Merge branch 'master' of git://repo.or.cz/org-mode

Makefile

@@ -18,8 +18,6 @@ prefix=/usr/local
 
 # Where local lisp files go.
 lispdir   = $(prefix)/share/emacs/site-lisp
-lispbdir  = $(lispdir)/babel
-lispbldir = $(lispbdir)/langs
 
 # Where info files go.
 infodir = $(prefix)/share/info
@@ -31,11 +29,7 @@ infodir = $(prefix)/share/info
 # Using emacs in batch mode.
 
 BATCH=$(EMACS) -batch -q -no-site-file -eval                             			\
-  "(setq load-path (cons (expand-file-name\
-                       \"langs\"\
-                       (expand-file-name \"babel\" (expand-file-name \"./lisp/\")))\
-                 (cons (expand-file-name \"babel\" (expand-file-name \"./lisp/\"))\
-                        (cons (expand-file-name \"./lisp/\") (cons \"$(lispdir)\" load-path)))))"
+  "(setq load-path (cons (expand-file-name \"./lisp/\") (cons \"$(lispdir)\" load-path)))"
 
 # Specify the byte-compiler for compiling org-mode files
 ELC= $(BATCH) -f batch-byte-compile
@@ -120,18 +114,17 @@ LISPF      = 	org.el			\
 		org-vm.el		\
 		org-w3m.el              \
 		org-wl.el		\
-		org-xoxo.el
-
-LISPBF     = 	ob.el			\
+		org-xoxo.el		\
+		ob.el			\
 		ob-table.el		\
 		ob-lob.el		\
 		ob-ref.el		\
 		ob-exp.el		\
 		ob-tangle.el		\
 		ob-comint.el		\
-		ob-keys.el
-
-LISPBLF   =	ob-C.el			\
+		ob-eval.el		\
+		ob-keys.el		\
+		ob-C.el			\
 		ob-ditaa.el		\
 		ob-haskell.el		\
 		ob-perl.el		\
@@ -156,11 +149,8 @@ LISPBLF   =	ob-C.el			\
 
 LISPFILES0  = $(LISPF:%=lisp/%)
 LISPFILES   = $(LISPFILES0) lisp/org-install.el
-LISPBFILES  = $(LISPBF:%=lisp/babel/%)
-LISPBLFILES = $(LISPBLF:%=lisp/babel/langs/%)
 ELCFILES0   = $(LISPFILES0:.el=.elc)
 ELCFILES    = $(LISPFILES:.el=.elc)
-ELCBFILES   = $(LISPBFILES:.el=.elc)
 DOCFILES    = doc/org.texi doc/org.pdf doc/org doc/dir \
               doc/pdflayout.sty doc/.nosearch \
               doc/orgguide.texi doc/orgguide.pdf
@@ -200,15 +190,10 @@ p:
 g:
 	${MAKE} pdf && open doc/orgguide.pdf
 
-install-lisp: $(LISPFILES) $(LISPBFILES) $(ELCFILES)
+install-lisp: $(LISPFILES) $(ELCFILES)
 	if [ ! -d $(lispdir) ]; then $(MKDIR) $(lispdir); else true; fi ;
-	if [ ! -d $(lispbdir) ]; then $(MKDIR) $(lispbdir); else true; fi ;
-	if [ ! -d $(lispbldir) ]; then $(MKDIR) $(lispbldir); else true; fi ;
 	$(CP) $(LISPFILES)  $(lispdir)
 	$(CP) $(ELCFILES)   $(lispdir)
-	$(CP) $(LISPBFILES) $(lispbdir)
-	$(CP) $(ELCBFILES)  $(lispbdir)
-	$(CP) $(LISPBLFILES) $(lispbldir)
 
 install-info: $(INFOFILES)
 	if [ ! -d $(infodir) ]; then $(MKDIR) $(infodir); else true; fi ;
@@ -224,13 +209,11 @@ install-noutline: xemacs/noutline.elc
 
 autoloads: lisp/org-install.el
 
-lisp/org-install.el: $(LISPFILES0) $(LISPBFILES) Makefile
+lisp/org-install.el: $(LISPFILES0) Makefile
 	$(BATCH) --eval "(require 'autoload)" \
 		--eval '(find-file "org-install.el")'  \
 		--eval '(erase-buffer)' \
-		--eval '(mapc (lambda (x) (generate-file-autoloads (symbol-name x))) (quote ($(LISPFILES0) $(LISPBFILES))))' \
-		--eval "(insert \"(add-to-list 'load-path (expand-file-name \\\"babel\\\" (file-name-directory (or load-file-name (buffer-file-name)))))\")" \
-		--eval "(insert \"\n(add-to-list 'load-path (expand-file-name \\\"langs\\\" (expand-file-name \\\"babel\\\" (file-name-directory (or load-file-name (buffer-file-name))))))\")\n" \
+		--eval '(mapc (lambda (x) (generate-file-autoloads (symbol-name x))) (quote ($(LISPFILES0))))' \
 		--eval '(insert "\n(provide (quote org-install))\n")' \
 		--eval '(save-buffer)'
 	mv org-install.el lisp
@@ -300,10 +283,7 @@ distfile:
 	$(MKDIR) org-$(TAG)/xemacs
 	$(MKDIR) org-$(TAG)/doc
 	$(MKDIR) org-$(TAG)/lisp
-	$(MKDIR) org-$(TAG)/lisp/babel
-	$(MKDIR) org-$(TAG)/lisp/babel/langs
 	cp -r $(LISPFILES) org-$(TAG)/lisp
-	cp -r $(LISPBFILES) org-$(TAG)/lisp/babel
 	cp -r $(DOCFILES) $(CARDFILES) org-$(TAG)/doc
 	cp -r $(DISTFILES_extra) org-$(TAG)/
 	cp -r README_DIST org-$(TAG)/README

doc/org.texi

@@ -260,7 +260,7 @@ Capture - Refile - Archive
 
 Capture
 
-* Setting up a capture location::  Where notes will be stored
+* Setting up capture::		Where notes will be stored
 * Using capture::		Commands to invoke and terminate capture
 * Capture templates::		Define the outline of different note types
 
@@ -5904,11 +5904,10 @@ trees to an archive file keeps the system compact and fast.
 @cindex capture
 
 Org's method for capturing new items is heavily inspired by John Wiegley
-excellent remember package.  Up to version 6.36 Org did actually use a
-special setup for @file{remember.el}.  @file{org-remember.el} is still part
-of Org-mode for backward compatibility with existing setups.  You can find
-the documentation for org-remember at
-@url{http://orgmode.org/org-remember.pdf}.
+excellent remember package.  Up to version 6.36 Org used a special setup
+for @file{remember.el}.  @file{org-remember.el} is still part of Org-mode for
+backward compatibility with existing setups.  You can find the documentation
+for org-remember at @url{http://orgmode.org/org-remember.pdf}.
 
 The new capturing setup described here is preferred and should be used by new
 users.  To convert your @code{org-remember-templates}, run the command
@@ -5917,32 +5916,32 @@ users.  To convert your @code{org-remember-templates}, run the command
 @end example
 @noindent and then customize the new variable with @kbd{M-x
 customize-variable org-capture-templates}, check the result, and save the
-customization.  You will then be able to use both remember and capture until
-you have gotten used to the new mechanism.
+customization.  You can then use both remember and capture until
+you are familiar with the new mechanism.
 
-Capture lets you store quick notes with little interruption of your work
+Capture lets you quickly store notes with little interruption of your work
 flow.  The basic process of capturing is very similar to remember, but Org
 does enhance it with templates and more.
 
 @menu
-* Setting up a capture location::  Where notes will be stored
+* Setting up capture::		Where notes will be stored
 * Using capture::		Commands to invoke and terminate capture
 * Capture templates::		Define the outline of different note types
 @end menu
 
-@node Setting up a capture location, Using capture, Capture, Capture
-@subsection Setting up a capture location
+@node Setting up capture, Using capture, Capture, Capture
+@subsection Setting up capture
 
 The following customization sets a default target file for notes, and defines
 a global key@footnote{Please select your own key, @kbd{C-c c} is only a
-suggestion.}  for capturing new stuff.
+suggestion.}  for capturing new material.
 
 @example
 (setq org-default-notes-file (concat org-directory "/notes.org"))
 (define-key global-map "\C-cc" 'org-capture)
 @end example
 
-@node Using capture, Capture templates, Setting up a capture location, Capture
+@node Using capture, Capture templates, Setting up capture, Capture
 @subsection Using capture
 
 @table @kbd
@@ -5956,14 +5955,14 @@ node.  You may then insert the information you want.
 
 @kindex C-c C-c
 @item C-c C-c
-Once you are done entering information into the capture buffer, 
+Once you have finished entering information into the capture buffer, 
 @kbd{C-c C-c} will return you to the window configuration before the capture
 process, so that you can resume your work without further distraction.
 
 @kindex C-c C-w
 @item C-c C-w
-When this command is used in the capture buffer, it will finalize the capture
-process by refiling (@pxref{Refiling notes}) the note to a different place.
+Finalize the capture process by refiling (@pxref{Refiling notes}) the note to
+a different place.
 
 @kindex C-c C-k
 @item C-c C-k
@@ -5979,8 +5978,8 @@ rather than to the current date.
 @subsection Capture templates
 @cindex templates, for Capture
 
-You can use templates to arrange for different types of capture items, and
-for different target locations.  The easiest way to set up such templates is
+You can use templates for different types of capture items, and
+for different target locations.  The easiest way to create such templates is
 through the customize interface.
 
 @table @kbd
@@ -5994,7 +5993,7 @@ an example.  Say you would like to use one template to create general TODO
 entries, and you want to put these entries under the heading @samp{Tasks} in
 your file @file{~/org/gtd.org}.  Also, a date tree in the file
 @file{journal.org} should capture journal entries.  A possible configuration
-would then look like this:
+would look like:
 
 @example
 (setq org-capture-templates
@@ -6015,7 +6014,7 @@ for you like this:
 During expansion of the template, @code{%a} has been replaced by a link to
 the location from where you called the capture command.  This can be
 extremely useful for deriving tasks from emails, for example.  You fill in
-the task definition, press @code{C-c C-c} and Org puts you back into the same
+the task definition, press @code{C-c C-c} and Org returns you to the same
 place where you started the capture process.
 
 
@@ -6056,15 +6055,15 @@ An Org-mode node, with a headline. Will be filed as the child of the
 target entry or as a top-level entry.  The target file should be an Org-mode
 file.
 @item item
-A plain list item, placed in the first plain  list a the target
+A plain list item, placed in the first plain  list at the target
 location.  Again the target file should be an Org file.
 @item checkitem
-A checkbox item.  This only differs from the plain lis item by the
+A checkbox item.  This only differs from the plain list item by the
 default template.
 @item table-line
-a new line in the first table at target location.  Where exactly the
+a new line in the first table at the target location.  Where exactly the
 line will be inserted depends on the properties @code{:prepend} and
-@code{:table-line-pos} (see below)
+@code{:table-line-pos} (see below).
 @item plain
 Text to be inserted as it is.
 @end table
@@ -6078,13 +6077,13 @@ body of this node.
 Valid values are:
 @table @code
 @item (file "path/to/file")
-Text will be placed at the beginning or end of that file
+Text will be placed at the beginning or end of that file.
 
 @item (id "id of existing org entry")
-Filing as child of this entry, or in the body of the entry
+Filing as child of this entry, or in the body of the entry.
 
 @item (file+headline "path/to/file" "node headline")
-Fast configuration if the target heading is unique in the file
+Fast configuration if the target heading is unique in the file.
 
 @item (file+olp "path/to/file" "Level 1 heading" "Level 2" ...)
 For non-unique headings, the full path is safer.
@@ -6109,7 +6108,7 @@ file and location.
 @item template
 The template for creating the capture item.  If you leave this
 empty, an appropriate default template will be used.  Otherwise this is a
-string with a number of escape code, which will be replaced depending on time
+string with  escape codes, which will be replaced depending on time
 and context of the capture call.  See below for more details.
 
 @item properties
@@ -6127,19 +6126,19 @@ file it away immediately.  This makes sense if the template only needs
 information that can be added automatically.
 
 @item :empty-lines
-Set this to the number of lines the should be inserted
+Set this to the number of lines to insert
 before and after the new item.  Default 0, only common other value is 1.
 
 @item :clock-in
 Start the clock in this item.
 
 @item :clock-resume
-If Starting the capture interrupted a clock, restart that clock when done
+If starting the capture interrupted a clock, restart that clock when finished
 with the capture.
 
 @item :unnarrowed
 Do not narrow the target buffer, simply show the full buffer.  Default is to
-narrow it so that you only see the new stuff.
+narrow it so that you only see the new material.
 @end table
 @end table
 
@@ -6149,6 +6148,8 @@ narrow it so that you only see the new stuff.
 In the template itself, special @kbd{%}-escapes@footnote{If you need one of
 these sequences literally, escape the @kbd{%} with a backslash.}  allow
 dynamic insertion of content:
+
+@comment SJE: should these sentences terminate in period?
 @smallexample
 %^@{@var{prompt}@}  @r{prompt the user for a string and replace this sequence with it.}
             @r{You may specify a default value and a completion table with}
@@ -6177,9 +6178,6 @@ dynamic insertion of content:
 %:keyword   @r{specific information for certain link types, see below}
 %[@var{file}]     @r{insert the contents of the file given by @var{file}}
 %(@var{sexp})     @r{evaluate Elisp @var{sexp} and replace with the result}
-%!          @r{immediately store note after completing the template}
-            @r{(skipping the @kbd{C-c C-c} that normally triggers storing)}
-%&          @r{jump to target location immediately after storing note}
 @end smallexample
 
 @noindent
@@ -6202,7 +6200,7 @@ vm, wl, mh, rmail  |  %:type %:subject %:message-id
 gnus               |  %:group, @r{for messages also all email fields}
 w3, w3m            |  %:url
 info               |  %:file %:node
-calendar           |  %:date"
+calendar           |  %:date
 @end smallexample
 
 @noindent
@@ -6220,7 +6218,7 @@ To place the cursor after template expansion use:
 @vindex org-attach-directory
 It is often useful to associate reference material with an outline node/task.
 Small chunks of plain text can simply be stored in the subtree of a project.
-Hyperlinks (@pxref{Hyperlinks}) can be used to establish associations with
+Hyperlinks (@pxref{Hyperlinks}) can establish associations with
 files that live elsewhere on your computer or in the cloud, like emails or
 source code files belonging to a project.  Another method is @i{attachments},
 which are files located in a directory belonging to an outline node.  Org
@@ -6237,14 +6235,14 @@ choice to an entry.  You can also make children inherit the attachment
 directory from a parent, so that an entire subtree uses the same attached
 directory.
 
-@noindent The following commands deal with attachments.
+@noindent The following commands deal with attachments:
 
 @table @kbd
 
 @kindex C-c C-a
 @item C-c C-a
 The dispatcher for commands related to the attachment system.  After these
-keys, a list of commands is displayed and you need to press an additional key
+keys, a list of commands is displayed and you must press an additional key
 to select a command:
 
 @table @kbd
@@ -6274,7 +6272,7 @@ attachments yourself.
 @kindex C-c C-a o
 @item o
 @vindex org-file-apps
-Open current task's attachment.  If there are more than one, prompt for a
+Open current task's attachment.  If there is more than one, prompt for a
 file name first.  Opening will follow the rules set by @code{org-file-apps}.
 For more details, see the information on following hyperlinks
 (@pxref{Handling links}).
@@ -6318,12 +6316,12 @@ same directory for attachments as the parent does.
 @section RSS feeds
 @cindex RSS feeds
 
-Org has the capability to add and change entries based on information found in
-RSS feeds.  You could use this to make a task out of each new podcast in a
-podcast feed.  Or you could use a phone-based note-creating service on the
-web to import tasks into Org.  To access feeds, you need to configure the
-variable @code{org-feed-alist}.  The docstring of this variable has detailed
-information.  Here is just an example:
+Org can add and change entries based on information found in RSS feeds.  You
+could use this to make a task out of each new podcast in a podcast feed.  Or
+you could use a phone-based note-creating service on the web to import tasks
+into Org.  To access feeds, configure the variable @code{org-feed-alist}.
+The docstring of this variable has detailed information.  Here is just an
+example:
 
 @example
 (setq org-feed-alist
@@ -6538,7 +6536,7 @@ Archived trees are excluded from column view unless the variable
 @code{org-columns-skip-archived-trees} is configured to @code{nil}.
 @end itemize
 
-The following commands help managing the ARCHIVE tag:
+The following commands help manage the ARCHIVE tag:
 
 @table @kbd
 @kindex C-c C-x a
@@ -11130,6 +11128,13 @@ Choose a file to tangle.
 @cindex code block, evaluating
 @cindex source code, evaluating
 
+@quotation
+Whenever code is evaluated there is a potential for that code to do harm.
+Org-mode provides a number of safeguards to ensure that it only evaluates
+code with explicit confirmation from the user.  For information on these
+safeguards (and on how to disable them) see @ref{Code evaluation security}.
+@end quotation
+
 Code blocks can be evaluated and the results placed in the Org-mode buffer.
 By default, evaluation is only turned on for @code{emacs-lisp} code blocks,
 however support exists for evaluating blocks in many languages.  See
@@ -11138,9 +11143,14 @@ code blocks} for information on the syntax used to define a code block.
 
 @kindex C-c C-c
 There are a number of ways to evaluate code blocks.  The simplest is to
-press @kbd{C-c C-c} with the point on a code block.  This will call the
-@code{org-babel-execute-src-block} function to evaluate the block and
-insert its results into the Org-mode buffer.
+press @kbd{C-c C-c} or @kbd{C-c C-v e} with the point on a code block.  This
+will call the @code{org-babel-execute-src-block} function to evaluate the
+block and insert its results into the Org-mode buffer.
+
+@quotation
+The @code{org-babel-no-eval-on-ctrl-c-ctrl-c} variable can be used to remove
+code evaluation from the @kbd{C-c C-c} key binding.
+@end quotation
 
 It is also possible to evaluate named code blocks from anywhere in an
 Org-mode buffer or an Org-mode table.  @code{#+call} (or synonymously
@@ -11214,22 +11224,33 @@ Language specific documentation is available for some languages.  If
 available, it can be found at
 @uref{http://orgmode.org/worg/org-contrib/babel/languages}.
 
+The @code{org-babel-load-languages} controls which languages are enabled for
+evaluation (by default only @code{emacs-lisp} is enabled).  This variable can
+be set using the customization interface or by adding code like the following
+to your emacs configuration.
 
-To add support for a particular language to your installation:
+@quotation
+The following disables @code{emacs-lisp} evaluation and enables evaluation of
+@code{R} code blocks.
+@end quotation
 
-@enumerate
-@item
-ensure that the language-specific requirements are met, then
-@item
-add a line to your Emacs configuration like
 @lisp
-(require 'ob-identifier)
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+ '((emacs-lisp . nil)
+   (R . t)))
 @end lisp
-where ``identifier'' is taken from the table above, e.g.,
+
+It is also possible to enable support for a language by loading the related
+elisp file with @code{require}.
+
+@quotation
+The following adds support for evaluating @code{clojure} code blocks.
+@end quotation
+
 @lisp
-(require 'ob-sass)
+(require 'ob-clojure)
 @end lisp
-@end enumerate
 
 @node Header arguments, Results of evaluation, Languages, Working With Source Code
 @section Header arguments
@@ -11396,6 +11417,7 @@ The following header arguments are defined:
 * exports::			Export code and/or results
 * tangle::			Toggle tangling and specify file name
 * no-expand::			Turn off variable assignment and noweb expansion during tangling
+* comments::                    Toggle insertion of comments in tangled code files
 * session::			Preserve the state of code evaluation
 * noweb::			Toggle expansion of noweb references
 * cache::			Avoid re-evaluating unchanged code blocks
@@ -11739,7 +11761,7 @@ Both the code and results are included in the exported file. E.g.,
 Nothing is included in the exported file.  E.g., @code{:exports none}.
 @end itemize
 
-@node tangle, no-expand, exports, Specific header arguments
+@node tangle, comments, exports, Specific header arguments
 @subsubsection @code{:tangle}
 
 The @code{:tangle} header argument specifies whether or not the code
@@ -11759,7 +11781,16 @@ as a file basename to which the block will be exported.  E.g., @code{:tangle
 basename}.
 @end itemize
 
-@node no-expand, session, tangle, Specific header arguments
+@node comments, no-expand, tangle, Specific header arguments
+@subsubsection @code{:comments}
+By default code blocks are tangled to source-code files without any insertion
+of comments beyond those which may already exist in the body of the code
+block.  The @code{:comments} header argument can be set to ``yes''
+e.g. @code{:comments yes} to enable the insertion of comments around code
+blocks during tangling.  The inserted comments contain pointers back to the
+original Org file from which the comment was tangled.
+
+@node no-expand, session, comments, Specific header arguments
 @subsubsection @code{:no-expand}
 
 By default, code blocks are expanded with @code{org-babel-expand-src-block}
@@ -12317,7 +12348,7 @@ Make sure you know what you are doing before customizing the variables
 which take of the default security brakes.
 
 @defopt org-confirm-babel-evaluate
-Does code evaluation have to be acknowledged by the user?
+When set to t user is queried before code block evaluation
 @end defopt
 
 @item Following @code{shell} and @code{elisp} links
@@ -12689,12 +12720,11 @@ more text                        |          more text
 
 @noindent
 
-If you are using at least Emacs 23.2 and version 6.29 of Org, this kind of
-view can be achieved dynamically at display time using
-@code{org-indent-mode}.  @i{Using this with earlier versions of Emacs can
-lead to crashes.} In this minor
-mode, all lines are prefixed for display with the necessary amount of
-space@footnote{@code{org-indent-mode} also sets the @code{wrap-prefix}
+If you are using at least Emacs 23.2@footnote{Emacs 23.1 can actually crash
+with @code{org-indent-mode}} and version 6.29 of Org, this kind of view can
+be achieved dynamically at display time using @code{org-indent-mode}.  In
+this minor mode, all lines are prefixed for display with the necessary amount
+of space@footnote{@code{org-indent-mode} also sets the @code{wrap-prefix}
 property, such that @code{visual-line-mode} (or purely setting
 @code{word-wrap}) wraps long lines (including headlines) correctly indented.
 }.  Also headlines are prefixed with additional stars, so that the amount of

lisp/babel/langs/ob-C.el → lisp/ob-C.el

@@ -32,10 +32,12 @@
 
 ;;; Code:
 (require 'ob)
+(require 'ob-eval)
 (require 'org)
 (require 'cc-mode)
 
-(declare-function org-entry-get "org" (&optional inherit))
+(declare-function org-entry-get "org"
+		  (pom property &optional inherit literal-nil))
 
 (add-to-list 'org-babel-tangle-lang-exts '("c++" . "cpp"))
 
@@ -112,14 +114,12 @@ or `org-babel-execute:c++'."
         (org-babel-reassemble-table
          (org-babel-read
           (org-babel-trim
-           (with-temp-buffer
-             (org-babel-shell-command-on-region
-              (point-min) (point-max)
-              (concat tmp-bin-file (if cmdline (concat " " cmdline) ""))
-              (current-buffer) 'replace)
-             (buffer-string))))
-         (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
-         (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params))))
+	   (org-babel-eval
+	    (concat tmp-bin-file (if cmdline (concat " " cmdline) "")) "")))
+         (org-babel-pick-name
+	  (nth 4 processed-params) (cdr (assoc :colnames params)))
+         (org-babel-pick-name
+	  (nth 5 processed-params) (cdr (assoc :rownames params))))
       (progn
         (with-current-buffer error-buf
           (goto-char (point-max))

lisp/babel/langs/ob-R.el → lisp/ob-R.el

@@ -28,6 +28,14 @@
 
 ;;; Code:
 (require 'ob)
+(require 'ob-ref)
+(require 'ob-comint)
+(require 'ob-eval)
+(eval-when-compile (require 'cl))
+
+(declare-function orgtbl-to-tsv "ob-table" (table params))
+(declare-function R "ext:essd-r" (&optional start-args))
+(declare-function inferior-ess-send-input "ext:ess-inf" ())
 
 (defconst org-babel-header-arg-names:R
   '(width height bg units pointsize antialias quality compression
@@ -37,26 +45,40 @@
 
 (defvar org-babel-default-header-args:R '())
 
+(defvar org-babel-R-command "R --slave --no-save"
+  "Name of command to use for executing R code.")
+
 (defun org-babel-expand-body:R (body params &optional processed-params)
   "Expand BODY according to PARAMS, return the expanded body."
   (let* ((processed-params (or processed-params
                                (org-babel-process-params params)))
-	 (vars (mapcar (lambda (i) (cons (car (nth i (nth 1 processed-params)))
-					 (org-babel-reassemble-table
-					  (cdr (nth i (nth 1 processed-params)))
-					  (cdr (nth i (nth 4 processed-params)))
-					  (cdr (nth i (nth 5 processed-params))))))
-		       (number-sequence 0 (1- (length (nth 1 processed-params))))))
+	 (vars (mapcar
+		(lambda (i)
+		  (cons (car (nth i (nth 1 processed-params)))
+			(org-babel-reassemble-table
+			 (cdr (nth i (nth 1 processed-params)))
+			 (cdr (nth i (nth 4 processed-params)))
+			 (cdr (nth i (nth 5 processed-params))))))
+		(number-sequence 0 (1- (length (nth 1 processed-params))))))
          (out-file (cdr (assoc :file params))))
-    (concat
-     (if out-file (concat (org-babel-R-construct-graphics-device-call out-file params) "\n") "")
-     (mapconcat ;; define any variables
-      (lambda (pair)
-	(org-babel-R-assign-elisp (car pair) (cdr pair)
-				  (equal "yes" (cdr (assoc :colnames params)))
-				  (equal "yes" (cdr (assoc :rownames params)))))
-      vars "\n")
-     "\n" body "\n" (if out-file "dev.off()\n" ""))))
+    (mapconcat ;; define any variables
+     #'org-babel-trim
+     ((lambda (inside)
+	(if out-file
+	    (append
+	     (list (org-babel-R-construct-graphics-device-call out-file params))
+	     inside
+	     (list "dev.off()"))
+	  inside))
+      (append
+       (mapcar
+	(lambda (pair)
+	  (org-babel-R-assign-elisp
+	   (car pair) (cdr pair)
+	   (equal "yes" (cdr (assoc :colnames params)))
+	   (equal "yes" (cdr (assoc :rownames params)))))
+	vars)
+       (list body))) "\n")))
 
 (defun org-babel-execute:R (body params)
   "Execute a block of R code with org-babel.  This function is
@@ -65,7 +87,8 @@ called by `org-babel-execute-src-block'."
   (save-excursion
     (let* ((processed-params (org-babel-process-params params))
            (result-type (nth 3 processed-params))
-           (session (org-babel-R-initiate-session (first processed-params) params))
+           (session (org-babel-R-initiate-session
+		     (first processed-params) params))
 	   (colnames-p (cdr (assoc :colnames params)))
 	   (rownames-p (cdr (assoc :rownames params)))
 	   (out-file (cdr (assoc :file params)))
@@ -77,6 +100,7 @@ called by `org-babel-execute-src-block'."
 		 (org-babel-pick-name (nth 4 processed-params) colnames-p))
 	     (or (equal "yes" rownames-p)
 		 (org-babel-pick-name (nth 5 processed-params) rownames-p)))))
+      (message "result is %S" result)
       (or out-file result))))
 
 (defun org-babel-prep-session:R (session params)
@@ -86,9 +110,9 @@ called by `org-babel-execute-src-block'."
 	 (var-lines
 	  (mapcar
 	   (lambda (pair) (org-babel-R-assign-elisp
-			   (car pair) (cdr pair)
-			   (equal (cdr (assoc :colnames params)) "yes")
-			   (equal (cdr (assoc :rownames params)) "yes")))
+		      (car pair) (cdr pair)
+		      (equal (cdr (assoc :colnames params)) "yes")
+		      (equal (cdr (assoc :rownames params)) "yes")))
 	   vars)))
     (org-babel-comint-in-buffer session
       (mapc (lambda (var)
@@ -136,9 +160,14 @@ called by `org-babel-execute-src-block'."
       (if (org-babel-comint-buffer-livep session)
 	  session
 	(save-window-excursion
-	  (R)
-	  (rename-buffer (if (bufferp session) (buffer-name session)
-			   (if (stringp session) session (buffer-name)))) (current-buffer))))))
+	  (require 'ess) (R)
+	  (rename-buffer
+	   (if (bufferp session)
+	       (buffer-name session)
+	     (if (stringp session)
+		 session
+	       (buffer-name))))
+	  (current-buffer))))))
 
 (defun org-babel-R-construct-graphics-device-call (out-file params)
   "Construct the call to the graphics device."
@@ -153,25 +182,36 @@ called by `org-babel-execute-src-block'."
 	   (:ps . "postscript")
 	   (:postscript . "postscript")))
 	(allowed-args '(:width :height :bg :units :pointsize
-			       :antialias :quality :compression :res :type
-			       :family :title :fonts :version :paper :encoding
-			       :pagecentre :colormodel :useDingbats :horizontal))
-	(device (and (string-match ".+\\.\\([^.]+\\)" out-file) (match-string 1 out-file)))
+			       :antialias :quality :compression :res
+			       :type :family :title :fonts :version
+			       :paper :encoding :pagecentre :colormodel
+			       :useDingbats :horizontal))
+	(device (and (string-match ".+\\.\\([^.]+\\)" out-file)
+		     (match-string 1 out-file)))
 	(extra-args (cdr (assq :R-dev-args params))) filearg args)
-    (setq device (or (and device (cdr (assq (intern (concat ":" device)) devices))) "png"))
-    (setq filearg (if (member device '("pdf" "postscript" "svg")) "file" "filename"))
-    (setq args (mapconcat (lambda (pair)
-			    (if (member (car pair) allowed-args)
-				(format ",%s=%s" (substring (symbol-name (car pair)) 1) (cdr pair)) ""))
-			  params ""))
-    (format "%s(%s=\"%s\"%s%s%s)\n" device filearg out-file args (if extra-args "," "") (or extra-args ""))))
+    (setq device (or (and device (cdr (assq (intern (concat ":" device))
+					    devices))) "png"))
+    (setq filearg
+	  (if (member device '("pdf" "postscript" "svg")) "file" "filename"))
+    (setq args (mapconcat
+		(lambda (pair)
+		  (if (member (car pair) allowed-args)
+		      (format ",%s=%s"
+			      (substring (symbol-name (car pair)) 1)
+			      (cdr pair)) ""))
+		params ""))
+    (format "%s(%s=\"%s\"%s%s%s)"
+	    device filearg out-file args
+	    (if extra-args "," "") (or extra-args ""))))
 
 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 (defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
 write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
+(defvar org-babel-R-wrapper-lastvar "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
 
-(defun org-babel-R-evaluate (session body result-type column-names-p row-names-p)
+(defun org-babel-R-evaluate
+  (session body result-type column-names-p row-names-p)
   "Pass BODY to the R process in SESSION.  If RESULT-TYPE equals
 'output then return a list of the outputs of the statements in
 BODY, if RESULT-TYPE equals 'value then return the value of the
@@ -179,65 +219,52 @@ last statement in BODY, as elisp."
   (if (not session)
       ;; external process evaluation
       (case result-type
-	(output
-	 (with-temp-buffer
-	   (insert body)
-	   (org-babel-shell-command-on-region (point-min) (point-max) "R --slave --no-save" 'current-buffer 'replace)
-	   (org-babel-trim (buffer-string))))
+	(output (org-babel-eval org-babel-R-command body))
 	(value
-	 (let* ((tmp-file (make-temp-file "R-out-functional-results")) exit-code
-		(stderr
-		 (with-temp-buffer
-		   (insert (format org-babel-R-wrapper-method
-				   body tmp-file (if row-names-p "TRUE" "FALSE") (if column-names-p (if row-names-p "NA" "TRUE") "FALSE")))
-		   (setq exit-code (org-babel-shell-command-on-region
-				    (point-min) (point-max) "R --no-save" nil 'replace (current-buffer)))
-		   (buffer-string))))
-	   (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
+	 (let ((tmp-file (make-temp-file "org-babel-R-results-")))
+	   (org-babel-eval org-babel-R-command
+			   (format org-babel-R-wrapper-method
+				   body tmp-file
+				   (if row-names-p "TRUE" "FALSE")
+				   (if column-names-p
+				       (if row-names-p "NA" "TRUE")
+				     "FALSE")))
 	   (org-babel-R-process-value-result
-	    (org-babel-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))
-	    column-names-p))))
+	    (org-babel-import-elisp-from-file
+	     (org-babel-maybe-remote-file tmp-file)) column-names-p))))
     ;; comint session evaluation
-    (org-babel-comint-in-buffer session
-      (let* ((tmp-file (make-temp-file "org-babel-R"))
-	     (full-body
-	      (case result-type
-		(value
-		 (mapconcat #'org-babel-chomp (list body
-						    (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)" tmp-file (if row-names-p "TRUE" "FALSE") (if column-names-p  (if row-names-p "NA" "TRUE") "FALSE"))
-						    org-babel-R-eoe-indicator) "\n"))
-		(output
-		 (mapconcat #'org-babel-chomp (list body org-babel-R-eoe-indicator) "\n"))))
-	     (raw
-	      (org-babel-comint-with-output (session org-babel-R-eoe-output)
-		(insert full-body) (inferior-ess-send-input)))
-	     (comint-prompt-regexp
-	      (concat "^\\("
-		      inferior-ess-primary-prompt
-		      "\\|"
-		      inferior-ess-secondary-prompt
-		      "\\)*"))
-	     broke results)
-        (case result-type
-          (value (org-babel-R-process-value-result
-		  (org-babel-import-elisp-from-file
-		   (org-babel-maybe-remote-file tmp-file))
-		  column-names-p))
-          (output
-	   (flet ((extractor
-		   (el)
-		   (if (or broke
-			   (and (string-match (regexp-quote org-babel-R-eoe-output) el)
-				(setq broke t)))
-		       nil
-		     (if (= (length el) 0)
-			 nil
-		       (if (string-match comint-prompt-regexp el)
-			   (org-babel-trim (substring el (match-end 0)))
-			 el)))))
-	     (mapconcat
-	      #'identity
-	      (delete nil (mapcar #'extractor (mapcar #'org-babel-chomp raw))) "\n"))))))))
+    (case result-type
+      (value
+       (let ((tmp-file (make-temp-file "org-babel-R"))
+	     broke)
+	 (org-babel-comint-with-output (session org-babel-R-eoe-output)
+	   (insert (mapconcat
+		    #'org-babel-chomp
+		    (list
+		     body
+		     (format org-babel-R-wrapper-lastvar
+			     tmp-file
+			     (if row-names-p "TRUE" "FALSE")
+			     (if column-names-p
+				 (if row-names-p "NA" "TRUE")
+			       "FALSE"))
+		     org-babel-R-eoe-indicator) "\n"))
+	   (inferior-ess-send-input))
+	 (org-babel-R-process-value-result
+	  (org-babel-import-elisp-from-file
+	   (org-babel-maybe-remote-file tmp-file))  column-names-p)))
+      (output
+       (mapconcat
+	#'org-babel-chomp
+	(butlast
+	 (delq nil
+	       (mapcar
+		#'identity
+		(org-babel-comint-with-output (session org-babel-R-eoe-output)
+		  (insert (mapconcat #'org-babel-chomp
+				     (list body org-babel-R-eoe-indicator)
+				     "\n"))
+		  (inferior-ess-send-input)))) 2) "\n")))))
 
 (defun org-babel-R-process-value-result (result column-names-p)
   "R-specific processing of return value prior to return to

lisp/babel/langs/ob-asymptote.el → lisp/ob-asymptote.el

@@ -46,6 +46,9 @@
 (require 'ob)
 (eval-when-compile (require 'cl))
 
+(declare-function orgtbl-to-generic "org-table" (table params))
+(declare-function org-combine-plists "org" (&rest plists))
+
 (add-to-list 'org-babel-tangle-lang-exts '("asymptote" . "asy"))
 
 (defvar org-babel-default-header-args:asymptote

lisp/babel/langs/ob-clojure.el → lisp/ob-clojure.el

@@ -39,9 +39,16 @@
 
 ;;; Code:
 (require 'ob)
-(require 'cl)
-(require 'slime)
-(require 'swank-clojure)
+(require 'ob-eval)
+(eval-when-compile (require 'cl))
+
+(declare-function slime-eval-async "ext:slime" (sexp &optional cont package))
+(declare-function slime-eval "ext:slime" (sexp &optional package))
+(declare-function swank-clojure-concat-paths "ext:slime" (paths))
+(declare-function org-babel-ref-variables "ext:slime" (params))
+(declare-function slime "ext:slime" (&optional command coding-system))
+(declare-function slime-output-buffer "ext:slime" (&optional noprompt))
+(declare-function slime-filter-buffers "ext:slime" (predicate))
 
 (add-to-list 'org-babel-tangle-lang-exts '("clojure" . "clj"))
 
@@ -63,7 +70,8 @@
   []
   %s)
 
-(spit \"%s\" (str (main)))") ;;" <-- syntax highlighting is messed without this double quote
+(spit \"%s\" (str (main)))")
+;;";; <-- syntax highlighting is messed without this double quote
 
 ;;taken mostly from clojure-test-mode.el
 (defun org-babel-clojure-clojure-slime-eval (string &optional handler)
@@ -76,16 +84,23 @@
   (slime-eval `(swank:eval-and-grab-output ,string)))
 
 ;;taken from swank-clojure.el
+(defvar swank-clojure-binary)
+(defvar swank-clojure-classpath)
+(defvar swank-clojure-java-path)
+(defvar swank-clojure-extra-vm-args)
+(defvar swank-clojure-library-paths)
+(defvar swank-clojure-extra-classpaths)
 (defun org-babel-clojure-babel-clojure-cmd ()
   "Create the command to start clojure according to current settings."
   (if (and (not swank-clojure-binary) (not swank-clojure-classpath))
-      (error "You must specifiy either a `swank-clojure-binary' or a `swank-clojure-jar-path'")
+      (error (concat "You must specifiy either a `swank-clojure-binary' "
+		     "or a `swank-clojure-jar-path'"))
     (if swank-clojure-binary
         (if (listp swank-clojure-binary)
             swank-clojure-binary
           (list swank-clojure-binary))
-      (delete-if
-       'null
+      (delq
+       nil
        (append
         (list swank-clojure-java-path)
         swank-clojure-extra-vm-args
@@ -123,15 +138,20 @@ specifying a var of the same value."
 
 (defun org-babel-clojure-build-full-form (body vars)
   "Construct a clojure let form with vars as the let vars."
-  (let ((vars-forms (mapconcat ;; define any variables
-                      (lambda (pair)
-                        (format "%s %s" (car pair) (org-babel-clojure-var-to-clojure (cdr pair))))
-                      vars "\n      "))
+  (let ((vars-forms
+	 (mapconcat ;; define any variables
+	  (lambda (pair)
+	    (format "%s %s"
+		    (car pair) (org-babel-clojure-var-to-clojure (cdr pair))))
+	  vars "\n      "))
 	(body (org-babel-trim body)))
-    (if (> (length vars-forms) 0) (format "(let [%s]\n  %s)" vars-forms body) body)))
+    (if (> (length vars-forms) 0)
+	(format "(let [%s]\n  %s)" vars-forms body)
+      body)))
 
 (defun org-babel-prep-session:clojure (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
+  (require 'slime) (require 'swank-clojure)
   (let* ((session-buf (org-babel-clojure-initiate-session session))
          (vars (org-babel-ref-variables params))
          (var-lines (mapcar ;; define any top level session variables
@@ -143,6 +163,7 @@ specifying a var of the same value."
 
 (defun org-babel-load-session:clojure (session body params)
   "Load BODY into SESSION."
+  (require 'slime) (require 'swank-clojure)
   (save-window-excursion
     (let ((buffer (org-babel-prep-session:clojure session params)))
       (with-current-buffer buffer
@@ -164,10 +185,11 @@ then create one.  Return the initialized session."
     (let* ((session (if session
                         (if (stringp session) (intern session)
                           session)
-                        :default))
+		      :default))
            (clojure-buffer (org-babel-clojure-session-buffer session)))
       (unless (and clojure-buffer (buffer-live-p clojure-buffer))
-        (setq org-babel-clojure-buffers (assq-delete-all session org-babel-clojure-buffers))
+        (setq org-babel-clojure-buffers
+	      (assq-delete-all session org-babel-clojure-buffers))
         (push session org-babel-clojure-pending-sessions)
         (slime)
         ;; we are waiting to finish setting up which will be done in
@@ -175,7 +197,8 @@ then create one.  Return the initialized session."
         (let ((timeout 9))
           (while (and (not (org-babel-clojure-session-buffer session))
                       (< 0 timeout))
-            (message "Waiting for clojure repl for session: %s ... %i" session timeout)
+            (message "Waiting for clojure repl for session: %s ... %i"
+		     session timeout)
             (sit-for 1)
             (decf timeout)))
         (setq org-babel-clojure-pending-sessions
@@ -188,8 +211,10 @@ then create one.  Return the initialized session."
 (defun org-babel-clojure-initiate-session (&optional session params)
   "Return the slime-clojure repl buffer bound to this session
 or nil if \"none\" is specified."
+  (require 'slime) (require 'swank-clojure)
   (unless (and (stringp session) (string= session "none"))
-    (org-babel-clojure-session-buffer (org-babel-clojure-initiate-session-by-key session))))
+    (org-babel-clojure-session-buffer
+     (org-babel-clojure-initiate-session-by-key session))))
 
 (defun org-babel-clojure-session-connected-hook ()
   "Finish setting up the bindings of org-babel session to a slime-clojure repl."
@@ -197,8 +222,11 @@ or nil if \"none\" is specified."
     (when pending-session
       (save-excursion
         (switch-to-buffer (slime-output-buffer))
-        (rename-buffer (if (stringp pending-session) pending-session (symbol-name pending-session)))
-        (org-babel-clojure-bind-session-to-repl-buffer pending-session (slime-output-buffer))))))
+        (rename-buffer
+	 (if (stringp pending-session)
+	     pending-session (symbol-name pending-session)))
+        (org-babel-clojure-bind-session-to-repl-buffer
+	 pending-session (slime-output-buffer))))))
 
 (add-hook 'slime-connected-hook 'org-babel-clojure-session-connected-hook)
 
@@ -222,48 +250,41 @@ repl buffer."
     (let ((repl-buf (read-buffer "Choose slime-clojure repl: " repl-bufs t)))
       (org-babel-clojure-bind-session-to-repl-buffer session repl-buf))))
 
-(defun org-babel-clojure-evaluate-external-process (buffer body &optional result-type)
+(defun org-babel-clojure-evaluate-external-process
+  (buffer body &optional result-type)
   "Evaluate the body in an external process."
-  (save-excursion
-    (let ((cmd (format "%s -" (mapconcat #'identity (org-babel-clojure-babel-clojure-cmd) " "))))
-      (case result-type
-	(output
-	 (with-temp-buffer
-	   (insert body)
-	   (org-babel-shell-command-on-region cmd (point-min) (point-max) 'current-buffer 'replace)
-	   (buffer-string)))
-	(value
-	 (let* ((tmp-file (make-temp-file "org-babel-clojure-results-")) exit-code
-		(stderr
-		 (with-temp-buffer
-		   (insert
-		    (format org-babel-clojure-wrapper-method body tmp-file tmp-file))
-		   (setq exit-code
-			 (org-babel-shell-command-on-region (point-min) (point-max) cmd nil 'replace (current-buffer)))
-		   (buffer-string))))
-	   (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
-	   (org-babel-clojure-table-or-string
-	    (with-temp-buffer
-	      (insert-file-contents (org-babel-maybe-remote-file tmp-file)) (buffer-string)))))))))
+  (let ((cmd (format "%s -" (mapconcat #'identity
+				       (org-babel-clojure-babel-clojure-cmd)
+				       " "))))
+    (case result-type
+      (output (org-babel-eval cmd body))
+      (value (let* ((tmp-file (make-temp-file "org-babel-clojure-results-")))
+	       (org-babel-eval cmd (format org-babel-clojure-wrapper-method
+					   body tmp-file tmp-file))
+	       (org-babel-clojure-table-or-string
+		(org-babel-eval-read-file tmp-file)))))))
 
 (defun org-babel-clojure-evaluate-session (buffer body &optional result-type)
   "Evaluate the body in the context of a clojure session."
+  (require 'slime) (require 'swank-clojure)
   (let ((raw nil)
         (results nil))
     (save-window-excursion
       (set-buffer buffer)
       (setq raw (org-babel-clojure-slime-eval-sync body))
       (setq results (reverse (mapcar #'org-babel-trim raw)))
-      (case result-type
-        (output (mapconcat #'identity (reverse (cdr results)) "\n"))
-        (value (org-babel-clojure-table-or-string (car results)))))))
+      (cond
+       ((equal result-type 'output)
+	(mapconcat #'identity (reverse (cdr results)) "\n"))
+       ((equal result-type 'value)
+	(org-babel-clojure-table-or-string (car results)))))))
 
 (defun org-babel-clojure-evaluate (buffer body &optional result-type)
   "Pass BODY to the Clojure process in BUFFER.  If RESULT-TYPE equals
 'output then return a list of the outputs of the statements in
 BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
-  (if session
+  (if buffer
       (org-babel-clojure-evaluate-session buffer body result-type)
     (org-babel-clojure-evaluate-external-process buffer body result-type)))
 
@@ -274,13 +295,17 @@ last statement in BODY, as elisp."
 
 (defun org-babel-execute:clojure (body params)
   "Execute a block of Clojure code with org-babel."
+  (require 'slime) (require 'swank-clojure)
   (let* ((processed-params (org-babel-process-params params))
          (body (org-babel-expand-body:clojure body params processed-params))
-         (session (org-babel-clojure-initiate-session (first processed-params))))
+         (session (org-babel-clojure-initiate-session
+		   (first processed-params))))
     (org-babel-reassemble-table
      (org-babel-clojure-evaluate session body (nth 3 processed-params))
-     (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
-     (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params))))))
+     (org-babel-pick-name
+      (nth 4 processed-params) (cdr (assoc :colnames params)))
+     (org-babel-pick-name
+      (nth 5 processed-params) (cdr (assoc :rownames params))))))
 
 (provide 'ob-clojure)
 

lisp/babel/ob-comint.el → lisp/ob-comint.el

@@ -33,6 +33,7 @@
 ;;; Code:
 (require 'ob)
 (require 'comint)
+(eval-when-compile (require 'cl))
 
 (defun org-babel-comint-buffer-livep (buffer)
   "Check if BUFFER is a comint buffer with a live process."
@@ -68,7 +69,7 @@ or user `keyboard-quit' during execution of body."
 	(remove-echo (cadr (cdr meta)))
 	(full-body (cadr (cdr (cdr meta)))))
     `(org-babel-comint-in-buffer ,buffer
-       (let ((string-buffer "") dangling-text)
+       (let ((string-buffer "") dangling-text raw)
 	 (flet ((my-filt (text)
 			 (setq string-buffer (concat string-buffer text))))
 	   ;; setup filter
@@ -106,7 +107,7 @@ or user `keyboard-quit' during execution of body."
 	 (if (and ,remove-echo ,full-body
 		  (string-match
 		   (replace-regexp-in-string
-		    "\n" "[\r\n]+" (regexp-quote ,full-body))
+		    "\n" "[\r\n]+" (regexp-quote (or ,full-body "")))
 		   string-buffer))
 	     (setq raw (substring string-buffer (match-end 0))))
 	 (split-string string-buffer comint-prompt-regexp)))))

lisp/babel/langs/ob-ditaa.el → lisp/ob-ditaa.el

@@ -46,6 +46,7 @@
 (defun org-babel-expand-body:ditaa (body params &optional processed-params)
   "Expand BODY according to PARAMS, return the expanded body." body)
 
+(defvar org-ditaa-jar-path)
 (defun org-babel-execute:ditaa (body params)
   "Execute a block of Ditaa code with org-babel.  This function is
 called by `org-babel-execute-src-block'."

lisp/ob-eval.el

@@ -0,0 +1,256 @@
+;;; ob-run.el --- org-babel functions for external code evaluation
+
+;; Copyright (C) 2009, 2010  Free Software Foundation, Inc.
+
+;; Author: Eric Schulte
+;; Keywords: literate programming, reproducible research, comint
+;; Homepage: http://orgmode.org
+;; Version: 0.01
+
+;; This file is part of GNU Emacs.
+
+;; GNU Emacs is free software: you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; GNU Emacs is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;; These functions build existing Emacs support for executing external
+;; shell commands.
+
+;;; Code:
+(require 'ob)
+(eval-when-compile (require 'cl))
+
+(defun org-babel-eval-error-notify (exit-code stderr)
+  "Open a buffer containing information from STDERR with a
+message about the value of EXIT-CODE."
+  (let ((buf (get-buffer-create "*Org-Babel Error Output*")))
+    (with-current-buffer buf
+      (goto-char (point-max))
+      (save-excursion (insert stderr)))
+    (display-buffer buf))
+  (message "Babel evaluation exited with code %d" exit-code))
+
+(defun org-babel-eval (cmd body)
+  "Run CMD on BODY, if CMD succeeds then return it's results,
+otherwise display STDERR with `org-babel-eval-error-notify'."
+  (let ((err-buff (get-buffer-create "*Org-Babel Error*")) exit-code)
+    (with-current-buffer err-buff (erase-buffer))
+    (with-temp-buffer
+      (insert body)
+      (setq exit-code
+	    (org-babel-shell-command-on-region
+	     (point-min) (point-max) cmd t 'replace err-buff))
+      (if (> exit-code 0)
+	  (progn
+	    (with-current-buffer err-buff
+	      (org-babel-eval-error-notify exit-code (buffer-string)))
+	    nil)
+	(buffer-string)))))
+
+(defun org-babel-eval-read-file (file)
+  "Return the contents of FILE as a string."
+  (with-temp-buffer (insert-file-contents
+		     (org-babel-maybe-remote-file file))
+		    (buffer-string)))
+
+(defun org-babel-shell-command-on-region (start end command
+				      &optional output-buffer replace
+				      error-buffer display-error-buffer)
+  "Execute string COMMAND in inferior shell with region as input.
+
+Fixes bugs in the emacs 23.1.1 version of `shell-command-on-region'
+
+Normally display output (if any) in temp buffer `*Shell Command Output*';
+Prefix arg means replace the region with it.  Return the exit code of
+COMMAND.
+
+To specify a coding system for converting non-ASCII characters in
+the input and output to the shell command, use
+\\[universal-coding-system-argument] before this command.  By
+default, the input (from the current buffer) is encoded in the
+same coding system that will be used to save the file,
+`buffer-file-coding-system'.  If the output is going to replace
+the region, then it is decoded from that same coding system.
+
+The noninteractive arguments are START, END, COMMAND,
+OUTPUT-BUFFER, REPLACE, ERROR-BUFFER, and DISPLAY-ERROR-BUFFER.
+Noninteractive callers can specify coding systems by binding
+`coding-system-for-read' and `coding-system-for-write'.
+
+If the command generates output, the output may be displayed
+in the echo area or in a buffer.
+If the output is short enough to display in the echo area
+\(determined by the variable `max-mini-window-height' if
+`resize-mini-windows' is non-nil), it is shown there.  Otherwise
+it is displayed in the buffer `*Shell Command Output*'.  The output
+is available in that buffer in both cases.
+
+If there is output and an error, a message about the error
+appears at the end of the output.
+
+If there is no output, or if output is inserted in the current buffer,
+then `*Shell Command Output*' is deleted.
+
+If the optional fourth argument OUTPUT-BUFFER is non-nil,
+that says to put the output in some other buffer.
+If OUTPUT-BUFFER is a buffer or buffer name, put the output there.
+If OUTPUT-BUFFER is not a buffer and not nil,
+insert output in the current buffer.
+In either case, the output is inserted after point (leaving mark after it).
+
+If REPLACE, the optional fifth argument, is non-nil, that means insert
+the output in place of text from START to END, putting point and mark
+around it.
+
+If optional sixth argument ERROR-BUFFER is non-nil, it is a buffer
+or buffer name to which to direct the command's standard error output.
+If it is nil, error output is mingled with regular output.
+If DISPLAY-ERROR-BUFFER is non-nil, display the error buffer if there
+were any errors.  (This is always t, interactively.)
+In an interactive call, the variable `shell-command-default-error-buffer'
+specifies the value of ERROR-BUFFER."
+  (interactive (let (string)
+		 (unless (mark)
+		   (error "The mark is not set now, so there is no region"))
+		 ;; Do this before calling region-beginning
+		 ;; and region-end, in case subprocess output
+		 ;; relocates them while we are in the minibuffer.
+		 (setq string (read-shell-command "Shell command on region: "))
+		 ;; call-interactively recognizes region-beginning and
+		 ;; region-end specially, leaving them in the history.
+		 (list (region-beginning) (region-end)
+		       string
+		       current-prefix-arg
+		       current-prefix-arg
+		       shell-command-default-error-buffer
+		       t)))
+  (let ((error-file
+	 (if error-buffer
+	     (make-temp-file
+	      (expand-file-name "scor"
+				(or (unless (featurep 'xemacs)
+				      small-temporary-file-directory)
+				    temporary-file-directory)))
+	   nil))
+	exit-status)
+    (if (or replace
+	    (and output-buffer
+		 (not (or (bufferp output-buffer) (stringp output-buffer)))))
+	;; Replace specified region with output from command.
+	(let ((swap (and replace (< start end))))
+	  ;; Don't muck with mark unless REPLACE says we should.
+	  (goto-char start)
+	  (and replace (push-mark (point) 'nomsg))
+	  (setq exit-status
+		(call-process-region start end shell-file-name t
+				     (if error-file
+					 (list output-buffer error-file)
+				       t)
+				     nil shell-command-switch command))
+	  ;; It is rude to delete a buffer which the command is not using.
+	  ;; (let ((shell-buffer (get-buffer "*Shell Command Output*")))
+	  ;;   (and shell-buffer (not (eq shell-buffer (current-buffer)))
+	  ;; 	 (kill-buffer shell-buffer)))
+	  ;; Don't muck with mark unless REPLACE says we should.
+	  (and replace swap (exchange-point-and-mark)))
+      ;; No prefix argument: put the output in a temp buffer,
+      ;; replacing its entire contents.
+      (let ((buffer (get-buffer-create
+		     (or output-buffer "*Shell Command Output*"))))
+	(unwind-protect
+	    (if (eq buffer (current-buffer))
+		;; If the input is the same buffer as the output,
+		;; delete everything but the specified region,
+		;; then replace that region with the output.
+		(progn (setq buffer-read-only nil)
+		       (delete-region (max start end) (point-max))
+		       (delete-region (point-min) (min start end))
+		       (setq exit-status
+			     (call-process-region (point-min) (point-max)
+						  shell-file-name t
+						  (if error-file
+						      (list t error-file)
+						    t)
+						  nil shell-command-switch
+						  command)))
+	      ;; Clear the output buffer, then run the command with
+	      ;; output there.
+	      (let ((directory default-directory))
+		(save-current-buffer
+		  (set-buffer buffer)
+		  (setq buffer-read-only nil)
+		  (if (not output-buffer)
+		      (setq default-directory directory))
+		  (erase-buffer)))
+	      (setq exit-status
+		    (call-process-region start end shell-file-name nil
+					 (if error-file
+					     (list buffer error-file)
+					   buffer)
+					 nil shell-command-switch command)))
+	  ;; Report the output.
+	  (with-current-buffer buffer
+	    (setq mode-line-process
+		  (cond ((null exit-status)
+			 " - Error")
+			((stringp exit-status)
+			 (format " - Signal [%s]" exit-status))
+			((not (equal 0 exit-status))
+			 (format " - Exit [%d]" exit-status)))))
+	  (if (with-current-buffer buffer (> (point-max) (point-min)))
+	      ;; There's some output, display it
+	      (display-message-or-buffer buffer)
+	    ;; No output; error?
+	    (let ((output
+		   (if (and error-file
+			    (< 0 (nth 7 (file-attributes error-file))))
+		       "some error output"
+		     "no output")))
+	      (cond ((null exit-status)
+		     (message "(Shell command failed with error)"))
+		    ((equal 0 exit-status)
+		     (message "(Shell command succeeded with %s)"
+			      output))
+		    ((stringp exit-status)
+		     (message "(Shell command killed by signal %s)"
+			      exit-status))
+		    (t
+		     (message "(Shell command failed with code %d and %s)"
+			      exit-status output))))
+	    ;; Don't kill: there might be useful info in the undo-log.
+	    ;; (kill-buffer buffer)
+	    ))))
+
+    (when (and error-file (file-exists-p error-file))
+      (if (< 0 (nth 7 (file-attributes error-file)))
+	  (with-current-buffer (get-buffer-create error-buffer)
+	    (let ((pos-from-end (- (point-max) (point))))
+	      (or (bobp)
+		  (insert "\f\n"))
+	      ;; Do no formatting while reading error file,
+	      ;; because that can run a shell command, and we
+	      ;; don't want that to cause an infinite recursion.
+	      (format-insert-file error-file nil)
+	      ;; Put point after the inserted errors.
+	      (goto-char (- (point-max) pos-from-end)))
+	    (and display-error-buffer
+		 (display-buffer (current-buffer)))))
+      (delete-file error-file))
+    exit-status))
+
+(provide 'ob-eval)
+
+;; arch-tag: 5328b17f-957d-42d9-94da-a2952682d04d
+
+;;; ob-comint.el ends here

lisp/babel/langs/ob-gnuplot.el → lisp/ob-gnuplot.el

@@ -40,7 +40,16 @@
 
 ;;; Code:
 (require 'ob)
-(require 'gnuplot)
+(require 'ob-ref)
+(require 'ob-comint)
+(eval-when-compile (require 'cl))
+
+(declare-function org-time-string-to-time "org" (s))
+(declare-function org-combine-plists "org" (&rest plists))
+(declare-function orgtbl-to-generic "org-table" (table params))
+(declare-function gnuplot-mode "ext:gnuplot-mode" ())
+(declare-function gnuplot-send-string-to-gnuplot "ext:gnuplot-mode" (str txt))
+(declare-function gnuplot-send-buffer-to-gnuplot "ext:gnuplot-mode" ())
 
 (defvar org-babel-default-header-args:gnuplot
   '((:results . "file") (:exports . "results") (:session . nil))
@@ -124,10 +133,12 @@ code."
   "Execute a block of Gnuplot code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
   (message "executing Gnuplot source code block")
+  (require 'gnuplot)
   (let ((session (cdr (assoc :session params)))
         (result-type (cdr (assoc :results params)))
         (out-file (cdr (assoc :file params)))
-        (body (org-babel-expand-body:gnuplot body params)))
+        (body (org-babel-expand-body:gnuplot body params))
+	output)
     (save-window-excursion
       ;; evaluate the code body with gnuplot
       (if (string= session "none")
@@ -170,18 +181,23 @@ called by `org-babel-execute-src-block'."
         (insert (org-babel-chomp body)))
       buffer)))
 
+(defvar gnuplot-buffer)
 (defun org-babel-gnuplot-initiate-session (&optional session params)
   "If there is not a current inferior-process-buffer in SESSION
 then create one.  Return the initialized session.  The current
 `gnuplot-mode' doesn't provide support for multiple sessions."
+  (require 'gnuplot)
   (unless (string= session "none")
-    (save-window-excursion (gnuplot-send-string-to-gnuplot "" "line")
-                           gnuplot-buffer)))
+    (save-window-excursion
+      (gnuplot-send-string-to-gnuplot "" "line")
+      gnuplot-buffer)))
 
 (defun org-babel-gnuplot-quote-timestamp-field (s)
   "Convert field S from timestamp to Unix time and export to gnuplot."
   (format-time-string org-babel-gnuplot-timestamp-fmt (org-time-string-to-time s)))
 
+(defvar org-table-number-regexp)
+(defvar org-ts-regexp3)
 (defun org-babel-gnuplot-quote-tsv-field (s)
   "Quote field S for export to gnuplot."
   (unless (stringp s)

lisp/babel/langs/ob-haskell.el → lisp/ob-haskell.el

@@ -41,8 +41,15 @@
 
 ;;; Code:
 (require 'ob)
-(require 'haskell-mode)
-(require 'inf-haskell)
+(require 'ob-comint)
+(require 'comint)
+(eval-when-compile (require 'cl))
+
+(declare-function org-remove-indentation "org" (code &optional n))
+(declare-function haskell-mode "ext:haskell-mode" ())
+(declare-function run-haskell "ext:inf-haskell" (&optional arg))
+(declare-function inferior-haskell-load-file
+		  "ext:inf-haskell" (&optional reload))
 
 (add-to-list 'org-babel-tangle-lang-exts '("haskell" . "hs"))
 
@@ -66,7 +73,7 @@
   "Execute a block of Haskell code with org-babel."
   (message "executing haskell source code block")
   (let* ((processed-params (org-babel-process-params params))
-         (session (first processed-params))
+         (session (nth 0 processed-params))
          (vars (nth 1 processed-params))
          (result-type (nth 3 processed-params))
          (full-body (org-babel-expand-body:haskell body params processed-params))
@@ -82,9 +89,11 @@
                    (cdr (member org-babel-haskell-eoe
                                 (reverse (mapcar #'org-babel-trim raw)))))))
     (org-babel-reassemble-table
-     (case result-type
-       (output (mapconcat #'identity (reverse (cdr results)) "\n"))
-       (value (org-babel-haskell-table-or-string (car results))))
+     (cond 
+      ((equal result-type 'output)
+       (mapconcat #'identity (reverse (cdr results)) "\n"))
+      ((equal result-type 'value)
+       (org-babel-haskell-table-or-string (car results))))
      (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
      (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params))))))
 
@@ -97,7 +106,7 @@
 (defun org-babel-haskell-initiate-session (&optional session params)
   "If there is not a current inferior-process-buffer in SESSION
 then create one.  Return the initialized session."
-  ;; TODO: make it possible to have multiple sessions
+  (require 'inf-haskell)
   (or (get-buffer "*haskell*")
       (save-window-excursion (run-haskell) (sleep-for 0.25) (current-buffer))))
 
@@ -114,13 +123,13 @@ then create one.  Return the initialized session."
       buffer)))
 
 (defun org-babel-prep-session:haskell
-  (session params &optional processesed-params)
+  (session params &optional processed-params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
   (save-window-excursion
     (let ((pp (or processed-params (org-babel-process-params params)))
 	  (buffer (org-babel-haskell-initiate-session session)))
       (org-babel-comint-in-buffer buffer
-      	(mapcar
+      	(mapc
       	 (lambda (pair)
       	   (insert (format "let %s = %s"
       			   (car pair)
@@ -150,6 +159,7 @@ specifying a var of the same value."
       (concat "[" (mapconcat #'org-babel-haskell-var-to-haskell var ", ") "]")
     (format "%S" var)))
 
+(defvar org-src-preserve-indentation)
 (defun org-babel-haskell-export-to-lhs (&optional arg)
   "Export to a .lhs file with all haskell code blocks escaped
 appropriately.  When called with a prefix argument the resulting

lisp/babel/ob-keys.el → lisp/ob-keys.el

@@ -51,7 +51,11 @@ functions.")
   (describe-bindings org-babel-key-prefix))
 
 (defvar org-babel-key-bindings
-  '(("\C-p" . org-babel-expand-src-block)
+  '(("e" . org-babel-execute-src-block)
+    ("\C-e" . org-babel-execute-src-block)
+    ("o" . org-babel-open-src-block-result)
+    ("\C-o" . org-babel-open-src-block-result)
+    ("\C-p" . org-babel-expand-src-block)
     ("p" . org-babel-expand-src-block)
     ("g" . org-babel-goto-named-source-block)
     ("\C-b" . org-babel-execute-buffer)

lisp/babel/langs/ob-latex.el → lisp/ob-latex.el

@@ -32,6 +32,7 @@
 
 ;;; Code:
 (require 'ob)
+(require 'org-latex)
 
 (add-to-list 'org-babel-tangle-lang-exts '("latex" . "tex"))
 
@@ -85,9 +86,12 @@ called by `org-babel-execute-src-block'."
   (with-temp-file tex-file
     (insert (org-splice-latex-header
 	       org-format-latex-header
-	       (remove-if
-                (lambda (el) (and (listp el) (string= "hyperref" (cadr el))))
-                org-export-latex-default-packages-alist)
+	       (delq
+		nil
+		(mapcar
+		 (lambda (el) (unless (and (listp el) (string= "hyperref" (cadr el)))
+			   el))
+		 org-export-latex-default-packages-alist))
 	       org-export-latex-packages-alist
 	       org-format-latex-header-extra)
             (if height (concat "\n" (format "\\pdfpageheight %s" height)) "")

lisp/babel/langs/ob-matlab.el → lisp/ob-matlab.el

@@ -36,43 +36,10 @@
 ;; http://matlab-emacs.sourceforge.net/
 
 ;;; Code:
-(require 'matlab)
+(require 'ob)
 (require 'ob-octave)
 
-(defvar org-babel-default-header-args:matlab '())
-
-(defvar org-babel-matlab-shell-command "matlab -nosplash"
-  "Shell command to use to run matlab as an external process.")
-
-(defun org-babel-expand-body:matlab (body params &optional processed-params)
-  "Expand BODY according to PARAMS, return the expanded body." body)
-
-(defvar org-babel-matlab-with-emacs-link nil
-  "If non-nil use matlab-shell-run-region for session
-  evaluation. This will use EmacsLink if (matlab-with-emacs-link)
-  evaluates to a non-nil value.")
-
-(defvar org-babel-matlab-emacs-link-wrapper-method
-   "%s
-if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
-else, save -ascii %s ans
-end
-delete('%s')
-")
-
-(defun org-babel-execute:matlab (body params)
-  "Execute a block of matlab code with org-babel."
-  (org-babel-execute:octave body params 'matlab))
-
-(defun org-babel-prep-session:matlab (session params)
-  "Prepare SESSION according to PARAMS."
-  (org-babel-prep-session:octave session params 'matlab))
-
-(defun org-babel-matlab-initiate-session (&optional session params)
-  "Create a matlab inferior process buffer.  If there is not a
-current inferior-process-buffer in SESSION then create. Return
-the initialized session."
-  (org-babel-octave-initiate-session session params 'matlab))
+;; see ob-octave for matlab implementation
 
 (provide 'ob-matlab)
 

lisp/babel/langs/ob-ocaml.el → lisp/ob-ocaml.el

@@ -37,7 +37,11 @@
 
 ;;; Code:
 (require 'ob)
-(require 'tuareg)
+(require 'ob-comint)
+(require 'comint)
+(eval-when-compile (require 'cl))
+
+(declare-function tuareg-run-caml "ext:taureg" ())
 
 (add-to-list 'org-babel-tangle-lang-exts '("ocaml" . "ml"))
 
@@ -60,7 +64,8 @@
   (let* ((processed-params (org-babel-process-params params))
          (vars (nth 1 processed-params))
          (full-body (org-babel-expand-body:ocaml body params processed-params))
-         (session (org-babel-prep-session:ocaml session params))
+         (session (org-babel-prep-session:ocaml
+		   (cdr (assoc :session params)) params))
          (raw (org-babel-comint-with-output
 		  (session org-babel-ocaml-eoe-output t full-body)
                 (insert (concat (org-babel-chomp full-body) " ;;"))
@@ -72,8 +77,10 @@
      (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
      (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params))))))
 
+(defvar tuareg-interactive-buffer-name)
 (defun org-babel-prep-session:ocaml (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
+  (require 'tuareg)
   (let ((tuareg-interactive-buffer-name (if (and (not (string= session "none"))
                                                  (not (string= session "default"))
                                                  (stringp session))

lisp/babel/langs/ob-octave.el → lisp/ob-octave.el

@@ -31,19 +31,29 @@
 
 ;;; Code:
 (require 'ob)
-(require 'octave-inf)
+(require 'ob-ref)
+(require 'ob-comint)
+(require 'ob-eval)
+(eval-when-compile (require 'cl))
 
+(declare-function matlab-shell "ext:matlab-mode")
+(declare-function matlab-shell-run-region "ext:matlab-mode")
+
+(defvar org-babel-default-header-args:matlab '())
 (defvar org-babel-default-header-args:octave '())
 
+(defvar org-babel-matlab-shell-command "matlab -nosplash"
+  "Shell command to use to run matlab as an external process.")
 (defvar org-babel-octave-shell-command "octave -q"
   "Shell command to use to run octave as an external process.")
 
+(defun org-babel-expand-body:matlab (body params &optional processed-params)
+  "Expand BODY according to PARAMS, return the expanded body."
+  (org-babel-expand-body:octave body params processed-params))
 (defun org-babel-expand-body:octave (body params &optional processed-params)
   "Expand BODY according to PARAMS, return the expanded body."
   (let ((vars (nth 1 (or processed-params (org-babel-process-params params)))))
     (concat
-     ;; prepend code to define all arguments passed to the code block
-     ;; (may not be appropriate for all languages)
      (mapconcat
       (lambda (pair)
         (format "%s=%s"
@@ -51,25 +61,60 @@
                 (org-babel-octave-var-to-octave (cdr pair))))
       vars "\n") "\n" body "\n")))
 
+(defvar org-babel-matlab-with-emacs-link nil
+  "If non-nil use matlab-shell-run-region for session
+  evaluation. This will use EmacsLink if (matlab-with-emacs-link)
+  evaluates to a non-nil value.")
+
+(defvar org-babel-matlab-emacs-link-wrapper-method
+   "%s
+if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
+else, save -ascii %s ans
+end
+delete('%s')
+")
+(defvar org-babel-octave-wrapper-method
+  "%s
+if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
+else, save -ascii %s ans
+end")
+
+(defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
+
+(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
+
+(defun org-babel-execute:matlab (body params)
+  "Execute a block of matlab code with org-babel."
+  (require 'matlab)
+  (org-babel-execute:octave body params 'matlab))
 (defun org-babel-execute:octave (body params &optional matlabp)
   "Execute a block of octave code with org-babel."
-  (message (format "executing %s source code block" (if matlabp "matlab" "octave")))
+  (message "executing %s source code block" (if matlabp "matlab" "octave"))
   (let* ((processed-params (org-babel-process-params params))
-         ;; set the session if the session variable is non-nil
-         (session (funcall (intern (format "org-babel-%s-initiate-session" lang))
-			   (first processed-params) params))
+         (session
+	  (funcall (intern (format "org-babel-%s-initiate-session"
+				   (if matlabp "matlab" "octave")))
+		   (nth 0 processed-params) params))
          (vars (nth 1 processed-params))
          (result-params (nth 2 processed-params))
          (result-type (nth 3 processed-params))
 	 (out-file (cdr (assoc :file params)))
-	 (augmented-body (org-babel-expand-body:octave body params processed-params))
-	 (result (org-babel-octave-evaluate session augmented-body result-type matlabp)))
+	 (augmented-body
+	  (org-babel-expand-body:octave body params processed-params))
+	 (result (org-babel-octave-evaluate
+		  session augmented-body result-type matlabp)))
     (or out-file
         (org-babel-reassemble-table
          result
-         (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
-         (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params)))))))
+         (org-babel-pick-name
+	  (nth 4 processed-params) (cdr (assoc :colnames params)))
+         (org-babel-pick-name
+	  (nth 5 processed-params) (cdr (assoc :rownames params)))))))
 
+(defun org-babel-prep-session:matlab (session params)
+  "Prepare SESSION according to PARAMS."
+  (require 'matlab)
+  (org-babel-prep-session:octave session params 'matlab))
 (defun org-babel-octave-var-to-octave (var)
   "Convert an emacs-lisp variable into an octave variable.
 Converts an emacs-lisp variable into a string of octave code
@@ -94,60 +139,53 @@ specifying a variable of the same value."
               (org-babel-comint-wait-for-output session)) var-lines))
     session))
 
+(defun org-babel-matlab-initiate-session (&optional session params)
+  "Create a matlab inferior process buffer.  If there is not a
+current inferior-process-buffer in SESSION then create. Return
+the initialized session."
+  (require 'matlab)
+  (org-babel-octave-initiate-session session params 'matlab))
 (defun org-babel-octave-initiate-session (&optional session params matlabp)
   "Create an octave inferior process buffer.  If there is not a
 current inferior-process-buffer in SESSION then create. Return
 the initialized session."
+  (require 'octave-inf)
   (unless (string= session "none")
-    (let ((session (or session (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
+    (let ((session (or session
+		       (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
       (if (org-babel-comint-buffer-livep session) session
 	(save-window-excursion
 	  (if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
 	    (run-octave))
 	  (rename-buffer (if (bufferp session) (buffer-name session)
-			   (if (stringp session) session (buffer-name)))) (current-buffer))))))
-
-(defvar org-babel-octave-wrapper-method
-   "%s
-if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
-else, save -ascii %s ans
-end")
-
-(defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
+			   (if (stringp session) session (buffer-name))))
+	  (current-buffer))))))
 
-(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
-
-(defun org-babel-octave-evaluate (session body result-type lang)
+(defun org-babel-octave-evaluate
+  (session body result-type lang &optional matlabp)
   "Pass BODY to the octave process in SESSION.  If RESULT-TYPE
 equals 'output then return the outputs of the statements in BODY,
 if RESULT-TYPE equals 'value then return the value of the last
 statement in BODY, as elisp."
   (if session
-    (org-babel-octave-evaluate-session session body result-type matlabp)
+      (org-babel-octave-evaluate-session session body result-type matlabp)
     (org-babel-octave-evaluate-external-process body result-type matlabp)))
 
 (defun org-babel-octave-evaluate-external-process (body result-type matlabp)
   "Evaluate BODY in an external octave process."
-  (let ((cmd (if matlabp org-babel-matlab-shell-command org-babel-octave-shell-command)))
-    (save-excursion
-      (case result-type
-	(output
-	 (with-temp-buffer
-	   (insert body)
-	   (org-babel-shell-command-on-region (point-min) (point-max) cmd 'current-buffer 'replace)
-	   (buffer-string)))
-	(value
-	 (let* ((tmp-file (make-temp-file "org-babel-results-")) exit-code
-		(stderr
-		 (with-temp-buffer
-		   (insert (format org-babel-octave-wrapper-method body tmp-file tmp-file))
-		   (setq exit-code (org-babel-shell-command-on-region
-				    (point-min) (point-max) cmd nil 'replace (current-buffer)))
-		   (buffer-string))))
-	   (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
-	   (org-babel-octave-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))))))))
-
-(defun org-babel-octave-evaluate-session (session body result-type &optional matlabp)
+  (let ((cmd (if matlabp
+		 org-babel-matlab-shell-command
+	       org-babel-octave-shell-command)))
+    (case result-type
+      (output (org-babel-eval cmd body))
+      (value (let ((tmp-file (make-temp-file "org-babel-results-")))
+	       (org-babel-eval
+		cmd
+		(format org-babel-octave-wrapper-method body tmp-file tmp-file))
+	       (org-babel-eval-read-file tmp-file))))))
+
+(defun org-babel-octave-evaluate-session
+  (session body result-type &optional matlabp)
   "Evaluate BODY in SESSION."
   (let* ((tmp-file (make-temp-file "org-babel-results-"))
 	 (wait-file (make-temp-file "org-babel-matlab-emacs-link-wait-signal-"))
@@ -164,7 +202,8 @@ statement in BODY, as elisp."
 			  body tmp-file tmp-file wait-file) "\n")
 	       (mapconcat
 		#'org-babel-chomp
-		(list (format org-babel-octave-wrapper-method body tmp-file tmp-file)
+		(list (format org-babel-octave-wrapper-method
+			      body tmp-file tmp-file)
 		      org-babel-octave-eoe-indicator) "\n")))))
 	 (raw (if (and matlabp org-babel-matlab-with-emacs-link)
 		  (save-window-excursion
@@ -187,16 +226,19 @@ statement in BODY, as elisp."
 		  (insert full-body) (comint-send-input nil t)))) results)
     (case result-type
       (value
-       (org-babel-octave-import-elisp-from-file (org-babel-maybe-remote-file tmp-file)))
+       (org-babel-octave-import-elisp-from-file
+	(org-babel-maybe-remote-file tmp-file)))
       (output
        (progn
 	 (setq results
 	       (if matlabp
-		   (cdr (reverse (delq "" (mapcar #'org-babel-octave-read-string
-						  (mapcar #'org-babel-trim raw)))))
+		   (cdr (reverse (delq "" (mapcar
+					   #'org-babel-octave-read-string
+					   (mapcar #'org-babel-trim raw)))))
 		 (cdr (member org-babel-octave-eoe-output
-			      (reverse (mapcar #'org-babel-octave-read-string
-					       (mapcar #'org-babel-trim raw)))))))
+			      (reverse (mapcar
+					#'org-babel-octave-read-string
+					(mapcar #'org-babel-trim raw)))))))
 	 (mapconcat #'identity (reverse results) "\n"))))))
 
 (defun org-babel-octave-import-elisp-from-file (file-name)

lisp/babel/langs/ob-perl.el → lisp/ob-perl.el

@@ -28,11 +28,16 @@
 
 ;;; Code:
 (require 'ob)
+(require 'ob-eval)
+(eval-when-compile (require 'cl))
 
 (add-to-list 'org-babel-tangle-lang-exts '("perl" . "pl"))
 
 (defvar org-babel-default-header-args:perl '())
 
+(defvar org-babel-perl-command "perl"
+  "Name of command to use for executing perl code.")
+
 (defun org-babel-expand-body:perl (body params &optional processed-params)
   "Expand BODY according to PARAMS, return the expanded body."
   (let ((vars (nth 1 (or processed-params (org-babel-process-params params)))))
@@ -49,17 +54,19 @@
 called by `org-babel-execute-src-block'."
   (message "executing Perl source code block")
   (let* ((processed-params (org-babel-process-params params))
-         (session (first processed-params))
+         (session (nth 0 processed-params))
          (vars (nth 1 processed-params))
          (result-params (nth 2 processed-params))
          (result-type (nth 3 processed-params))
          (full-body (org-babel-expand-body:perl
-                     body params processed-params)) ;; then the source block body
+                     body params processed-params))
 	(session (org-babel-perl-initiate-session session)))
     (org-babel-reassemble-table
      (org-babel-perl-evaluate session full-body result-type)
-     (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
-     (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params))))))
+     (org-babel-pick-name
+      (nth 4 processed-params) (cdr (assoc :colnames params)))
+     (org-babel-pick-name
+      (nth 5 processed-params) (cdr (assoc :rownames params))))))
 
 (defun org-babel-prep-session:perl (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
@@ -97,33 +104,14 @@ print o join(\"\\n\", @r), \"\\n\"")
 'output then return a list of the outputs of the statements in
 BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
-  (if (not session)
-      ;; external process evaluation
-      (save-excursion
-        (case result-type
-          (output
-           (with-temp-buffer
-             (insert body)
-             ;; (message "buffer=%s" (buffer-string)) ;; debugging
-             (org-babel-shell-command-on-region (point-min) (point-max) "perl" 'current-buffer 'replace)
-             (buffer-string)))
-          (value
-           (let* ((tmp-file (make-temp-file "perl-functional-results")) exit-code
-		 (stderr
-		  (with-temp-buffer
-		    (insert
-		     (format
-		      (if (member "pp" result-params)
-			  (error "Pretty-printing not implemented for perl")
-			org-babel-perl-wrapper-method) body tmp-file))
-		    (setq exit-code
-			  (org-babel-shell-command-on-region
-			   (point-min) (point-max) "perl" nil 'replace (current-buffer)))
-		    (buffer-string))))
-	     (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
-	     (org-babel-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))))))
-    ;; comint session evaluation
-    (error "Sessions are not supported for Perl.")))
+  (when session (error "Sessions are not supported for Perl."))
+  (case result-type
+    (output (org-babel-eval org-babel-perl-command body))
+    (value (let ((tmp-file (make-temp-file "org-babel-perl-results-")))
+	     (org-babel-eval
+	      org-babel-perl-command
+	      (format org-babel-perl-wrapper-method body tmp-file))
+	     (org-babel-eval-read-file tmp-file)))))
 
 (provide 'ob-perl)
 

lisp/babel/langs/ob-python.el → lisp/ob-python.el

@@ -28,14 +28,21 @@
 
 ;;; Code:
 (require 'ob)
-(require 'ob-tangle)
+(require 'ob-ref)
 (require 'ob-comint)
+(require 'ob-eval)
 (require (if (featurep 'xemacs) 'python-mode 'python))
+(eval-when-compile (require 'cl))
+
+(declare-function org-remove-indentation "org" )
 
 (add-to-list 'org-babel-tangle-lang-exts '("python" . "py"))
 
 (defvar org-babel-default-header-args:python '())
 
+(defvar org-babel-python-command "python"
+  "Name of command to use for executing python code.")
+
 (defun org-babel-expand-body:python (body params &optional processed-params)
   "Expand BODY according to PARAMS, return the expanded body."
   (concat
@@ -56,13 +63,16 @@ called by `org-babel-execute-src-block'."
          (result-params (nth 2 processed-params))
          (result-type (nth 3 processed-params))
          (full-body (org-babel-expand-body:python
-                     body params processed-params)) ;; then the source block body
-         (result (org-babel-python-evaluate session full-body result-type)))
+                     body params processed-params))
+         (result (org-babel-python-evaluate
+		  session full-body result-type result-params)))
     (or (cdr (assoc :file params))
         (org-babel-reassemble-table
          result
-         (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
-         (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params)))))))
+         (org-babel-pick-name (nth 4 processed-params)
+			      (cdr (assoc :colnames params)))
+         (org-babel-pick-name (nth 5 processed-params)
+			      (cdr (assoc :rownames params)))))))
 
 (defun org-babel-prep-session:python (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
@@ -136,31 +146,25 @@ then create.  Return the initialized session."
 	;; `py-shell' creates a buffer whose name is the value of
 	;; `py-which-bufname' with '*'s at the beginning and end
 	(let* ((bufname (if python-buffer
-			    (replace-regexp-in-string "^\\*\\([^*]+\\)\\*$" "\\1" python-buffer) ; zap surrounding *
+			    (replace-regexp-in-string ;; zap surrounding *
+			     "^\\*\\([^*]+\\)\\*$" "\\1" python-buffer)
 			  (concat "Python-" (symbol-name session))))
-	       (py-which-bufname bufname)) ; avoid making a mess with buffer-local
+	       (py-which-bufname bufname))
 	  (py-shell)
 	  (setq python-buffer (concat "*" bufname "*"))))
        (t
 	(error "No function available for running an inferior python.")))
-	
-      (setq org-babel-python-buffers (cons (cons session python-buffer)
-					   (assq-delete-all session org-babel-python-buffers)))
+      (setq org-babel-python-buffers
+	    (cons (cons session python-buffer)
+		  (assq-delete-all session org-babel-python-buffers)))
       session)))
 
 (defun org-babel-python-initiate-session (&optional session params)
   "Create a session named SESSION according to PARAMS."
   (unless (string= session "none")
-    (org-babel-python-session-buffer (org-babel-python-initiate-session-by-key session))))
-
-(defvar org-babel-python-last-value-eval "_"
-  "When evaluated by Python this returns the return value of the last statement.")
-(defvar org-babel-python-pp-last-value-eval
-  '("results = _"
-    "import pprint"
-    "org_babel_pp = pprint.PrettyPrinter()"
-    "org_babel_pp.pprint(results)")
-  "When evaluated by Python this pretty prints the value of the last statement.")
+    (org-babel-python-session-buffer
+     (org-babel-python-initiate-session-by-key session))))
+
 (defvar org-babel-python-eoe-indicator "'org_babel_python_eoe'"
   "Used to indicate that evaluation is has completed.")
 (defvar org-babel-python-wrapper-method
@@ -177,77 +181,74 @@ def main():
 
 open('%s', 'w').write( pprint.pformat(main()) )")
 
-(defun org-babel-python-evaluate (buffer body &optional result-type)
+(defun org-babel-python-evaluate
+  (buffer body &optional result-type result-params)
   "Pass BODY to the Python process in BUFFER.  If RESULT-TYPE equals
 'output then return a list of the outputs of the statements in
 BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
-  (if (not session)
+  (if (not buffer)
       ;; external process evaluation
-      (save-excursion
-        (case result-type
-          (output
-           (with-temp-buffer
-             (insert body)
-             ;; (message "buffer=%s" (buffer-string)) ;; debugging
-             (org-babel-shell-command-on-region (point-min) (point-max) "python" 'current-buffer 'replace)
-             (buffer-string)))
-          (value
-           (let* ((tmp-file (make-temp-file "org-babel-python-results-")) exit-code
-		  (stderr
-		   (with-temp-buffer
-		     (insert
-		      (format
-		       (if (member "pp" result-params)
-			   org-babel-python-pp-wrapper-method
-			 org-babel-python-wrapper-method)
-		       (mapconcat
-			(lambda (line) (format "\t%s" line))
-			(split-string
-			 (org-remove-indentation (org-babel-trim body)) "[\r\n]") "\n")
-		       tmp-file))
-		     ;; (message "buffer=%s" (buffer-string)) ;; debugging
-		     (setq exit-code (org-babel-shell-command-on-region
-				      (point-min) (point-max) "python" nil 'replace (current-buffer)))
-		     (buffer-string))))
-	     (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
-             (let ((raw (with-temp-buffer
-			  (insert-file-contents (org-babel-maybe-remote-file tmp-file))
-			  (buffer-string))))
-               (if (or (member "code" result-params) (member "pp" result-params))
-                   raw
-                 (org-babel-python-table-or-string raw)))))))
+      (case result-type
+	(output (org-babel-eval org-babel-python-command body))
+	(value (let ((tmp-file (make-temp-file "org-babel-python-results-")))
+		 (org-babel-eval org-babel-python-command
+				 (format
+				  (if (member "pp" result-params)
+				      org-babel-python-pp-wrapper-method
+				    org-babel-python-wrapper-method)
+				  (mapconcat
+				   (lambda (line) (format "\t%s" line))
+				   (split-string
+				    (org-remove-indentation
+				     (org-babel-trim body))
+				    "[\r\n]") "\n")
+				  tmp-file))
+		 ((lambda (raw)
+		    (if (or (member "code" result-params)
+			    (member "pp" result-params))
+			raw
+		      (org-babel-python-table-or-string raw)))
+		  (org-babel-eval-read-file tmp-file)))))
     ;; comint session evaluation
-    (org-babel-comint-in-buffer buffer
-      (let* ((raw (org-babel-comint-with-output
-		      (buffer org-babel-python-eoe-indicator t full-body)
-                    ;; for some reason python is fussy, and likes enters after every input
-		    (let ((comint-process-echoes nil))
-		      (mapc (lambda (statement) (insert statement) (comint-send-input))
-			    (split-string (org-babel-trim body) "[\r\n]+"))
-		      (comint-send-input) (comint-send-input)
-		      (if (member "pp" result-params)
-			  (mapc (lambda (statement) (insert statement) (comint-send-input))
-				org-babel-python-pp-last-value-eval)
-			(insert org-babel-python-last-value-eval))
-		      (comint-send-input) (comint-send-input)
-		      (insert org-babel-python-eoe-indicator)
-		      (comint-send-input))))
-	     (raw (apply #'append ; split further
-			 (mapcar #'(lambda (r)
-				     (split-string r "[\r\n]+"))
-				 raw)))
-             (results (delete org-babel-python-eoe-indicator
-                              (cdr (member org-babel-python-eoe-indicator
-                                           (mapcar #'org-babel-trim raw))))))
-        (unless (or (member "code" result-params) (member "pp" result-params))
-          (setq results (mapcar #'org-babel-python-read-string results)))
-        (case result-type
-	  (output (org-babel-trim (mapconcat #'identity (reverse (cdr results)) "\n")))
-	  (value
-           (if (or (member "code" result-params) (member "pp" result-params))
-               (car results)
-             (org-babel-python-table-or-string (org-babel-trim (car results))))))))))
+    (flet ((dump-last-value (tmp-file pp)
+	    (mapc
+	     (lambda (statement) (insert statement) (comint-send-input))
+	     (if pp
+		 (list
+		  "import pp"
+		  (format "open('%s', 'w').write(pprint.pformat(_))" tmp-file))
+	       (list (format "open('%s', 'w').write(str(_))" tmp-file)))))
+	   (input-body (body)
+	    (mapc (lambda (statement) (insert statement) (comint-send-input))
+		  (split-string (org-babel-trim body) "[\r\n]+"))
+	    (comint-send-input) (comint-send-input)))
+      (case result-type
+	(output
+	 (mapconcat
+	  #'org-babel-trim
+	  (butlast
+	   (org-babel-comint-with-output
+	       (buffer org-babel-python-eoe-indicator t body)
+	     (let ((comint-process-echoes nil))
+	       (input-body body)
+	       (insert org-babel-python-eoe-indicator)
+	       (comint-send-input))) 2) "\n"))
+	(value
+	 ((lambda (results)
+	    (if (or (member "code" result-params) (member "pp" result-params))
+		results
+	      (org-babel-python-table-or-string results)))
+	  (let ((tmp-file (make-temp-file "org-babel-python-results-")))
+	    (org-babel-comint-with-output
+		(buffer org-babel-python-eoe-indicator t body)
+	      (let ((comint-process-echoes nil))
+		(input-body body)
+		(dump-last-value tmp-file (member "pp" result-params))
+		(comint-send-input) (comint-send-input)
+		(insert org-babel-python-eoe-indicator)
+		(comint-send-input)))
+	    (org-babel-eval-read-file tmp-file))))))))
 
 (defun org-babel-python-read-string (string)
   "Strip 's from around python string"

lisp/babel/langs/ob-ruby.el → lisp/ob-ruby.el

@@ -38,14 +38,23 @@
 
 ;;; Code:
 (require 'ob)
-(require 'inf-ruby)
+(require 'ob-ref)
+(require 'ob-comint)
+(require 'ob-eval)
+(eval-when-compile (require 'cl))
+
+(declare-function run-ruby "ext:inf-ruby" (&optional command name))
 
 (add-to-list 'org-babel-tangle-lang-exts '("ruby" . "rb"))
 
 (defvar org-babel-default-header-args:ruby '())
 
+(defvar org-babel-ruby-command "ruby"
+  "Name of command to use for executing ruby code.")
+
 (defun org-babel-expand-body:ruby (body params &optional processed-params)
   "Expand BODY according to PARAMS, return the expanded body."
+  (require 'inf-ruby)
   (let ((vars (nth 1 (or processed-params (org-babel-process-params params)))))
     (concat
      (mapconcat ;; define any variables
@@ -65,7 +74,8 @@ called by `org-babel-execute-src-block'."
          (result-type (nth 3 processed-params))
          (full-body (org-babel-expand-body:ruby
                      body params processed-params))
-         (result (org-babel-ruby-evaluate session full-body result-type)))
+         (result (org-babel-ruby-evaluate
+		  session full-body result-type result-params)))
     (or (cdr (assoc :file params))
         (org-babel-reassemble-table
          result
@@ -114,7 +124,6 @@ specifying a var of the same value."
 (defun org-babel-ruby-table-or-string (results)
   "If RESULTS look like a table, then convert them into an
 Emacs-lisp table, otherwise return the results as a string."
-  (message "converting %S" results)
   (org-babel-read
    (if (and (stringp results) (string-match "^\\[.+\\]$" results))
        (org-babel-read
@@ -123,12 +132,13 @@ Emacs-lisp table, otherwise return the results as a string."
                  "\\[" "(" (replace-regexp-in-string
                             "\\]" ")" (replace-regexp-in-string
                                        ", " " " (replace-regexp-in-string
-                                                 "'" "\"" results))))))
+						 "'" "\"" results))))))
      results)))
 
 (defun org-babel-ruby-initiate-session (&optional session params)
   "If there is not a current inferior-process-buffer in SESSION
 then create one.  Return the initialized session."
+  (require 'inf-ruby)
   (unless (string= session "none")
     (let ((session-buffer (save-window-excursion
 			    (run-ruby nil session) (current-buffer))))
@@ -137,12 +147,12 @@ then create one.  Return the initialized session."
         (sit-for .5)
         (org-babel-ruby-initiate-session session)))))
 
-(defvar org-babel-ruby-last-value-eval "_"
-  "When evaluated by Ruby this returns the return value of the last statement.")
-(defvar org-babel-ruby-pp-last-value-eval "require 'pp'; pp(_)"
-  "When evaluated by Ruby this pretty prints value of the last statement.")
 (defvar org-babel-ruby-eoe-indicator ":org_babel_ruby_eoe"
   "Used to indicate that evaluation is has completed.")
+(defvar org-babel-ruby-f-write
+  "File.open('%s','w'){|f| f.write((_.class == String) ? _ : _.inspect)}")
+(defvar org-babel-ruby-pp-f-write
+  "File.open('%s','w'){|f| $stdout = f; pp(results); $stdout = orig_out}")
 (defvar org-babel-ruby-wrapper-method
   "
 def main()
@@ -164,66 +174,70 @@ File.open('%s', 'w') do |f|
 end
 ")
 
-(defun org-babel-ruby-evaluate (buffer body &optional result-type)
+(defun org-babel-ruby-evaluate
+  (buffer body &optional result-type result-params)
   "Pass BODY to the Ruby process in BUFFER.  If RESULT-TYPE equals
 'output then return a list of the outputs of the statements in
 BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
-  (if (not session)
+  (if (not buffer)
       ;; external process evaluation
-      (save-excursion
-        (case result-type
-          (output
-           (with-temp-buffer
-             (insert body)
-             ;; (message "buffer=%s" (buffer-string)) ;; debugging
-             (org-babel-shell-command-on-region
-	      (point-min) (point-max) "ruby" 'current-buffer 'replace)
-             (buffer-string)))
-          (value
-           (let* ((tmp-file (make-temp-file "ruby-functional-results"))
-		  exit-code
-		  (stderr
-		   (with-temp-buffer
-		     (insert (format (if (member "pp" result-params)
-					 org-babel-ruby-pp-wrapper-method
-				       org-babel-ruby-wrapper-method)
-				     body tmp-file))
-		     (setq exit-code
-			   (org-babel-shell-command-on-region
-			    (point-min) (point-max) "ruby"
-			    nil 'replace (current-buffer)))
-		     (buffer-string))))
-	     (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
-             (let ((raw (with-temp-buffer
-			  (insert-file-contents
-			   (org-babel-maybe-remote-file tmp-file))
-			  (buffer-string))))
-               (if (or (member "code" result-params)
-		       (member "pp" result-params))
-                   raw
-                 (org-babel-ruby-table-or-string raw)))))))
-    ;; comint session evaluation
-    (let* ((full-body
-	    (mapconcat
-	     #'org-babel-chomp
-	     (list body (if (member "pp" result-params)
-                            org-babel-ruby-pp-last-value-eval
-                          org-babel-ruby-last-value-eval)
-                   org-babel-ruby-eoe-indicator) "\n"))
-           (raw (org-babel-comint-with-output
-		    (buffer org-babel-ruby-eoe-indicator t full-body)
-                  (insert full-body) (comint-send-input nil t)))
-           (results (cdr (member
-			  org-babel-ruby-eoe-indicator
-			  (reverse (mapcar #'org-babel-ruby-read-string
-					   (mapcar #'org-babel-trim raw)))))))
       (case result-type
-        (output (mapconcat #'identity (reverse (cdr results)) "\n"))
-        (value
-         (if (or (member "code" result-params) (member "pp" result-params))
-             (car results)
-           (org-babel-ruby-table-or-string (car results))))))))
+	(output (org-babel-eval org-babel-ruby-command body))
+	(value (let ((tmp-file (make-temp-file "org-babel-ruby-results-")))
+		 (org-babel-eval org-babel-ruby-command
+				 (format (if (member "pp" result-params)
+					     org-babel-ruby-pp-wrapper-method
+					   org-babel-ruby-wrapper-method)
+					 body tmp-file))
+		 ((lambda (raw)
+		    (if (or (member "code" result-params)
+			    (member "pp" result-params))
+			raw
+		      (org-babel-ruby-table-or-string raw)))
+		  (org-babel-eval-read-file tmp-file)))))
+    ;; comint session evaluation
+    (case result-type
+      (output
+       (mapconcat
+	#'identity
+	(butlast
+	 (split-string
+	  (mapconcat
+	   #'org-babel-trim
+	   (butlast
+	    (org-babel-comint-with-output
+		(buffer org-babel-ruby-eoe-indicator t body)
+	      (mapc
+	       (lambda (line)
+		 (insert (org-babel-chomp line)) (comint-send-input nil t))
+	       (list body org-babel-ruby-eoe-indicator))
+	      (comint-send-input nil t)) 2)
+	   "\n") "[\r\n]")) "\n"))
+      (value
+       ((lambda (results)
+	  (if (or (member "code" result-params) (member "pp" result-params))
+	      results
+	    (org-babel-ruby-table-or-string results)))
+	(let* ((tmp-file (make-temp-file "org-babel-ruby-results-"))
+	       (ppp (or (member "code" result-params)
+			(member "pp" result-params))))
+	  (org-babel-comint-with-output
+	      (buffer org-babel-ruby-eoe-indicator t body)
+	    (when ppp (insert "require 'pp';") (comint-send-input nil t))
+	    (mapc
+	     (lambda (line)
+	       (insert (org-babel-chomp line)) (comint-send-input nil t))
+	     (append
+	      (list body)
+	      (if (not ppp)
+		  (list (format org-babel-ruby-f-write tmp-file))
+		(list
+		 "results=_" "require 'pp'" "orig_out = $stdout"
+		 (format org-babel-ruby-pp-f-write tmp-file)))
+	      (list org-babel-ruby-eoe-indicator)))
+	    (comint-send-input nil t))
+	  (org-babel-eval-read-file tmp-file)))))))
 
 (defun org-babel-ruby-read-string (string)
   "Strip \\\"s from around a ruby string."

lisp/babel/langs/ob-sass.el → lisp/ob-sass.el

@@ -40,7 +40,6 @@
 
 ;;; Code:
 (require 'ob)
-(require 'sass-mode)
 
 (defvar org-babel-default-header-args:sass '())
 

lisp/babel/langs/ob-screen.el → lisp/ob-screen.el

@@ -35,6 +35,7 @@
 
 ;;; Code:
 (require 'ob)
+(require 'ob-ref)
 
 (defvar org-babel-screen-location "screen"
   "The command location for screen. 
@@ -53,7 +54,7 @@ In case you want to use a different screen than one selected by your $PATH")
   (message "Sending source code block to interactive terminal session...")
   (save-window-excursion
     (let* ((processed-params (org-babel-process-params params))
-           (session (first processed-params))
+           (session (nth 0 processed-params))
            (socket (org-babel-screen-session-socketname session)))
       (unless socket (org-babel-prep-session:screen session params))
       (org-babel-screen-session-execute-string
@@ -62,7 +63,7 @@ In case you want to use a different screen than one selected by your $PATH")
 (defun org-babel-prep-session:screen (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
   (let* ((processed-params (org-babel-process-params params))
-         (session (first processed-params))
+         (session (nth 0 processed-params))
          (vars (nth 1 processed-params))
          (socket (org-babel-screen-session-socketname session))
          (vars (org-babel-ref-variables params))
@@ -94,14 +95,22 @@ In case you want to use a different screen than one selected by your $PATH")
 (defun org-babel-screen-session-socketname (session)
   "Check if SESSION exist by parsing output of \"screen -ls\"."
   (let* ((screen-ls (shell-command-to-string "screen -ls"))
-         (sockets (remove-if-not
-                   '(lambda (x)
-                     (string-match (rx (or "(Attached)" "(Detached)")) x))
-                   (split-string screen-ls "\n")))
-         (match-socket (find-if
-                        '(lambda (x)
-                          (string-match (concat "org-babel-session-" session) x))
-                        sockets)))
+         (sockets (delq
+		   nil
+                   (mapcar
+		    (lambda (x)
+		      (when (string-match (rx (or "(Attached)" "(Detached)")) x)
+			x))
+		    (split-string screen-ls "\n"))))
+         (match-socket (car
+			(delq
+			 nil
+			 (mapcar
+			  (lambda (x)
+			    (when (string-match
+				   (concat "org-babel-session-" session) x)
+			      x))
+			  sockets)))))
     (when match-socket (car (split-string match-socket)))))
 
 (defun org-babel-screen-session-write-temp-file (session body)

lisp/babel/langs/ob-sh.el → lisp/ob-sh.el

@@ -28,9 +28,10 @@
 
 ;;; Code:
 (require 'ob)
+(require 'ob-comint)
+(require 'ob-eval)
 (require 'shell)
-(eval-when-compile
-  (require 'cl))
+(eval-when-compile (require 'cl))
 
 (declare-function org-babel-ref-variables "ob-ref" (params))
 (declare-function org-babel-comint-in-buffer "ob-comint" (buffer &rest body))
@@ -142,52 +143,30 @@ Emacs-lisp table, otherwise return the results as a string."
 'output then return a list of the outputs of the statements in
 BODY, if RESULT-TYPE equals 'value then return the value of the
 last statement in BODY."
-  (if (not session)
-      ;; external process evaluation
-      (save-window-excursion
-        (with-temp-buffer
-          (insert body)
-          ;; (message "buffer=%s" (buffer-string)) ;; debugging
-          (org-babel-shell-command-on-region (point-min) (point-max) org-babel-sh-command 'current-buffer 'replace)
-	  (cond
-	   ((member "output" result-params) (buffer-string))
-	   ;; TODO: figure out how to return non-output values from shell scripts
-	   (t ;; if not "output" then treat as "value"
-	    (if (member "scalar" result-params)
-		(buffer-string)
-	      (let ((tmp-file (make-temp-file "org-babel-sh"))
-		    (results (buffer-string)))
-		(with-temp-file tmp-file (insert results))
-		(org-babel-import-elisp-from-file tmp-file)))))))
-    ;; comint session evaluation
-    (flet ((strip-empty (lst)
-                        (delq nil (mapcar (lambda (el) (unless (= (length el) 0) el)) lst))))
-      (let ((tmp-file (make-temp-file "org-babel-sh"))
-            (results
-             (cdr (member
-                   org-babel-sh-eoe-output
-                   (strip-empty
-                    (reverse
-                     (mapcar #'org-babel-sh-strip-weird-long-prompt
-                             (mapcar #'org-babel-trim
-                                     (org-babel-comint-with-output
-                                         (session org-babel-sh-eoe-output t body)
-                                       (mapc (lambda (line) (insert line) (comint-send-input))
-                                             (strip-empty (split-string body "\n")))
-                                       (insert org-babel-sh-eoe-indicator)
-                                       (comint-send-input))))))))))
-        ;; (message (replace-regexp-in-string
-        ;;           "%" "%%" (format "processed-results=%S" results))) ;; debugging
-        (or (and results
-                 (cond
-		  ((member "output" result-params)
-		   (org-babel-trim (mapconcat #'org-babel-trim
-					      (reverse results) "\n")))
-		  (t ;; if not "output" then treat as "value"
-		   (with-temp-file tmp-file
-		     (insert (car results)) (insert "\n"))
-		   (org-babel-import-elisp-from-file tmp-file))))
-            "")))))
+  ((lambda (results)
+     (if (or (member "scalar" result-params)
+	     (member "output" result-params))
+	 (buffer-string)
+       (let ((tmp-file (make-temp-file "org-babel-sh")))
+	 (with-temp-file tmp-file (insert results))
+	 (org-babel-import-elisp-from-file tmp-file))))
+   (if (not session)
+       (org-babel-eval org-babel-sh-command (org-babel-trim body))
+     (let ((tmp-file (make-temp-file "org-babel-sh")))
+       (mapconcat
+	#'org-babel-sh-strip-weird-long-prompt
+	(mapcar
+	 #'org-babel-trim
+	 (butlast
+	  (org-babel-comint-with-output
+	      (session org-babel-sh-eoe-output t body)
+	    (mapc
+	     (lambda (line)
+	       (insert line) (comint-send-input nil t) (sleep-for 0.25))
+	     (append
+	      (split-string (org-babel-trim body) "\n")
+	      (list org-babel-sh-eoe-indicator))))
+	  2)) "\n")))))
 
 (defun org-babel-sh-strip-weird-long-prompt (string)
   "Remove prompt cruft from a string of shell output."

lisp/babel/langs/ob-sql.el → lisp/ob-sql.el

@@ -44,6 +44,9 @@
 
 ;;; Code:
 (require 'ob)
+(eval-when-compile (require 'cl))
+
+(declare-function org-table-import "org-table" (file arg))
 
 (defvar org-babel-default-header-args:sql '())
 
@@ -55,6 +58,7 @@
 called by `org-babel-execute-src-block'."
   (message "executing Sql source code block")
   (let* ((result-params (split-string (or (cdr (assoc :results params)) "")))
+	 (processed-params (org-babel-process-params params))
          (cmdline (cdr (assoc :cmdline params)))
          (engine (cdr (assoc :engine params)))
          (in-file (make-temp-file "org-babel-sql-in"))
@@ -63,7 +67,7 @@ called by `org-babel-execute-src-block'."
          (command (case (intern engine)
                     ('mysql (format "mysql %s -e \"source %s\" > %s"
                                     (or cmdline "") in-file out-file))
-                    (t (error "no support for the %s sql engine")))))
+                    (t (error "no support for the %s sql engine" engine)))))
     (with-temp-file in-file
       (insert (org-babel-expand-body:sql body params)))
     (message command)

lisp/babel/langs/ob-sqlite.el → lisp/ob-sqlite.el

@@ -28,9 +28,18 @@
 
 ;;; Code:
 (require 'ob)
+(require 'ob-ref)
+
+(declare-function org-fill-template "org" (template alist))
+(declare-function org-table-convert-region
+		  "org-table" (beg0 end0 &optional separator))
 
 (defvar org-babel-default-header-args:sqlite '())
 
+(defvar org-babel-header-arg-names:sqlite
+  '(db header echo bail csv column html line list separator nullvalue)
+  "Sqlite specific header args.")
+
 (defun org-babel-expand-body:sqlite
   (body params &optional processed-params) body)
 
@@ -42,16 +51,44 @@ called by `org-babel-execute-src-block'."
   (message "executing Sqlite source code block")
   (let ((result-params (split-string (or (cdr (assoc :results params)) "")))
 	(vars (org-babel-ref-variables params))
-	(headers-p (equal "yes" (cdr (assoc :colnames params)))))
+	(db (cdr (assoc :db params)))
+	(separator (cdr (assoc :separator params)))
+	(nullvalue (cdr (assoc :nullvalue params)))
+	(headers-p (equal "yes" (cdr (assoc :colnames params))))
+	(others (delq nil (mapcar
+			   (lambda (arg) (car (assoc arg params)))
+			   (list :header :echo :bail :column
+				 :csv :html :line :list))))
+	exit-code)
+    (message "others:%s" others)
+    (unless db (error "ob-sqlite: can't evaluate without a database."))
     (with-temp-buffer
       (insert
        (shell-command-to-string
-	(format "%s %s -csv %s %S"
-		org-babel-sqlite3-command
-		(if headers-p "-header" "")
-		(cdr (assoc :db params))
-		(org-babel-sqlite-expand-vars body vars))))
+	(org-fill-template
+	 "%cmd %header %separator %nullvalue %others %csv %db  %body"
+	 (list
+	  (cons "cmd" org-babel-sqlite3-command)
+	  (cons "header" (if headers-p "-header" "-noheader"))
+	  (cons "separator"
+		(if separator (format "-separator %s" separator) ""))
+	  (cons "nullvalue"
+		(if nullvalue (format "-nullvalue %s" nullvalue) ""))
+	  (cons "others"
+		(mapconcat
+		 (lambda (arg) (format "-%s" (substring (symbol-name arg) 1)))
+		 others " "))
+	  ;; for easy table parsing, default header type should be -csv
+	  (cons "csv" (if (or (member :csv others) (member :column others)
+			      (member :line others) (member :list others)
+			      (member :html others) separator)
+			  ""
+			"-csv"))
+	  (cons "db " db)
+	  (cons "body" (format "%S" (org-babel-sqlite-expand-vars
+				     body vars)))))))
       (if (or (member "scalar" result-params)
+	      (member "html" result-params)
 	      (member "code" result-params))
 	  (buffer-string)
 	(org-table-convert-region (point-min) (point-max))
@@ -74,8 +111,11 @@ called by `org-babel-execute-src-block'."
   "If RESULT looks like a trivial table, then unwrap it."
   (if (and (equal 1 (length result))
 	   (equal 1 (length (car result))))
-      (caar result)
-    result))
+      (org-babel-read (caar result))
+    (mapcar (lambda (row)
+	      (if (equal 'hline row)
+		  'hline
+		(mapcar #'org-babel-read row))) result)))
 
 (defun org-babel-sqlite-offset-colnames (table headers-p)
   "If HEADERS-P is non-nil then offset the first row as column names."

lisp/babel/ob-tangle.el → lisp/ob-tangle.el

@@ -34,13 +34,6 @@
 
 (declare-function org-link-escape "org" (text &optional table))
 
-(defcustom org-babel-tangle-w-comments nil
-  "Control the insertion of comments into tangled code.  Non-nil
-value will result in the insertion of comments for those
-languages with comment support."
-  :group 'org-babel-tangle
-  :type 'boolean)
-
 (defcustom org-babel-tangle-lang-exts
   '(("emacs-lisp" . "el"))
   "Alist mapping languages to their file extensions.
@@ -247,8 +240,7 @@ form
 	(body (nth 3 spec))
 	(commentable (string= (cdr (assoc :comments (nth 2 spec))) "yes")))
     (flet ((insert-comment (text)
-			   (when (and commentable
-				      org-babel-tangle-w-comments)
+			   (when commentable
 			     (insert "\n")
 			     (comment-region (point)
 					     (progn (insert text) (point)))

lisp/babel/ob.el → lisp/ob.el

@@ -61,6 +61,34 @@
 (declare-function org-babel-ref-variables "ob-ref" (params))
 (declare-function org-babel-ref-resolve-reference "ob-ref" (ref &optional params))
 
+(defcustom org-confirm-babel-evaluate t
+    "Require confirmation before interactively evaluating code
+blocks in Org-mode buffers.  The default value of this variable
+is t, meaning confirmation is required for any code block
+evaluation.  This variable can be set to nil to inhibit any
+future confirmation requests.  This variable can also be set to a
+function which takes two arguments the language of the code block
+and the body of the code block.  Such a function should then
+return a non-nil value if the user should be prompted for
+execution or nil if no prompt is required.
+
+Warning: Disabling confirmation may result in accidental
+evaluation of potentially harmful code.  It may be advisable
+remove code block execution from C-c C-c as further protection
+against accidental code block evaluation.  The
+`org-babel-no-eval-on-ctrl-c-ctrl-c' variable can be used to
+remove code block execution from the C-c C-c keybinding."
+    :group 'org-babel
+    :type '(choice boolean function))
+;; don't allow this variable to be changed through file settings
+(put 'org-confirm-babel-evaluate 'safe-local-variable (lambda (x) (eq x t)))
+
+(defcustom org-babel-no-eval-on-ctrl-c-ctrl-c nil
+  "This variable can be set to remove code block evaluation from
+the C-c C-c key binding."
+  :group 'org-babel
+  :type 'boolean)
+
 (defvar org-babel-source-name-regexp
   "^[ \t]*#\\+\\(srcname\\|source\\|function\\):[ \t]*"
   "Regular expression used to match a source name line.")
@@ -134,15 +162,34 @@ added to the header-arguments-alist."
           (org-babel-parse-inline-src-block-match)
         nil))))
 
+(defun org-babel-confirm-evaluate (info)
+  "Confirm that the user wishes to evaluate the code block
+defined by INFO.  This behavior can be suppressed by setting the
+value of `org-confirm-babel-evaluate' to nil, in which case all
+future interactive code block evaluations will proceed without
+any confirmation from the user.
+
+Note disabling confirmation may result in accidental evaluation
+of potentially harmful code."
+  (unless (or (not (if (functionp org-confirm-babel-evaluate)
+		       (funcall org-confirm-babel-evaluate
+				(nth 0 info) (nth 1 info))
+		     org-confirm-babel-evaluate))
+	      (yes-or-no-p
+	       (format "Evaluate this%scode on your system?"
+		       (if info (format " %s " (nth 0 info)) " "))))
+    (error "evaluation aborted")))
+
 ;;;###autoload
 (defun org-babel-execute-src-block-maybe ()
   "Detect if this is context for a org-babel src-block and if so
 then run `org-babel-execute-src-block'."
   (interactive)
-  (let ((info (org-babel-get-src-block-info)))
-    (if info
-        (progn (org-babel-execute-src-block current-prefix-arg info) t) nil)))
-
+  (if (not org-babel-no-eval-on-ctrl-c-ctrl-c)
+      (let ((info (org-babel-get-src-block-info)))
+	(if info
+	    (progn (org-babel-execute-src-block current-prefix-arg info) t) nil))
+    nil))
 (add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-execute-src-block-maybe)
 
 ;;;###autoload
@@ -241,6 +288,10 @@ the header arguments specified at the front of the source code
 block."
   (interactive)
   (let* ((info (or info (org-babel-get-src-block-info)))
+	 ;; note the `evaluation-confirmed' variable is currently not
+	 ;; used, but could be used later to avoid the need for
+	 ;; chaining confirmations
+	 (evaluation-confirmed (org-babel-confirm-evaluate info))
          (lang (nth 0 info))
 	 (params (setf (nth 2 info)
                        (sort (org-babel-merge-params (nth 2 info) params)
@@ -1022,7 +1073,7 @@ code ---- the results are extracted in the syntax of the source
 					  (listp (cdr (car result)))))
 				 result (list result))
 			     '(:fmt (lambda (cell) (format "%s" cell)))) "\n"))
-	    (goto-char beg) (org-table-align))
+	    (goto-char beg) (when (org-at-table-p) (org-table-align)))
 	   ((member "file" result-params)
 	    (insert result))
 	   ((member "html" result-params)
@@ -1298,16 +1349,6 @@ block but are passed literally to the \"example-block\"."
         (nb-add (buffer-substring index (point-max)))))
     new-body))
 
-(defun org-babel-error-notify (exit-code stderr)
-  "Open a buffer containing information from STDERR with a
-message about the value of EXIT-CODE."
-  (message (format "Shell command exited with code %d" exit-code))
-  (let ((buf (get-buffer-create "*Org-Babel Error Output*")))
-    (with-current-buffer buf
-      (goto-char (point-max))
-      (save-excursion (insert stderr)))
-    (display-buffer buf)))
-
 (defun org-babel-clean-text-properties (text)
   "Strip all properties from text return."
   (when text
@@ -1420,191 +1461,6 @@ the remote connection."
         (concat "/" user (when user "@") host ":" file))
     file))
 
-(defun org-babel-shell-command-on-region (start end command
-				      &optional output-buffer replace
-				      error-buffer display-error-buffer)
-  "Execute string COMMAND in inferior shell with region as input.
-
-Fixes bugs in the emacs 23.1.1 version of `shell-command-on-region'
-
-Normally display output (if any) in temp buffer `*Shell Command Output*';
-Prefix arg means replace the region with it.  Return the exit code of
-COMMAND.
-
-To specify a coding system for converting non-ASCII characters in
-the input and output to the shell command, use
-\\[universal-coding-system-argument] before this command.  By
-default, the input (from the current buffer) is encoded in the
-same coding system that will be used to save the file,
-`buffer-file-coding-system'.  If the output is going to replace
-the region, then it is decoded from that same coding system.
-
-The noninteractive arguments are START, END, COMMAND,
-OUTPUT-BUFFER, REPLACE, ERROR-BUFFER, and DISPLAY-ERROR-BUFFER.
-Noninteractive callers can specify coding systems by binding
-`coding-system-for-read' and `coding-system-for-write'.
-
-If the command generates output, the output may be displayed
-in the echo area or in a buffer.
-If the output is short enough to display in the echo area
-\(determined by the variable `max-mini-window-height' if
-`resize-mini-windows' is non-nil), it is shown there.  Otherwise
-it is displayed in the buffer `*Shell Command Output*'.  The output
-is available in that buffer in both cases.
-
-If there is output and an error, a message about the error
-appears at the end of the output.
-
-If there is no output, or if output is inserted in the current buffer,
-then `*Shell Command Output*' is deleted.
-
-If the optional fourth argument OUTPUT-BUFFER is non-nil,
-that says to put the output in some other buffer.
-If OUTPUT-BUFFER is a buffer or buffer name, put the output there.
-If OUTPUT-BUFFER is not a buffer and not nil,
-insert output in the current buffer.
-In either case, the output is inserted after point (leaving mark after it).
-
-If REPLACE, the optional fifth argument, is non-nil, that means insert
-the output in place of text from START to END, putting point and mark
-around it.
-
-If optional sixth argument ERROR-BUFFER is non-nil, it is a buffer
-or buffer name to which to direct the command's standard error output.
-If it is nil, error output is mingled with regular output.
-If DISPLAY-ERROR-BUFFER is non-nil, display the error buffer if there
-were any errors.  (This is always t, interactively.)
-In an interactive call, the variable `shell-command-default-error-buffer'
-specifies the value of ERROR-BUFFER."
-  (interactive (let (string)
-		 (unless (mark)
-		   (error "The mark is not set now, so there is no region"))
-		 ;; Do this before calling region-beginning
-		 ;; and region-end, in case subprocess output
-		 ;; relocates them while we are in the minibuffer.
-		 (setq string (read-shell-command "Shell command on region: "))
-		 ;; call-interactively recognizes region-beginning and
-		 ;; region-end specially, leaving them in the history.
-		 (list (region-beginning) (region-end)
-		       string
-		       current-prefix-arg
-		       current-prefix-arg
-		       shell-command-default-error-buffer
-		       t)))
-  (let ((error-file
-	 (if error-buffer
-	     (make-temp-file
-	      (expand-file-name "scor"
-				(or (unless (featurep 'xemacs)
-				      small-temporary-file-directory)
-				    temporary-file-directory)))
-	   nil))
-	exit-status)
-    (if (or replace
-	    (and output-buffer
-		 (not (or (bufferp output-buffer) (stringp output-buffer)))))
-	;; Replace specified region with output from command.
-	(let ((swap (and replace (< start end))))
-	  ;; Don't muck with mark unless REPLACE says we should.
-	  (goto-char start)
-	  (and replace (push-mark (point) 'nomsg))
-	  (setq exit-status
-		(call-process-region start end shell-file-name t
-				     (if error-file
-					 (list output-buffer error-file)
-				       t)
-				     nil shell-command-switch command))
-	  ;; It is rude to delete a buffer which the command is not using.
-	  ;; (let ((shell-buffer (get-buffer "*Shell Command Output*")))
-	  ;;   (and shell-buffer (not (eq shell-buffer (current-buffer)))
-	  ;; 	 (kill-buffer shell-buffer)))
-	  ;; Don't muck with mark unless REPLACE says we should.
-	  (and replace swap (exchange-point-and-mark)))
-      ;; No prefix argument: put the output in a temp buffer,
-      ;; replacing its entire contents.
-      (let ((buffer (get-buffer-create
-		     (or output-buffer "*Shell Command Output*"))))
-	(unwind-protect
-	    (if (eq buffer (current-buffer))
-		;; If the input is the same buffer as the output,
-		;; delete everything but the specified region,
-		;; then replace that region with the output.
-		(progn (setq buffer-read-only nil)
-		       (delete-region (max start end) (point-max))
-		       (delete-region (point-min) (min start end))
-		       (setq exit-status
-			     (call-process-region (point-min) (point-max)
-						  shell-file-name t
-						  (if error-file
-						      (list t error-file)
-						    t)
-						  nil shell-command-switch
-						  command)))
-	      ;; Clear the output buffer, then run the command with
-	      ;; output there.
-	      (let ((directory default-directory))
-		(save-current-buffer
-		  (set-buffer buffer)
-		  (setq buffer-read-only nil)
-		  (if (not output-buffer)
-		      (setq default-directory directory))
-		  (erase-buffer)))
-	      (setq exit-status
-		    (call-process-region start end shell-file-name nil
-					 (if error-file
-					     (list buffer error-file)
-					   buffer)
-					 nil shell-command-switch command)))
-	  ;; Report the output.
-	  (with-current-buffer buffer
-	    (setq mode-line-process
-		  (cond ((null exit-status)
-			 " - Error")
-			((stringp exit-status)
-			 (format " - Signal [%s]" exit-status))
-			((not (equal 0 exit-status))
-			 (format " - Exit [%d]" exit-status)))))
-	  (if (with-current-buffer buffer (> (point-max) (point-min)))
-	      ;; There's some output, display it
-	      (display-message-or-buffer buffer)
-	    ;; No output; error?
-	    (let ((output
-		   (if (and error-file
-			    (< 0 (nth 7 (file-attributes error-file))))
-		       "some error output"
-		     "no output")))
-	      (cond ((null exit-status)
-		     (message "(Shell command failed with error)"))
-		    ((equal 0 exit-status)
-		     (message "(Shell command succeeded with %s)"
-			      output))
-		    ((stringp exit-status)
-		     (message "(Shell command killed by signal %s)"
-			      exit-status))
-		    (t
-		     (message "(Shell command failed with code %d and %s)"
-			      exit-status output))))
-	    ;; Don't kill: there might be useful info in the undo-log.
-	    ;; (kill-buffer buffer)
-	    ))))
-
-    (when (and error-file (file-exists-p error-file))
-      (if (< 0 (nth 7 (file-attributes error-file)))
-	  (with-current-buffer (get-buffer-create error-buffer)
-	    (let ((pos-from-end (- (point-max) (point))))
-	      (or (bobp)
-		  (insert "\f\n"))
-	      ;; Do no formatting while reading error file,
-	      ;; because that can run a shell command, and we
-	      ;; don't want that to cause an infinite recursion.
-	      (format-insert-file error-file nil)
-	      ;; Put point after the inserted errors.
-	      (goto-char (- (point-max) pos-from-end)))
-	    (and display-error-buffer
-		 (display-buffer (current-buffer)))))
-      (delete-file error-file))
-    exit-status))
-
 (provide 'ob)
 
 ;; arch-tag: 01a7ebee-06c5-4ee4-a709-e660d28c0af1

lisp/org-capture.el

@@ -336,7 +336,7 @@ for a Remember buffer.")
 (defun org-capture (&optional goto keys)
   "Capture something.
 
-This will let you select a template from org-capture-templates, and then
+This will let you select a template from `org-capture-templates', and then
 file new captured information.  The text is immediately inserted at the
 target location, and an indirect buffer is shown where you can edit it.
 Pressing `C-c C-c' brings you back to the previous state of Emacs,
@@ -454,6 +454,7 @@ bypassed."
 			 '(entry item checkitem plain)))
 	(save-excursion
 	  (goto-char end)
+	  (or (bolp) (newline))
 	  (org-capture-empty-lines-after
 	   (or (org-capture-get :empty-lines 'local) 0))))
       ;; Postprocessing:  Update Statistics cookies, do the sorting
@@ -567,9 +568,10 @@ already gone."
 	(goto-char (point-min))
 	(if (re-search-forward (nth 2 target) nil t)
 	    (progn
-	      (goto-char (match-beginning 0))
+	      (goto-char (if (org-capture-get :prepend)
+			     (match-beginning 0) (match-end 0)))
+	      (org-capture-put :exact-position (point))
 	      (setq target-entry-p (and (org-mode-p) (org-at-heading-p))))
-	  (kill-buffer (current-buffer))
 	  (error "No match for target regexp in file %s" (nth 1 target))))
 
        ((eq (car target) 'file+datetree)
@@ -588,6 +590,12 @@ already gone."
        ((eq (car target) 'file+function)
 	(set-buffer (org-capture-target-buffer (nth 1 target)))
 	(funcall (nth 2 target))
+	(org-capture-put :exact-position (point))
+	(setq target-entry-p (and (org-mode-p) (org-at-heading-p))))
+
+       ((eq (car target) 'function)
+	(funcall (nth 1 target))
+	(org-capture-put :exact-position (point))
 	(setq target-entry-p (and (org-mode-p) (org-at-heading-p))))
 
        ((eq (car target) 'clock)
@@ -640,6 +648,8 @@ already gone."
 	 (target-entry-p (org-capture-get :target-entry-p))
 	 level beg end)
     (cond
+     ((org-capture-get :exact-position)
+      (goto-char (org-capture-get :exact-position)))
      ((not target-entry-p)
       ;; Insert as top-level entry, either at beginning or at end of file
       (setq level 1)
@@ -674,8 +684,11 @@ already gone."
   "Place the template as a new plain list item."
   (let* ((txt (org-capture-get :template))
 	 (target-entry-p (org-capture-get :target-entry-p))
-	 ind beg end)
+	 (ind 0)
+	 beg end)
     (cond
+     ((org-capture-get :exact-position)
+      (goto-char (org-capture-get :exact-position)))
      ((not target-entry-p)
       ;; Insert as top-level entry, either at beginning or at end of file
       (setq beg (point-min) end (point-max)))
@@ -731,6 +744,8 @@ already gone."
 	 (table-line-pos (org-capture-get :table-line-pos))
 	 ind beg end)
     (cond
+     ((org-capture-get :exact-position)
+      (goto-char (org-capture-get :exact-position)))
      ((not target-entry-p)
       ;; Table is not necessarily under a heading
       (setq beg (point-min) end (point-max)))
@@ -804,7 +819,10 @@ already gone."
   "Place the template plainly."
   (let* ((txt (org-capture-get :template))
 	 beg end)
-    (goto-char (if (org-capture-get :prepend) (point-min) (point-max)))
+    (goto-char (cond
+		((org-capture-get :exact-position))
+		((org-capture-get :prepend) (point-min))
+		(t (point-max))))
     (or (bolp) (newline))
     (org-capture-empty-lines-before)
     (setq beg (point))

lisp/org-feed.el

@@ -45,7 +45,7 @@
 ;;  With this setup, the command `M-x org-feed-update-all' will
 ;;  collect new entries in the feed at the given URL and create
 ;;  entries as subheadings under the "ReQall Entries" heading in the
-;;  file "~/org-feeds.org".  Each feed should normally have its own
+;;  file "~/org/feeds.org".  Each feed should normally have its own
 ;;  heading - however see the `:drawer' parameter.
 ;;
 ;;  Besides these standard elements that need to be specified for each

lisp/org-indent.el

@@ -127,45 +127,56 @@ Internally this works by adding `line-prefix' properties to all non-headlines.
 These properties are updated locally in idle time.
 FIXME:  How to update when broken?"
   nil " Ind" nil
-  (if (org-bound-and-true-p org-inhibit-startup)
-      (setq org-indent-mode nil)
-    (if org-indent-mode
-	(progn
-	  (org-set-local 'indent-tabs-mode nil)
-	  (or org-indent-strings (org-indent-initialize))
-	  (when org-indent-mode-turns-off-org-adapt-indentation
-	    (org-set-local 'org-adapt-indentation nil))
-	  (when org-indent-mode-turns-on-hiding-stars
-	    (org-set-local 'org-hide-leading-stars-before-indent-mode
-			   org-hide-leading-stars)
-	    (org-set-local 'org-hide-leading-stars t))
-	  (make-local-variable 'buffer-substring-filters)
-	  (add-to-list 'buffer-substring-filters
-		       'org-indent-remove-properties-from-string)
-	  (org-add-hook 'org-after-demote-entry-hook
-			'org-indent-refresh-section nil 'local)
-	  (org-add-hook 'org-after-promote-entry-hook
-			'org-indent-refresh-section nil 'local)
-	  (org-add-hook 'org-font-lock-hook
-			'org-indent-refresh-to nil 'local)
-	  (and font-lock-mode (org-restart-font-lock))
-	  )
-      (save-excursion
-	(save-restriction
-	  (org-indent-remove-properties (point-min) (point-max))
-	  (kill-local-variable 'org-adapt-indentation)
-	  (when (boundp 'org-hide-leading-stars-before-indent-mode)
-	    (org-set-local 'org-hide-leading-stars
-			   org-hide-leading-stars-before-indent-mode))
-	  (setq buffer-substring-filters
-		(delq 'org-indent-remove-properties-from-string
-		      buffer-substring-filters))
-	  (remove-hook 'org-after-promote-entry-hook
-		       'org-indent-refresh-section 'local)
-	  (remove-hook 'org-after-demote-entry-hook
-		       'org-indent-refresh-section 'local)
-	  (and font-lock-mode (org-restart-font-lock))
-	  (redraw-display))))))
+  (cond
+   ((org-bound-and-true-p org-inhibit-startup)
+    (setq org-indent-mode nil))
+   ((and org-indent-mode
+	 (or (< emacs-major-version 23)
+	     (and (= emacs-major-version 23)
+		  (< emacs-minor-version 2))))
+    (message "org-indent-mode is can crash Emacs 23.1 - refused to turn it on!")
+    (ding)
+    (sit-for 1)
+    (setq org-indent-mode nil))
+   (org-indent-mode
+    ;; mode was turned on.
+    (org-set-local 'indent-tabs-mode nil)
+    (or org-indent-strings (org-indent-initialize))
+    (when org-indent-mode-turns-off-org-adapt-indentation
+      (org-set-local 'org-adapt-indentation nil))
+    (when org-indent-mode-turns-on-hiding-stars
+      (org-set-local 'org-hide-leading-stars-before-indent-mode
+		     org-hide-leading-stars)
+      (org-set-local 'org-hide-leading-stars t))
+    (make-local-variable 'buffer-substring-filters)
+    (add-to-list 'buffer-substring-filters
+		 'org-indent-remove-properties-from-string)
+    (org-add-hook 'org-after-demote-entry-hook
+		  'org-indent-refresh-section nil 'local)
+    (org-add-hook 'org-after-promote-entry-hook
+		  'org-indent-refresh-section nil 'local)
+    (org-add-hook 'org-font-lock-hook
+		  'org-indent-refresh-to nil 'local)
+    (and font-lock-mode (org-restart-font-lock))
+    )
+   (t
+    ;; mode was turned off (or we refused to turn it on)
+    (save-excursion
+      (save-restriction
+	(org-indent-remove-properties (point-min) (point-max))
+	(kill-local-variable 'org-adapt-indentation)
+	(when (boundp 'org-hide-leading-stars-before-indent-mode)
+	  (org-set-local 'org-hide-leading-stars
+			 org-hide-leading-stars-before-indent-mode))
+	(setq buffer-substring-filters
+	      (delq 'org-indent-remove-properties-from-string
+		    buffer-substring-filters))
+	(remove-hook 'org-after-promote-entry-hook
+		     'org-indent-refresh-section 'local)
+	(remove-hook 'org-after-demote-entry-hook
+		     'org-indent-refresh-section 'local)
+	(and font-lock-mode (org-restart-font-lock))
+	(redraw-display))))))
 
 
 (defface org-indent

lisp/org-latex.el

@@ -1894,7 +1894,7 @@ The conversion is made depending of STRING-BEFORE and STRING-AFTER."
 	     (t (insert "\\texttt{" desc "}")))))))
 
 
-(defun org-export-latex-format-image (path caption label attr)
+(defun org-export-latex-format-image (path caption label attr &optional shortn)
   "Format the image element, depending on user settings."
   (let (ind floatp wrapp multicolumnp placement figenv)
     (setq floatp (or caption label))

lisp/org.el

@@ -119,7 +119,62 @@
 (require 'ob-tangle)
 (require 'ob-comint)
 (require 'ob-keys)
-(require 'ob-emacs-lisp)
+
+;; load languages based on value of `org-babel-load-languages'
+(defvar org-babel-load-languages)
+(defun org-babel-do-load-languages (sym value)
+  "Load the languages defined in `org-babel-load-languages'."
+  (set-default sym value)
+  (mapc (lambda (pair)
+	  (let ((active (cdr pair)) (lang (symbol-name (car pair))))
+	    (if active
+		(progn
+		  (require (intern (concat "ob-" lang))))
+	      (progn
+		(funcall 'fmakunbound
+			 (intern (concat "org-babel-execute:" lang)))
+		(funcall 'fmakunbound
+			 (intern (concat "org-babel-expand-body:" lang)))))))
+	org-babel-load-languages))
+
+(defcustom org-babel-load-languages '((emacs-lisp . t))
+  "Languages which can be evaluated in Org-mode buffers.  This
+list can be used to load support for any of the languages below,
+note that each language will depend on a different set of system
+executables and/or Emacs modes.  When a language is \"loaded\",
+then code blocks in that language can be evaluated with
+`org-babel-execute-src-block' bound by default to C-c C-c (note
+the `org-babel-no-eval-on-ctrl-c-ctrl-c' variable can be set to
+remove code block evaluation from the C-c C-c keybinding.  By
+default only Emacs Lisp (which has no requirements) is loaded."
+  :group 'org-babel
+  :set 'org-babel-do-load-languages
+  :type '(alist :tag "Babel Languages"
+		:key-type
+		(choice
+		 (const :tag "C" C)
+		 (const :tag "R" R)
+		 (const :tag "Asymptote" asymptote)
+		 (const :tag "Clojure" clojure)
+		 (const :tag "CSS" css)
+		 (const :tag "Ditaa" ditaa)
+		 (const :tag "Dot" dot)
+		 (const :tag "Emacs Lisp" emacs-lisp)
+		 (const :tag "Gnuplot" gnuplot)
+		 (const :tag "Haskell" haskell)
+		 (const :tag "Latex" latex)
+		 (const :tag "Matlab" matlab)
+		 (const :tag "Ocaml" ocaml)
+		 (const :tag "Octave" octave)
+		 (const :tag "Perl" perl)
+		 (const :tag "Python" python)
+		 (const :tag "Ruby" ruby)
+		 (const :tag "Sass" sass)
+		 (const :tag "Screen" screen)
+		 (const :tag "Shell Script" sh)
+		 (const :tag "Sql" sql)
+		 (const :tag "Sqlite" sqlite))
+		:value-type (boolean :tag "Activate" :value t)))
 
 ;;;; Customization variables
 (defcustom org-clone-delete-id nil
@@ -17021,7 +17076,13 @@ This command does many different things, depending on context:
 - If the cursor is on a numbered item in a plain list, renumber the
   ordered list.
 
-- If the cursor is on a checkbox, toggle it."
+- If the cursor is on a checkbox, toggle it.
+
+- If the cursor is on a code block, evaluate it.  The variable
+  `org-confirm-babel-evaluate' can be used to control prompting
+  before code block evaluation, by default every code block
+  evaluation requires confirmation.  Code block evaluation can be
+  inhibited by setting `org-babel-no-eval-on-ctrl-c-ctrl-c'."
   (interactive "P")
   (let  ((org-enable-table-editor t))
     (cond