `temporary-file-directory' instead of "/tmp" -- thanks to Uday S Reddy for catching this 2010-05-04 09:49:07 -06:00
Dan Davison 2d1025298e babel: More concise matlab/octave code template
Patch by Christopher Long
2010-05-03 21:45:27 -04:00
Dan Davison 245d98786d babel: matlab: detect end of evaluation under Emacs Link
Currently, this uses the presence of a temporary file to signal that
Matlab Emacs Link evaluation is not yet complete.

Emacs Link support added in collaboration with Christopher Long.
2010-05-03 21:45:01 -04:00
Benjamin Andresen c133dd394e babel: Fix org-babel-screen after expand changes 2010-05-02 21:30:13 -04:00
Dan Davison d2b9343029 babel: Avoid trouble with '%' in matlab/octave output
Patch by Christopher Long
2010-05-02 18:26:22 -04:00
Dan Davison 65a98e3282 babel: fix editing error in org-babel-octave.el 2010-05-02 00:41:53 -04:00
Dan Davison 1a43a5939b Merge branch 'octave-matlab' 2010-04-30 18:26:37 -04:00
Dan Davison a61de7b130 babel: matlab: don't try matlab-shell if using emacs link 2010-04-30 18:23:36 -04:00
Eric Schulte a3cc050a96 babel: `org-babel-get-colnames' no longer requires hline 2010-04-30 13:03:46 -06:00
Dan Davison 6f399c20b6 babel: Allow EmacsLink to be used for matlab session evaluation
To use EmacsLink, the user will need to set
org-babel-matlab-with-emacs-link to a non-nil value, and also arrange
that (matlab-with-emacs-link) evaluates to a non-nil value.
2010-04-30 14:39:31 -04:00
Dan Davison 10a07a644b babel: R: allow forcing of colnames without hline 2010-04-30 14:14:27 -04:00
Dan Davison 7f3e64bfb4 babel: R: output colnames when other languages would 2010-04-30 14:14:13 -04:00
Robert P. Goldman 413e6b4eee Add handling of blockquote and output formats that must be flowed.
Added a handler for blockquotes.

Also added :body-newline-paragraph to the org-set-generic-type.  This is
intended to help handling output formats (like tikiwiki) where newlines are
treated as paragraph separators, instead of being used to fill (i.e., the
destination is expected to do the word-wrapping).  If this is set to T then
org-export-generic will emit a newline character when it sees a blank
line.  This should be used in concert with a value like "%s " for
:body-line-format and nil for :body-line-wrap.
2010-04-29 15:57:03 +02:00
Eric Schulte 6a1f5b2bcb babel: ob-emacs-lisp now wraps body in a progn on execute 2010-04-27 13:55:48 -06:00
Dan Davison 837e898936 babel: Fall back to generic expand function during tangling 2010-04-27 15:02:55 -04:00
Eric Schulte 44bb82d38e babel: `org-babel-ref-resolve-reference' doesn't break paren nesting when resolving indicies 2010-04-24 13:26:34 -06:00
Eric Schulte b8adc74894 babel: ob-emacs-lisp and ob-clojure now only wrap bodies in `let' forms when variables are present 2010-04-24 09:21:14 -06:00
Eric Schulte bc0a6c624d babel: adding :no-expand option to code blocks to inhibit body expansion 2010-04-24 09:08:27 -06:00
Eric Schulte c12e18b6cf babel: org-babel-reassemble-table checks for matching table/name dimensions 2010-04-23 11:54:31 -06:00
Dan Davison b8c4bb27ba babel: Use org-src edit buffer for expanded body preview 2010-04-23 10:10:01 -06:00
Eric Schulte 2f71d79e5e org-babel-c: now using org-babel-read on outline-property parameters 2010-04-23 10:10:00 -06:00
Eric Schulte 9124e9055d fixed bug in org-babel-execute:C 2010-04-23 10:10:00 -06:00
Eric Schulte 59251c8d08 babel: fixed bug in org-babel-execute:gnuplot related to body-expand changes 2010-04-23 10:10:00 -06:00
Dan Davison d0dde7c6d5 babel: flip default values of :hlines header arg 2010-04-23 10:10:00 -06:00
Dan Davison 9fdd058669 org-babel-expand-body:R 2010-04-23 10:10:00 -06:00
Eric Schulte 32c7ae42c3 babel: remove superfluous newlines from tangled C code bodies 2010-04-23 10:10:00 -06:00
Eric Schulte 03f13106fb babel: adding org-babel-expand-body:generic for languages w/o body expansion support 2010-04-23 10:10:00 -06:00
Eric Schulte 626cb079e4 babel: fixed bug in org-babel-expand-body:sass 2010-04-23 10:10:00 -06:00
Dan Davison 7decdec3b2 babel: erase previous contents of preview buffer 2010-04-23 10:10:00 -06:00
Dan Davison 8872454566 org-babel-expand-body:R 2010-04-23 10:10:00 -06:00
Eric Schulte 0917218da5 babel: fixed bug in org-babel-expand-body:python 2010-04-23 10:10:00 -06:00
Eric Schulte 9ff31a5110 babel: bound `org-babel-expand-src-block' to (C-c M-b p) 2010-04-23 10:09:59 -06:00
Eric Schulte 0734bf96ba org-babel-expand-body:sql 2010-04-23 10:09:59 -06:00
Eric Schulte 1fdc012e3d org-babel-expand-body:sh 2010-04-23 10:09:59 -06:00
Eric Schulte e6c979f0d7 org-babel-expand-body:screen 2010-04-23 10:09:59 -06:00
Eric Schulte 35434e1389 org-babel-expand-body:sass 2010-04-23 10:09:59 -06:00
Eric Schulte 394031eb38 org-babel-expand-body:ruby 2010-04-23 10:09:59 -06:00
Eric Schulte 1bcafa5d9f org-babel-expand-body:python 2010-04-23 10:09:59 -06:00
Eric Schulte 598dc1ad67 org-babel-expand-body:perl 2010-04-23 10:09:59 -06:00
Eric Schulte 41663b0ce4 org-babel-expand-body:oz 2010-04-23 10:09:59 -06:00
Eric Schulte 2759b6621d org-babel-expand-body:octave 2010-04-23 10:09:59 -06:00
Eric Schulte 8e9f4eec88 org-babel-expand-body:ocaml 2010-04-23 10:09:58 -06:00
Eric Schulte e07aced178 org-babel-expand-body:matlab 2010-04-23 10:09:58 -06:00
Eric Schulte 7bd0712ac2 org-babel-expand-body:latex 2010-04-23 10:09:58 -06:00
Eric Schulte dd500005ef org-babel-expand-body:haskell 2010-04-23 10:09:58 -06:00
Eric Schulte 58c8ddd5c6 org-babel-expand-body:gnuplot 2010-04-23 10:09:58 -06:00
Eric Schulte 01918dffc4 org-babel-expand-body:dot 2010-04-23 10:09:58 -06:00
Eric Schulte 4d862912b2 org-babel-expand-body:ditaa 2010-04-23 10:09:58 -06:00
Eric Schulte b805089eb8 org-babel-expand-body:css 2010-04-23 10:09:58 -06:00
Eric Schulte 6d61edd1ea org-babel-expand-body:clojure 2010-04-23 10:09:58 -06:00
Eric Schulte 4ba08f9b5b org-babel-expand-body:asymptote 2010-04-23 10:09:58 -06:00
Eric Schulte 34eed9b48d org-babel-expand-body:c, org-babel-expand-body:c++ 2010-04-23 10:09:58 -06:00
Eric Schulte 8c8c96972e org-babel-expand-body:emacs-lisp 2010-04-23 10:09:58 -06:00
Eric Schulte 2fe12b99f4 babel: adding new function `org-babel-expand-src-block'
org-babel-expand-body:lang function needs to be implemented by every
  language, and is used to expand the body of a code block for
  execution or tangling
2010-04-23 10:09:57 -06:00
Dan Davison 788779e16c babel: typo in org-babel-get-rownames 2010-04-23 10:09:57 -06:00
Dan Davison c777e729fb babel: bring R row- and col-names into line with others 2010-04-23 10:09:57 -06:00
Julien Barnier bd3c85ed60 babel: add :rownames header arg for R 2010-04-23 10:09:57 -06:00
Dan Davison d5dd160b23 babel: bug fix in org-babel-get-colnames 2010-04-23 10:09:57 -06:00
Eric Schulte b9aa92ba21 org-babel: splitting `org-babel-pick-name' into it's own function
also renaming org-babel-manicure-tables to org-babel-disassemble-tables
2010-04-23 10:09:57 -06:00
Eric Schulte bfc93ca808 babel: added row/col-name support to all applicable languages 2010-04-23 10:09:57 -06:00
Eric Schulte 10b3da72fc babel: adding row/col-names functions
adding a suite of functions to org-babel.el which can be used to
  handle hlines, rownames, and columnnames in input tables.  These
  functions can be called from any org-babel-language.el file.

  done in close collaboration with Dan Davison
2010-04-23 10:09:57 -06:00
Eric Schulte 0c8b86e9a9 org-babel: keep within 80 columns
this is exclusively whitespace and indentation changes, with the
  goal of cleaning up the file, and keep all lines within 80 columns
2010-04-23 10:09:57 -06:00
Eric Schulte 927ff1125b babel: `org-babel-ref-index-list' now converts trivial lists to scalars
Thanks to Darlan Cavalcante Moreira for this suggestion.
2010-04-21 09:35:13 -06:00
Carsten Dominik c6ea2a1457 Use overlay-in and overlay-at instead of compatibility functions 2010-04-20 12:17:06 +02:00
Carsten Dominik 97e20048b2 Use `add-to-invisibility-spec' directly 2010-04-18 19:41:05 +02:00
Carsten Dominik b35b9914e6 Revert "Use `add-to-invisibility-spec' directly"
This reverts commit c2e5b13a2d.
2010-04-18 19:38:10 +02:00
Carsten Dominik c2e5b13a2d Use `add-to-invisibility-spec' directly 2010-04-18 19:26:30 +02:00
Carsten Dominik bb0ef787b7 Require calendar already on top level in org.el 2010-04-18 16:50:13 +02:00
Carsten Dominik f45e6a28b1 Use the normal overlay API, not Org's one 2010-04-18 16:49:58 +02:00
Eric Schulte 3652689944 org-mime: removed short string " xx " from semi syntax 2010-04-16 09:21:36 -06:00
Eric Schulte 3b5c85fb95 org-mime: WL is now fully supported -- thanks to Eric S. Fraga 2010-04-15 09:40:03 -06:00
Eric Schulte a2769bef61 org-mime: bug fixes, thanks to Eric S Fraga and Andrew Hyatt for their debugging help 2010-04-14 09:12:41 -06:00
Eric Schulte b617a457ae org-mime: change `org-mime-org-export' to more closely mimic `org-run-like-in-org-mode' 2010-04-12 11:21:59 -06:00
Eric Schulte 70ba21e699 babel: new function `org-babel-tangle-publish' allows for tangling during project publish 2010-04-11 23:58:44 -06:00
Eric Schulte 7cbb35920d org-babel-c: new header argument ":main no" allows inhibiting main wrap 2010-04-10 15:54:40 -06:00
Eric Schulte 99a07f1d4a org-babel-c: cleaning up header arguments 2010-04-10 15:43:31 -06:00
Eric Schulte 0e8c9f7a49 org-babel: no longer over evaluating header arguments 2010-04-10 15:43:19 -06:00
Eric Schulte 3386a702f8 org-babel: all languages now returning lists as pure emacs-lisp, not quoted emacs-lisp 2010-04-10 15:15:06 -06:00
Eric Schulte 722dd7eb5c org-mime: cleaned `org-mime-default-header' from text/plain exports 2010-04-10 15:15:05 -06:00
Dan Davison 59d499ff51 babel: Allow table to end neatly with terminal hline
Prior to this, a terminal hline would leave dangling empty cells:

 #+TBLNAME: A
 |---+---+---|
 | a | b | c |
 |---+---+---|

 #+begin_src emacs-lisp :var tab=A
 tab
 #+end_src

 #+results:
 |---+---+---|
 | a | b | c |
 |---+---+---|
 |   |   |   |
2010-04-10 16:49:40 -04:00
Dan Davison 8c827ba5ba babel: Allow output tables to start with 'hline 2010-04-10 16:12:28 -04:00
Eric Schulte 98b4ae28a9 babel: allow lisp quoted expansion of variable values when starting with ` 2010-04-09 19:06:07 -06:00
Eric Schulte 8258daf439 added org-mime.el to contrib -- allows HTML email composition with Org-mode
see http://orgmode.org/worg/org-contrib/org-mime.php for
  documentation

  much thanks to everyone on the "using orgmode to send html mail"
  thread (see http://thread.gmane.org/gmane.emacs.orgmode/23153)
  especially David Maus for ideas, discussion, and suggestions
2010-04-09 10:26:57 -06:00
Dan Davison f846663ce6 babel: Do not add indentation to perl code.
Thanks to Łukasz Stelmach.
2010-04-09 08:45:18 -04:00
Dan Davison 0f83b2d203 babel: allow disabling of noweb expansion during tangling 2010-04-08 16:14:28 -04:00
Dan Davison 38d6bf3f6c babel: allow assigning of variables when preparing R session
This is already in place for other languages, but seems to have been
forgotten for R.
2010-04-08 15:26:08 -04:00
Eric Schulte caaf755192 babel: org-babel-latex adjusts to the new org latex setup 2010-04-07 22:43:37 -06:00
Dan Davison e48b8bf577 babel: return string results from matlab as strings
Thanks to Bob Jansen
2010-04-07 18:44:58 -04:00
Dan Davison f03c981fc0 babel: return string results from octave as strings
Thanks to Darlan Cavalcante
2010-04-07 15:51:04 -04:00
Eric Schulte 8d405783cb babel: safer modification of `call-process-region' 2010-04-04 17:15:12 -06:00
Eric Schulte 8ef104195f babel: use wildcard "*" characters in `org-babel-ref-index-list' to index entire ranges 2010-04-02 08:46:13 -06:00
Dan Davison 40a8933ba6 babel: allow R to produce svg format output 2010-04-01 18:45:59 -04:00
Carsten Dominik c1ee3cc3d9 Merge branch 'master' of git+ssh://repo.or.cz/srv/git/org-mode 2010-03-31 00:16:13 +02:00
Carsten Dominik 28b1059f09 Snow Leopard compatibility for org-mac-iCal.el 2010-03-31 00:16:07 +02:00
Dan Davison 3637efe647 babel: Don't use language major-mode when expanding noweb references
There is no longer any need for the language major mode.
2010-03-30 10:20:18 -04:00
Dan Davison e32c066874 babel: check that language major-mode is available during tangling 2010-03-30 10:20:10 -04:00
Eric Schulte 2675848d37 babel: org-babel-c now responds to :cmdline header argument 2010-03-29 12:26:53 -06:00
Bernt Hansen f2abb650fb Add completions for checkbox targets
Add the new property values to the completion list.
2010-03-28 22:10:24 -04:00
Eric Schulte e8a125bed7 babel: now taking headline properties into account for lob calls 2010-03-28 16:53:00 -06:00
Dan Davison a23ca4529f babel: Get rid of parameter inheritance by reference blocks 2010-03-27 18:49:00 -04:00
Dan Davison 36351d26a9 Merge branch 'master' of git://repo.or.cz/org-mode 2010-03-27 16:18:27 -04:00
Dan Davison 47571965d4 babel: don't process emacs-lisp params twice 2010-03-27 15:59:53 -04:00
Eric Schulte 8ecc86d49e babel: better variable initialization for org-babel-c 2010-03-27 08:20:38 -06:00
Eric Schulte fc28dd538b babel: shorter language names no longer shadow larger names
Previously "R" could overshadow "Ruby", and "C" could overshadow
  "Clojure", causing blocks of the longer language name to fail to
  load. This issue has now been fixed
2010-03-26 20:54:16 -06:00
Eric Schulte 22e4cd9b6d babel: org-babel-c more robust, better error messages and c++ support 2010-03-26 19:35:31 -06:00
Eric Schulte b61019489c babel: org-babel-C now displays compilation error messages 2010-03-26 17:12:43 -06:00
Eric Schulte e3fbc98b26 babel: removed errant reference to R from org-babel.el 2010-03-26 16:28:25 -06:00
Eric Schulte 17790c7dad babel: limited initial support for C and similar languages 2010-03-26 16:28:23 -06:00
Eric Schulte f400632f94 babel: when passing values from a table an extra '$' prefix forces literal
thanks to Maurizio Vitale for the suggestion.  This allows literal
  values to be passed to code blocks through `sbe' without forcing the
  use of quotes inside the table.
2010-03-25 11:09:38 -06:00
Eric Schulte 727aa263cb babel: src block regexps are more robust to embedded "[begin|end]_src" in block body 2010-03-22 15:19:33 -06:00
Eric Schulte 32bbd3f3bb babel: variable references which look like lisp forms are now evaluated
for example, the following simple example
    #+begin_src emacs-lisp :var two=(+ 1 1)
      (sqrt two)
    #+end_src

    #+results:
    : 1.4142135623730951

  Or this more interesting usage, which pulls variable values from
  headline properties
    *** example headline w/property
        :PROPERTIES:
        :special:  89
        :last-name: schulte
        :END:

    #+begin_src emacs-lisp :var special=(string-to-number (org-entry-get nil "special" t))
      (+ special 1)
    #+end_src

    #+results:
    : 90

    #+begin_src emacs-lisp :var last-name=(org-entry-get nil "last-name" t))
      (message "hello %s" last-name)
    #+end_src

    #+results:
    : hello schulte
2010-03-22 15:19:32 -06:00
Dan Davison abf0a50d1b babel: Ensure that inline code blocks produce string output on export 2010-03-19 10:08:16 -04:00
Dan Davison adb2f3f590 babel: Add octave and matlab support 2010-03-18 14:45:39 -04:00
Dan Davison aa0e4b86ce babel: Fix org-babel-load-file
This was broken by 29a2ab0047
2010-03-18 14:30:54 -04:00
Dan Davison 73d8e57685 babel: Allow tramp syntax when supplying :tangle filename
Patch by Rémi Vanicat.
2010-03-17 21:03:21 -04:00
Dan Davison 29a2ab0047 babel: when tangling do not add extension if filename supplied 2010-03-17 20:09:06 -04:00
Dan Davison 6976d9fc79 babel: org-babel-switch-to-session [C-c M-b z]
org-babel-pop-to-session is an alias of this
2010-03-16 12:57:28 -04:00
Dan Davison 485781ed40 babel: set default-directory in org-babel-pop-to-session 2010-03-13 14:02:47 -05:00
Dan Davison f4ae431706 babel: Make code block params available when initiating session 2010-03-13 14:02:31 -05:00
Dan Davison 215d11c092 babel: New hook org-babel-after-execute-hook
Runs at the end of org-babel-execute-src-block
2010-03-13 14:02:22 -05:00
Dan Davison ba4d698fa1 babel: Provide notification of errors during code execution
This deals with external process :results value mode for R, ruby,
python, perl and clojure: if the shell process has a non-zero exit
code, a buffer containing stderr is displayed.
2010-03-05 11:32:18 +00:00
Dan Davison 4e9a2d4efd babel: Fix bug in shell-command-on-region
Prior to this commit,

OUTPUT-BUFFER nil
REPLACE 'replace
ERROR-BUFFER 'current-buffer

resulted in stdout going with stderr to the current buffer, contra the
docstring. With this change stdout is discarded in this case. The
docstring does stipulate that stdout always should go to *Shell
Command Output*; this change does not make that happen in this case.
2010-03-05 11:32:11 +00:00
Dan Davison 05986e95ea babel: Introduce org-babel copy of shell-command-on-region
At this commit, org-babel-shell-command-on-region is a direct copy of
shell-command-on-region. In addition to switching to use the org-babel
version, we change the argument passed so that they agree with the
docstring of s-c-o-r.

Despite the change in arguments, the same behaviour results because
s-c-o-r does not behave as documented in emacs23. Future commits will
be able to fix these bugs in the org-babel version, as necessary.
2010-03-05 11:32:04 +00:00
Dan Davison ed7b8bfcca babel: clojure: read results remotely when necessary 2010-03-03 22:00:08 +00:00
Dan Davison 54c7b04734 babel: clojure: use shell-command-on-region 2010-03-03 21:59:32 +00:00
Dan Davison a8c1a49b77 babel: Read perl results remotely when necessary. 2010-03-03 16:11:04 +00:00
Dan Davison 9c36b20a25 babel: make output file links track changed directory 2010-03-02 14:51:01 +00:00
Dan Davison 486bc2fe64 babel: Use file-name-as-directory to form default-directory 2010-03-02 14:51:01 +00:00
Eric Schulte f0f511916a babel: org-babel-oz.el now uses unix-style newline characters 2010-03-01 08:31:05 -07:00
Dan Davison 44c8487e2d babel: fix bug with remote working directory
This change fixes a bug in the remote execution branch, involving the
way that org-babel-tramp-handle-call-process-region is used
to (conditionally) handle calls to call-process-region. When
org-babel-execute-src-block called itself recursively (e.g. when
resolving a reference to another src block), a circular binding of
symbols and values resulted.
2010-02-27 18:19:18 -05:00
Dan Davison 322fe431c5 babel: Write R input data remotely when necessary. 2010-02-27 18:19:09 -05:00
Eric Schulte a705bf5925 babel: wrapped `org-babel-make-remote-file-name' in conditional as `org-babel-maybe-remote-file' 2010-02-27 18:18:37 -05:00
Dan Davison 24cdeea122 babel: read remote results from remote files
When using ':results value' in certain situations, results are written
to file by the foreign language process and subsequently read from
file by emacs into an elisp table structure. If the foreign language
process is running remotely, then the results are written
remotely. These changes ensure that in that case, an appropriate
remote file name is constructed to read the remote data.
2010-02-27 14:14:08 -05:00
Dan Davison 2056d7d419 babel: Allow shell-command-on-region to execute remotely
These changes solve two problems: both are discussed in the following thread

http://lists.gnu.org/archive/html/tramp-devel/2010-02/msg00025.html

of which a summary follows.

Firstly, shell-command-on-region does not work with tramp in the same
way that shell-command does. I.e. whereas

(let ((default-directory "/user@remote-host:"))
  (shell-command "hostname" t))

gives the remote hostname,

(let ((default-directory "/user@remote-host:"))
  (shell-command-on-region (point) (mark) "hostname" t))

does not.

The reason is that shell-command-on-region calls call-process-region,
which does not use a tramp handler for remote files. However, such a
file handler does exist (unused) in the tramp sources:
tramp-handle-call-process-region. There is a slight problem in that
there is a bug in that function definition in current tramp (which has
persisted because the function is not normally used).

Therefore, we define an org-babel version of
tramp-handle-call-process-region which fixes the bug, and we bind
call-process-region to org-babel-tramp-handle-call-process-region for
the duration of org-babel-execute-src-block.
2010-02-27 14:14:08 -05:00
Dan Davison b3d5a1eb39 babel: working directories and remote execution
This introduces a new header argument :dir. For the duration of source
block execution, default-directory is set to the value of this header
argument. Consequences include:

- external interpreter processes run in that directory
- new session processes run in that directory (but existing ones are unaffected)
- relative paths for file output are relative to that directory

The name of a directory on a remote machine may be specified with
tramp syntax (/user@host:path), in which case the interpreter
executable will be sought in tramp-remote-path, and if found will
execute on the remote machine in the specified remote directory.
2010-02-27 14:14:08 -05:00
Dan Davison 5f8a57ad48 babel: change implementation of external R process evaluation
Use shell-command-on-region, bringing R into line with ruby, python,
clojure, shell. In addition to consistency (and perhaps efficiency),
this will also be preferable in the case of a remote R process because
it means that transfer of the input to the remote process is dealt
with automatically by tramp.
2010-02-27 14:14:08 -05:00
Eric Schulte 522f30bc9f babel: tiny doc tweak 2010-02-27 14:14:07 -05:00
Dan Davison cc7052540b babel: allow point to move to end of comint buffer 2010-02-27 14:14:07 -05:00
Dan Davison 283ebcb43b babel: New const variable org-babel-header-arg-names
This is used when checking for babel header args in org properties.
2010-02-27 14:14:07 -05:00
Dan Davison 82d7585810 babel: Tighten result and source line regexps
Anchored to beginning of line, with optional whitespace indenting.
2010-02-25 17:58:46 -05:00
Dan Davison 5833fbd358 babel: Make colnames header arg expect use "yes" for true. 2010-02-25 17:58:46 -05:00
Dan Davison 4064c31fa7 babel: get rid of unused variable 2010-02-25 17:58:46 -05:00
Dan Davison fc693eb5e2 babel: treat python tuples as lists 2010-02-25 17:58:45 -05:00
Dan Davison a95c05773e babel: Fix unquoting of strings
Before this change we have

 #+begin_src ruby :results value :session
 ["1", "3"]
 #+end_src

 #+results:
 : 1", "3

 After, we have

 #+begin_src ruby :results value :session
 ["1", "3"]
 #+end_src

 #+results:
 | 1 | 3 |
2010-02-25 17:58:45 -05:00
Dan Davison 6f62066ac6 babel: Fix export bug.
Introduced at 747f425f00
2010-02-25 15:12:47 -05:00
Dan Davison eb521ae95e Remove org-R from contrib
org-babel should be used to execute R code from org-mode.
2010-02-24 12:42:48 -05:00
Eric Schulte 8625e5c0bc babel: gnuplot can now return it's string output -- when session is set to "none" 2010-02-23 08:16:25 -07:00
Dan Davison a2d94ffc8e babel: prevent quoting of strings in shell variables 2010-02-23 07:31:43 -07:00
Carsten Dominik 6a5f6deaac Fix bug in org-git-link.el.
Patch by David Maus
2010-02-20 20:34:39 +01:00
Eric Schulte 753d1402d8 babel: avoid infinite loop in org-babel-execute-buffer -- Thanks to Stephan Schmitt 2010-02-16 13:34:09 -07:00
Eric Schulte 574f1b590e babel: adding support for the OZ programming language -- Thanks to Torsten Anders!
For information on the OZ programming language see
  http://www.mozart-oz.org/, for information on using Org-babel with
  OZ see the OZ specific documentation on Worg at
  http://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-oz.php
2010-02-16 13:28:08 -07:00
Dan Davison 1e96482389 babel: check pdf file existence before deleting 2010-02-15 10:29:56 -07:00
Dan Davison 747f425f00 babel: only add srcname property for source blocks which actually have names 2010-02-15 10:07:23 -07:00
Eric Schulte 692c569215 babel: smarter `org-babel-ref-split-args' -- fixes bug parsing indexed function-style args 2010-02-14 11:48:28 -07:00
Eric Schulte 25f76ffa44 babel: now including source code block arguments w/source name on export
This change provides for better export of named source-code blocks,
  with specific support for more attractive html export.  The arguments
  are included with the source code name, and both the source code name
  and code body are wrapped in a div to support styling with css.  For
  example the following CSS can be used to associate a source-code block
  name with it's code body, and to slightly indent the body.

.org-src-container {
  border-left: 4px solid gray;
  padding: 0.5em 0.5em 0.5em 1em; }
  .org-src-container pre {
    margin-left: 1em; }
2010-02-10 13:34:00 -07:00
Carsten Dominik 9196dc9bbe Fix list export in org-export-generic
Patch by Robert Goldman
2010-02-10 11:36:58 +01:00
Eric Schulte 2531d704c0 babel: now able to reference links as results 2010-02-09 20:30:28 -07:00