From 0c8b86e9a9786ed12a8724d5911df262d6bfe9b9 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sat, 17 Apr 2010 14:03:30 -0600
Subject: [PATCH 01/46] org-babel: keep within 80 columns

  this is exclusively whitespace and indentation changes, with the
  goal of cleaning up the file, and keep all lines within 80 columns
---
 contrib/babel/lisp/org-babel.el | 271 ++++++++++++++++++++------------
 1 file changed, 168 insertions(+), 103 deletions(-)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index b2dd5b9ba..910ffc85f 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -36,7 +36,8 @@
 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 info
+        (progn (org-babel-execute-src-block current-prefix-arg info) t) nil)))
 
 (add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-execute-src-block-maybe)
 
@@ -50,8 +51,9 @@ prefix argument from inside of a source-code block."
            (lang (first info))
            (params (third info))
            (session (cdr (assoc :session params))))
-      (when (and info session) ;; if we are in a source-code block which has a session
-        (funcall (intern (concat "org-babel-prep-session:" lang)) session params))))
+      (when (and info session) ;; we are in a source-code block with a session
+        (funcall
+         (intern (concat "org-babel-prep-session:" lang)) session params))))
   ad-do-it)
 
 (defadvice org-open-at-point (around org-babel-open-at-point activate)
@@ -86,7 +88,8 @@ individual languages may define their own language specific
 header arguments as well.")
 
 (defvar org-babel-default-header-args
-  '((:session . "none") (:results . "replace") (:exports . "code") (:cache . "no") (:noweb . "no"))
+  '((:session . "none") (:results . "replace") (:exports . "code")
+    (:cache . "no") (:noweb . "no"))
   "Default arguments to use when evaluating a source block.")
 
 (defvar org-babel-default-inline-header-args
@@ -133,13 +136,14 @@ can not be resolved.")
 
 (defun org-babel-set-interpreters (var value)
   (set-default var value)
-  (setq org-babel-src-block-regexp
-	(concat "^[ \t]*#\\+begin_src[ \t]+\\("       ;; (1)   lang
-		(mapconcat 'regexp-quote value "\\|")
-		"\\)[ \t]*"
-		"\\([^\":\n]*\"[^\"\n*]*\"[^\":\n]*\\|[^\":\n]*\\)" ;; (2)   switches
-		"\\([^\n]*\\)\n"                      ;; (3)   header arguments
-                "\\([^\000]+?\n\\)[ \t]*#\\+end_src"));; (4)   body
+  (setq
+   org-babel-src-block-regexp
+   (concat "^[ \t]*#\\+begin_src[ \t]+\\("       ;; (1)   lang
+           (mapconcat 'regexp-quote value "\\|")
+           "\\)[ \t]*"
+           "\\([^\":\n]*\"[^\"\n*]*\"[^\":\n]*\\|[^\":\n]*\\)" ;; (2)   switches
+           "\\([^\n]*\\)\n"                      ;; (3)   header arguments
+           "\\([^\000]+?\n\\)[ \t]*#\\+end_src"));; (4)   body
   (setq org-babel-inline-src-block-regexp
 	(concat "[ \f\t\n\r\v]\\(src_"                ;; (1)   replacement target
 		"\\("                                 ;; (2)   lang
@@ -206,14 +210,15 @@ block."
                        (sort (org-babel-merge-params (third info) params)
                              (lambda (el1 el2) (string< (symbol-name (car el1))
                                                    (symbol-name (car el2)))))))
-         (new-hash (if (and (cdr (assoc :cache params))
-                            (string= "yes" (cdr (assoc :cache params)))) (org-babel-sha1-hash info)))
+         (new-hash
+          (if (and (cdr (assoc :cache params))
+                   (string= "yes" (cdr (assoc :cache params))))
+              (org-babel-sha1-hash info)))
          (old-hash (org-babel-result-hash info))
          (body (setf (second info)
 		     (if (and (cdr (assoc :noweb params))
                               (string= "yes" (cdr (assoc :noweb params))))
-			 (org-babel-expand-noweb-references info) (second info))))
-
+                         (org-babel-expand-noweb-references info) (second info))))
          (result-params (split-string (or (cdr (assoc :results params)) "")))
          (result-type (cond ((member "output" result-params) 'output)
 			    ((member "value" result-params) 'value)
@@ -228,7 +233,7 @@ block."
          result)
     (unwind-protect
         (flet ((call-process-region (&rest args)
-                                    (apply 'org-babel-tramp-handle-call-process-region args)))
+                 (apply 'org-babel-tramp-handle-call-process-region args)))
           (unless (member lang org-babel-interpreters)
             (error "Language is not in `org-babel-interpreters': %s" lang))
           (if (and (not arg) new-hash (equal new-hash old-hash))
@@ -236,7 +241,8 @@ block."
                 (goto-char (org-babel-where-is-src-block-result nil info))
                 (move-end-of-line 1) (forward-char 1)
                 (setq result (org-babel-read-result))
-                (message (replace-regexp-in-string "%" "%%" (format "%S" result))) result)
+                (message (replace-regexp-in-string "%" "%%"
+                                                   (format "%S" result))) result)
             (setq result (funcall cmd body params))
             (if (eq result-type 'value)
                 (setq result (if (and (or (member "vector" result-params)
@@ -262,7 +268,9 @@ session.  After loading the body this pops open the session."
     (unless (member lang org-babel-interpreters)
       (error "Language is not in `org-babel-interpreters': %s" lang))
     ;; if called with a prefix argument, then process header arguments
-    (pop-to-buffer (funcall (intern (concat "org-babel-load-session:" lang)) session body params))
+    (pop-to-buffer
+     (funcall (intern (concat "org-babel-load-session:" lang))
+              session body params))
     (move-end-of-line 1)))
 
 (defun org-babel-switch-to-session (&optional arg info)
@@ -282,11 +290,15 @@ of the source block to the kill ring."
     (unless (member lang org-babel-interpreters)
       (error "Language is not in `org-babel-interpreters': %s" lang))
     ;; copy body to the kill ring
-    (with-temp-buffer (insert (org-babel-trim body)) (copy-region-as-kill (point-min) (point-max)))
+    (with-temp-buffer (insert (org-babel-trim body))
+                      (copy-region-as-kill (point-min) (point-max)))
     ;; if called with a prefix argument, then process header arguments
-    (if arg (funcall (intern (concat "org-babel-prep-session:" lang)) session params))
+    (when arg
+      (funcall (intern (concat "org-babel-prep-session:" lang)) session params))
     ;; just to the session using pop-to-buffer
-    (pop-to-buffer (funcall (intern (format "org-babel-%s-initiate-session" lang)) session params))
+    (pop-to-buffer
+     (funcall (intern (format "org-babel-%s-initiate-session" lang))
+              session params))
     (move-end-of-line 1)))
 
 (defalias 'org-babel-pop-to-session 'org-babel-switch-to-session)
@@ -355,18 +367,22 @@ added to the header-arguments-alist."
 	  (goto-char head)
 	  (setq info (org-babel-parse-src-block-match))
 	  (forward-line -1)
-	  (when (looking-at (concat org-babel-source-name-regexp
-                                    "\\([^ ()\f\t\n\r\v]+\\)\\(\(\\(.*\\)\)\\|\\)"))
-	    (setq info (append info (list (org-babel-clean-text-properties (match-string 2)))))
+	  (when (looking-at
+                 (concat org-babel-source-name-regexp
+                         "\\([^ ()\f\t\n\r\v]+\\)\\(\(\\(.*\\)\)\\|\\)"))
+	    (setq info (append info (list (org-babel-clean-text-properties
+                                           (match-string 2)))))
 	    ;; Note that e.g. "name()" and "name( )" result in ((:var . "")).
 	    ;; We maintain that behaviour, and the resulting non-nil sixth
-	    ;; element is relied upon in org-babel-exp-code to detect a functional-style
-	    ;; block in those cases. However, "name" without any
-	    ;; parentheses would result in the same thing, so we
-	    ;; explicitly avoid that.
+	    ;; element is relied upon in org-babel-exp-code to detect
+	    ;; a functional-style block in those cases. However,
+	    ;; "name" without any parentheses would result in the same
+	    ;; thing, so we explicitly avoid that.
 	    (if (setq args (match-string 4))
-		(setq info (append info (list (mapcar (lambda (ref) (cons :var ref))
-						      (org-babel-ref-split-args args))))))
+                (setq info
+                      (append info (list
+                                    (mapcar (lambda (ref) (cons :var ref))
+                                            (org-babel-ref-split-args args))))))
 	    (unless header-vars-only
 	      (setf (third info)
 		    (org-babel-merge-params (sixth info) (third info)))))
@@ -543,7 +559,7 @@ may be specified in the properties of the current outline entry."
 	 (preserve-indentation (or org-src-preserve-indentation
 				   (string-match "-i\\>" switches))))
     (list lang
-          ;; get src block body removing properties, protective commas, and indentation
+          ;; get block body less properties, protective commas, and indentation
           (with-temp-buffer
             (save-match-data
               (insert (org-babel-strip-protective-commas body))
@@ -553,19 +569,22 @@ may be specified in the properties of the current outline entry."
 	   org-babel-default-header-args
            (org-babel-params-from-properties)
 	   (if (boundp lang-headers) (eval lang-headers) nil)
-	   (org-babel-parse-header-arguments (org-babel-clean-text-properties (or (match-string 3) ""))))
+	   (org-babel-parse-header-arguments
+            (org-babel-clean-text-properties (or (match-string 3) ""))))
 	  switches)))
 
 (defun org-babel-parse-inline-src-block-match ()
   (let* ((lang (org-babel-clean-text-properties (match-string 2)))
          (lang-headers (intern (concat "org-babel-default-header-args:" lang))))
     (list lang
-          (org-babel-strip-protective-commas (org-babel-clean-text-properties (match-string 5)))
+          (org-babel-strip-protective-commas
+           (org-babel-clean-text-properties (match-string 5)))
           (org-babel-merge-params
            org-babel-default-inline-header-args
            (org-babel-params-from-properties)
            (if (boundp lang-headers) (eval lang-headers) nil)
-           (org-babel-parse-header-arguments (org-babel-clean-text-properties (or (match-string 4) "")))))))
+           (org-babel-parse-header-arguments
+            (org-babel-clean-text-properties (or (match-string 4) "")))))))
 
 (defun org-babel-parse-header-arguments (arg-string)
   "Parse a string of header arguments returning an alist."
@@ -573,10 +592,13 @@ may be specified in the properties of the current outline entry."
       (delq nil
 	    (mapcar
 	     (lambda (arg)
-	       (if (string-match "\\([^ \f\t\n\r\v]+\\)[ \f\t\n\r\v]+\\([^ \f\t\n\r\v]+.*\\)" arg)
+	       (if (string-match
+                    "\\([^ \f\t\n\r\v]+\\)[ \f\t\n\r\v]+\\([^ \f\t\n\r\v]+.*\\)"
+                    arg)
 		   (cons (intern (concat ":" (match-string 1 arg)))
                          (let ((raw (org-babel-chomp (match-string 2 arg))))
-                           (if (org-babel-number-p raw) raw (org-babel-read raw))))
+                           (if (org-babel-number-p raw)
+                               raw (org-babel-read raw))))
 		 (cons (intern (concat ":" arg)) nil)))
 	     (split-string (concat " " arg-string) "[ \f\t\n\r\v]+:" t)))))
 
@@ -644,7 +666,8 @@ buffer or nil if no such result exists."
   (save-excursion
     (goto-char (point-min))
     (when (re-search-forward
-           (concat org-babel-result-regexp "[ \t]" (regexp-quote name) "[ \t\n\f\v\r]") nil t)
+           (concat org-babel-result-regexp
+                   "[ \t]" (regexp-quote name) "[ \t\n\f\v\r]") nil t)
       (move-beginning-of-line 0) (point))))
 
 (defun org-babel-where-is-src-block-result (&optional insert info hash)
@@ -668,13 +691,18 @@ following the source block."
 			       (progn ;; unnamed results line already exists
 				 (re-search-forward "[^ \f\t\n\r\v]" nil t)
 				 (move-beginning-of-line 1)
-                                 (looking-at (concat org-babel-result-regexp "\n"))))
-			  ;; or (with optional insert) back up and make one ourselves
+                                 (looking-at
+                                  (concat org-babel-result-regexp "\n"))))
+			  ;; or (with optional insert) back up and
+			  ;; make one ourselves
                           (when insert
                             (goto-char end)
-			    (if (looking-at "[\n\r]") (forward-char 1) (insert "\n"))
-                            (insert (concat "#+results" (if hash (concat "["hash"]"))
-                                            ":"(if name (concat " " name)) "\n"))
+			    (if (looking-at "[\n\r]")
+                                (forward-char 1) (insert "\n"))
+                            (insert (concat "#+results"
+                                            (when hash (concat "["hash"]"))
+                                            ":"
+                                            (when name (concat " " name)) "\n"))
                             (move-beginning-of-line 0)
                             (if hash (org-babel-hide-hash)) t)))
                (point))))))
@@ -689,12 +717,14 @@ following the source block."
      ((looking-at ": ")
       (setq result-string
 	    (org-babel-trim
-	     (mapconcat (lambda (line) (if (and (> (length line) 1)
-						(string= ": " (substring line 0 2)))
-					   (substring line 2)
-					 line))
+	     (mapconcat (lambda (line)
+                          (if (and (> (length line) 1)
+                                   (string= ": " (substring line 0 2)))
+                              (substring line 2)
+                            line))
 			(split-string
-			 (buffer-substring (point) (org-babel-result-end)) "[\r\n]+")
+			 (buffer-substring
+                          (point) (org-babel-result-end)) "[\r\n]+")
 			"\n")))
       (or (org-babel-number-p result-string) result-string))
      ((looking-at org-babel-result-regexp)
@@ -776,7 +806,8 @@ code ---- the results are extracted in the syntax of the source
         (setq result (concat result "\n")))
       (save-excursion
 	(let ((existing-result (org-babel-where-is-src-block-result t info hash))
-	      (results-switches (cdr (assoc :results_switches (third info)))) beg)
+	      (results-switches
+               (cdr (assoc :results_switches (third info)))) beg)
 	  (when existing-result (goto-char existing-result) (forward-line 1))
 	  (setq results-switches
                 (if results-switches (concat " " results-switches) ""))
@@ -794,11 +825,14 @@ code ---- the results are extracted in the syntax of the source
 	   ((member "file" result-params)
 	    (insert result))
 	   ((member "html" result-params)
-	    (insert (format "#+BEGIN_HTML%s\n%s#+END_HTML\n" results-switches result)))
+	    (insert (format "#+BEGIN_HTML%s\n%s#+END_HTML\n"
+                            results-switches result)))
 	   ((member "latex" result-params)
-	    (insert (format "#+BEGIN_LaTeX%s\n%s#+END_LaTeX\n" results-switches result)))
+	    (insert (format "#+BEGIN_LaTeX%s\n%s#+END_LaTeX\n"
+                            results-switches result)))
 	   ((member "code" result-params)
-	    (insert (format "#+BEGIN_SRC %s%s\n%s#+END_SRC\n" lang results-switches result)))
+	    (insert (format "#+BEGIN_SRC %s%s\n%s#+END_SRC\n"
+                            lang results-switches result)))
 	   ((or (member "raw" result-params) (member "org" result-params))
 	    (save-excursion (insert result)) (if (org-at-table-p) (org-cycle)))
 	   (t
@@ -852,7 +886,8 @@ directory then expand relative links."
    (if (and default-directory
             buffer-file-name
             (not (string= (expand-file-name default-directory)
-                          (expand-file-name (file-name-directory buffer-file-name)))))
+                          (expand-file-name
+                           (file-name-directory buffer-file-name)))))
        (expand-file-name result default-directory)
      result)))
 
@@ -863,7 +898,8 @@ directory then expand relative links."
 		      (line-number-at-pos beg)))))
     (save-excursion
       (cond ((= size 0)
-	     (error "This should be impossible: a newline was appended to result if missing"))
+	     (error (concat "This should be impossible:"
+                            "a newline was appended to result if missing")))
 	    ((< size org-babel-min-lines-for-block-output)
 	     (goto-char beg)
 	     (dotimes (n size)
@@ -882,66 +918,85 @@ elements of PLISTS override the values of previous element.  This
 takes into account some special considerations for certain
 parameters when merging lists."
   (let ((results-exclusive-groups
-	 '(("file" "vector" "table" "scalar" "raw" "org" "html" "latex" "code" "pp")
+	 '(("file" "vector" "table" "scalar" "raw" "org"
+            "html" "latex" "code" "pp")
 	   ("replace" "silent")
 	   ("output" "value")))
 	(exports-exclusive-groups
 	 '(("code" "results" "both" "none")))
 	params results exports tangle noweb cache vars var ref shebang comments)
     (flet ((e-merge (exclusive-groups &rest result-params)
-                    ;; maintain exclusivity of mutually exclusive parameters
-                    (let (output)
-                      (mapc (lambda (new-params)
-                              (mapc (lambda (new-param)
-                                      (mapc (lambda (exclusive-group)
-                                              (when (member new-param exclusive-group)
-                                                (mapcar (lambda (excluded-param)
-                                                          (setq output (delete excluded-param output)))
-                                                        exclusive-group)))
-                                            exclusive-groups)
-                                      (setq output (org-uniquify (cons new-param output))))
-                                    new-params))
-                            result-params)
-                      output)))
+             ;; maintain exclusivity of mutually exclusive parameters
+             (let (output)
+               (mapc (lambda (new-params)
+                       (mapc (lambda (new-param)
+                               (mapc (lambda (exclusive-group)
+                                       (when (member new-param exclusive-group)
+                                         (mapcar (lambda (excluded-param)
+                                                   (setq output
+                                                         (delete
+                                                          excluded-param
+                                                          output)))
+                                                 exclusive-group)))
+                                     exclusive-groups)
+                               (setq output (org-uniquify
+                                             (cons new-param output))))
+                             new-params))
+                     result-params)
+               output)))
       (mapc (lambda (plist)
               (mapc (lambda (pair)
                       (case (car pair)
                         (:var
                          ;; we want only one specification per variable
-                         (when (string-match "^\\([^= \f\t\n\r\v]+\\)[ \t]*=[ \t]*\\([^\f\n\r\v]+\\)$" (cdr pair))
+                         (when (string-match
+                                (concat "^\\([^= \f\t\n\r\v]+\\)[ \t]*="
+                                        "[ \t]*\\([^\f\n\r\v]+\\)$") (cdr pair))
                            ;; TODO: When is this not true?
                            (setq var (intern (match-string 1 (cdr pair)))
                                  ref (match-string 2 (cdr pair))
-                                 vars (cons (cons var ref) (assq-delete-all var vars)))))
+                                 vars (cons (cons var ref)
+                                            (assq-delete-all var vars)))))
                         (:results
                          (setq results
-			       (e-merge results-exclusive-groups results (split-string (cdr pair)))))
+			       (e-merge results-exclusive-groups
+                                        results (split-string (cdr pair)))))
 			(:file
 			 (when (cdr pair)
-			   (setq results (e-merge results-exclusive-groups results '("file")))
+			   (setq results (e-merge results-exclusive-groups
+                                                  results '("file")))
 			   (unless (or (member "both" exports)
                                        (member "none" exports)
                                        (member "code" exports))
-			     (setq exports (e-merge exports-exclusive-groups exports '("results"))))
-			   (setq params (cons pair (assq-delete-all (car pair) params)))))
+			     (setq exports (e-merge exports-exclusive-groups
+                                                    exports '("results"))))
+			   (setq params
+                                 (cons pair
+                                       (assq-delete-all (car pair) params)))))
                         (:exports
-                         (setq exports (e-merge exports-exclusive-groups
-                                                exports (split-string (cdr pair)))))
+                         (setq exports
+                               (e-merge exports-exclusive-groups
+                                        exports (split-string (cdr pair)))))
                         (:tangle ;; take the latest -- always overwrite
                          (setq tangle (or (list (cdr pair)) tangle)))
                         (:noweb
-                         (setq noweb (e-merge '(("yes" "no"))
-                                              noweb (split-string (or (cdr pair) "")))))
+                         (setq noweb
+                               (e-merge '(("yes" "no")) noweb
+                                        (split-string (or (cdr pair) "")))))
                         (:cache
-                         (setq cache (e-merge '(("yes" "no"))
-                                              cache (split-string (or (cdr pair) "")))))
+                         (setq cache
+                               (e-merge '(("yes" "no")) cache
+                                        (split-string (or (cdr pair) "")))))
                         (:shebang ;; take the latest -- always overwrite
                          (setq shebang (or (list (cdr pair)) shebang)))
                         (:comments
-                         (setq comments (e-merge '(("yes" "no"))
-                                                 comments (split-string (or (cdr pair) "")))))
+                         (setq comments
+                               (e-merge '(("yes" "no")) comments
+                                        (split-string (or (cdr pair) "")))))
                         (t ;; replace: this covers e.g. :session
-                         (setq params (cons pair (assq-delete-all (car pair) params))))))
+                         (setq params
+                               (cons pair
+                                     (assq-delete-all (car pair) params))))))
                     plist))
             plists))
     (setq vars (mapcar (lambda (pair) (format "%s=%s" (car pair) (cdr pair))) vars))
@@ -951,9 +1006,12 @@ parameters when merging lists."
                 (cons (cons :cache (mapconcat 'identity cache " "))
                       (cons (cons :noweb (mapconcat 'identity noweb " "))
                             (cons (cons :tangle (mapconcat 'identity tangle " "))
-                                  (cons (cons :exports (mapconcat 'identity exports " "))
-                                        (cons (cons :results (mapconcat 'identity results " "))
-                                              params)))))))))
+                                  (cons (cons :exports
+                                              (mapconcat 'identity exports " "))
+                                        (cons
+                                         (cons :results
+                                               (mapconcat 'identity results " "))
+                                         params)))))))))
 
 (defun org-babel-expand-noweb-references (&optional info parent-buffer)
   "This function expands Noweb style references in the body of
@@ -999,9 +1057,10 @@ block but are passed literally to the \"example-block\"."
           (save-match-data (setf source-name (match-string 1)))
           (save-match-data (setq evaluate (string-match "\(.*\)" source-name)))
           (save-match-data
-            (setq prefix (buffer-substring (match-beginning 0)
-                                           (save-excursion
-                                             (move-beginning-of-line 1) (point)))))
+            (setq prefix
+                  (buffer-substring (match-beginning 0)
+                                    (save-excursion
+                                      (move-beginning-of-line 1) (point)))))
           ;; add interval to new-body (removing noweb reference)
           (goto-char (match-beginning 0))
           (nb-add (buffer-substring index (point)))
@@ -1020,13 +1079,15 @@ block but are passed literally to the \"example-block\"."
                           (if point
                               (save-excursion
                                 (goto-char point)
-                                (org-babel-trim (org-babel-expand-noweb-references
-                                                 (org-babel-get-src-block-info))))
+                                (org-babel-trim
+                                 (org-babel-expand-noweb-references
+                                  (org-babel-get-src-block-info))))
                             ;; optionally raise an error if named
                             ;; source-block doesn't exist
                             (if (member lang org-babel-noweb-error-langs)
                                 (error
-                                 "<<%s>> could not be resolved (see `org-babel-noweb-error-langs')"
+                                 (concat "<<%s>> could not be resolved "
+                                         "(see `org-babel-noweb-error-langs')")
                                  source-name)
                               "")))) "[\n\r]") (concat "\n" prefix)))))
         (nb-add (buffer-substring index (point-max)))))
@@ -1107,14 +1168,16 @@ the table is trivial, then return it as a scalar."
 STRING.  Default regexp used is \"[ \f\t\n\r\v]\" but can be
 overwritten by specifying a regexp as a second argument."
   (let ((regexp (or regexp "[ \f\t\n\r\v]")))
-    (while (and (> (length string) 0) (string-match regexp (substring string -1)))
+    (while (and (> (length string) 0)
+                (string-match regexp (substring string -1)))
       (setq string (substring string 0 -1)))
     string))
 
 (defun org-babel-trim (string &optional regexp)
   "Like `org-babel-chomp' only it runs on both the front and back of the string"
   (org-babel-chomp (org-babel-reverse-string
-                    (org-babel-chomp (org-babel-reverse-string string) regexp)) regexp))
+                    (org-babel-chomp (org-babel-reverse-string string) regexp))
+                   regexp))
 
 (defun org-babel-tramp-handle-call-process-region
   (start end program &optional delete buffer display &rest args)
@@ -1125,12 +1188,14 @@ Fixes a bug in `tramp-handle-call-process-region'."
 	(write-region start end tmpfile)
 	(when delete (delete-region start end))
 	(unwind-protect
-	    ;;	(apply 'call-process program tmpfile buffer display args) ;; bug in tramp
+	    ;;	(apply 'call-process program tmpfile buffer display args)
+            ;; bug in tramp
 	    (apply 'process-file program tmpfile buffer display args)
 	  (delete-file tmpfile)))
     ;; call-process-region-original is the original emacs definition. It
     ;; is in scope from the let binding in org-babel-execute-src-block
-    (apply call-process-region-original start end program delete buffer display args)))
+    (apply call-process-region-original
+           start end program delete buffer display args)))
 
 (defun org-babel-maybe-remote-file (file)
   (if (file-remote-p default-directory)
@@ -1151,12 +1216,13 @@ 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.
+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.
@@ -1323,6 +1389,5 @@ specifies the value of ERROR-BUFFER."
       (delete-file error-file))
     exit-status))
 
-
 (provide 'org-babel)
 ;;; org-babel.el ends here

From 10b3da72fc0262aa147e60ae7f9ee043d95de417 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Mon, 19 Apr 2010 07:26:02 -0600
Subject: [PATCH 02/46] babel: adding row/col-names functions

  adding a suite of functions to org-babel.el which can be used to
  handle hlines, rownames, and columnnames in input tables.  These
  functions can be called from any org-babel-language.el file.

  done in close collaboration with Dan Davison
---
 contrib/babel/lisp/org-babel.el | 101 ++++++++++++++++++++++++++++++--
 1 file changed, 97 insertions(+), 4 deletions(-)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index 910ffc85f..9987b8690 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -89,7 +89,7 @@ header arguments as well.")
 
 (defvar org-babel-default-header-args
   '((:session . "none") (:results . "replace") (:exports . "code")
-    (:cache . "no") (:noweb . "no"))
+    (:cache . "no") (:noweb . "no") (:hlines . "yes"))
   "Default arguments to use when evaluating a source block.")
 
 (defvar org-babel-default-inline-header-args
@@ -605,14 +605,107 @@ may be specified in the properties of the current outline entry."
 (defun org-babel-process-params (params)
   "Parse params and resolve references.
 
-Return a list (session vars result-params result-type)."
+Return a list (session vars result-params result-type colnames rownames)."
   (let* ((session (cdr (assoc :session params)))
-	 (vars (org-babel-ref-variables params))
+         (vars-and-names (org-babel-manicure-tables
+                          (org-babel-ref-variables params)
+                          (cdr (assoc :hlines params))
+                          (cdr (assoc :colnames params))
+                          (cdr (assoc :rownames params))))
+         (vars     (car   vars-and-names))
+         (colnames (cadr  vars-and-names))
+         (rownames (caddr vars-and-names))
 	 (result-params (split-string (or (cdr (assoc :results params)) "")))
 	 (result-type (cond ((member "output" result-params) 'output)
 			    ((member "value" result-params) 'value)
 			    (t 'value))))
-    (list session vars result-params result-type)))
+    (list session vars result-params result-type colnames rownames)))
+
+;; row and column names
+(defun org-babel-del-hlines (table)
+  "Remove all 'hlines from TABLE."
+  (remove 'hline table))
+
+(defun org-babel-get-colnames (table)
+  "Return a cons cell, the `car' of which contains the TABLE
+        less colnames, and the `cdr' of which contains a list of the
+        column names"
+  (if (equal 'hline (second table))
+      (cons (cddr table) (car table))
+    table))
+
+(defun org-babel-get-rownames (table)
+  "Return a cons cell, the `car' of which contains the TABLE less
+     colnames, and the `cdr' of which contains a list of the column
+     names.  Note: this function removes any hlines in TABLE"
+  (flet ((trans (table) (apply #'mapcar* #'list table)))
+    (let* ((width (apply 'max (mapcar (lambda (el) (if (listp el) (length el) 0)) table)))
+           (table (trans (mapcar (lambda (row)
+                                   (if (not (equal row 'hline))
+                                       row
+                                     (setq row '())
+                                     (dotimes (n width) (setq row (cons 'hline row)))
+                                     row))
+                                 tab))))
+      (cons (mapcar (lambda (row) (if (equal (car row) 'hline) 'hline row))
+                    (trans (cdr table)))
+            (remove 'hline (car table))))))
+
+(defun org-babel-put-colnames (table colnames)
+  "Add COLNAMES to TABLE if they exist."
+  (if colnames (apply 'list colnames 'hline table) table))
+
+(defun org-babel-put-rownames (table rownames)
+  "Add ROWNAMES to TABLE if they exist."
+  (if rownames
+      (mapcar (lambda (row)
+                (if (listp row)
+                    (cons (or (pop rownames) "") row)
+                  row)) table)
+    table))
+
+(defun org-babel-manicure-tables (vars hlines colnames rownames)
+  "Process the variables in VARS according to the HLINES,
+ROWNAMES and COLNAMES header arguments.  Return a list consisting
+of the vars, cnames and rnames."
+  (flet ((pick (names sel)
+           (when names
+             (if (and sel (symbolp sel) (not (equal t sel)))
+                 (cdr (assoc sel names))
+               (if (integerp sel)
+                   (nth (- sel 1) names)
+                 (cdr (car (last names))))))))
+    (let (cnames rnames)
+      (list
+       (mapcar
+        (lambda (var)
+          (when (listp (cdr var))
+            (when (and (not (equal colnames "no"))
+                       (or colnames (and (equal (second (cdr var)) 'hline)
+                                         (not (member 'hline (cddr (cdr var)))))))
+              (let ((both (org-babel-get-colnames (cdr var))))
+                (setq cnames (cons (cons (car var) (cdr both))
+                                   cnames))
+                (setq var (cons (car var) (car both)))))
+            (when (and rownames (not (equal rownames "no")))
+              (let ((both (org-babel-get-rownames (cdr var))))
+                (setq rnames (cons (cons (car var) (cdr both))
+                                   rnames))
+                (setq var (cons (car var) (car both)))))
+            (when (and hlines (not (equal hlines "yes")))
+              (setq var (cons (car var) (org-babel-del-hlines (cdr var))))))
+          var)
+        vars)
+       (pick cnames colnames) (pick rnames rownames)))))
+
+(defun org-babel-reassemble-table (table colnames rownames)
+  "Given a TABLE and set of COLNAMES and ROWNAMES add the names
+to the table for reinsertion to org-mode."
+  (if (listp table)
+      ((lambda (table)
+         (if colnames (org-babel-put-colnames table colnames) table))
+       (if rownames (org-babel-put-rownames table rownames) table))
+    table))
 
 (defun org-babel-where-is-src-block-head ()
   "Return the point at the beginning of the current source

From bfc93ca8084dd2c2887c3fd00a574f3c0c9c7053 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sun, 18 Apr 2010 19:06:34 -0600
Subject: [PATCH 03/46] babel: added row/col-name support to all applicable
 languages

---
 contrib/babel/lisp/langs/org-babel-C.el       | 18 +++++++++--------
 contrib/babel/lisp/langs/org-babel-clojure.el |  4 +++-
 .../babel/lisp/langs/org-babel-emacs-lisp.el  | 20 ++++++++++++-------
 contrib/babel/lisp/langs/org-babel-haskell.el |  8 +++++---
 contrib/babel/lisp/langs/org-babel-ocaml.el   |  4 +++-
 contrib/babel/lisp/langs/org-babel-octave.el  |  4 +++-
 contrib/babel/lisp/langs/org-babel-oz.el      |  5 +++--
 contrib/babel/lisp/langs/org-babel-perl.el    |  4 +++-
 contrib/babel/lisp/langs/org-babel-python.el  |  4 +++-
 contrib/babel/lisp/langs/org-babel-ruby.el    |  4 +++-
 contrib/babel/lisp/langs/org-babel-sh.el      |  4 +++-
 contrib/babel/lisp/langs/org-babel-sql.el     |  5 ++++-
 12 files changed, 56 insertions(+), 28 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-C.el b/contrib/babel/lisp/langs/org-babel-C.el
index 67ef7384d..fe6f359c3 100644
--- a/contrib/babel/lisp/langs/org-babel-C.el
+++ b/contrib/babel/lisp/langs/org-babel-C.el
@@ -116,14 +116,16 @@ called by `org-babel-execute-src-block'."
                        tmp-src-file)
                (current-buffer) 'replace error-buf)))))
     (if (= compile 0)
-        (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-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))))
+         (nth 4 processed-params) (nth 5 processed-params))
       (progn
         (with-current-buffer error-buf
           (goto-char (point-max))
diff --git a/contrib/babel/lisp/langs/org-babel-clojure.el b/contrib/babel/lisp/langs/org-babel-clojure.el
index f34b6343b..d23fecc60 100644
--- a/contrib/babel/lisp/langs/org-babel-clojure.el
+++ b/contrib/babel/lisp/langs/org-babel-clojure.el
@@ -269,6 +269,8 @@ last statement in BODY, as elisp."
          (vars (second processed-params))
          (body (org-babel-clojure-build-full-form body vars))
          (session (org-babel-clojure-initiate-session (first processed-params))))
-    (org-babel-clojure-evaluate session body (fourth processed-params))))
+    (org-babel-reassemble-table
+     (org-babel-clojure-evaluate session body (fourth processed-params))
+     (nth 4 processed-params) (nth 5 processed-params))))
 
 (provide 'org-babel-clojure)
diff --git a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
index 1472ea9c5..67fad7cea 100644
--- a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
+++ b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
@@ -35,6 +35,10 @@
 
 (add-to-list 'org-babel-tangle-langs '("emacs-lisp" "el"))
 
+(defvar org-babel-default-header-args:emacs-lisp
+  '((:hlines . "no") (:colnames . "no"))
+  "Default arguments to use when evaluating an emacs-lisp source block.")
+
 (defun org-babel-execute:emacs-lisp (body params)
   "Execute a block of emacs-lisp code with org-babel."
   (message "executing emacs-lisp code block...")
@@ -43,13 +47,15 @@
            (result-params (third processed-params))
            (vars (second processed-params))
            (print-level nil) (print-length nil))
-      (eval `(let ,(mapcar (lambda (var) `(,(car var) ',(cdr var)))
-                           vars)
-	       ,(read (concat "(progn "
-			      (if (or (member "code" result-params)
-				      (member "pp" result-params))
-				  (concat "(pp " body ")") body)
-			      ")")))))))
+      (org-babel-reassemble-table
+       (eval `(let ,(mapcar (lambda (var) `(,(car var) ',(cdr var)))
+                            vars)
+                ,(read (concat "(progn "
+                               (if (or (member "code" result-params)
+                                       (member "pp" result-params))
+                                   (concat "(pp " body ")") body)
+                               ")"))))
+       (nth 4 processed-params) (nth 5 processed-params)))))
 
 (provide 'org-babel-emacs-lisp)
 ;;; org-babel-emacs-lisp.el ends here
diff --git a/contrib/babel/lisp/langs/org-babel-haskell.el b/contrib/babel/lisp/langs/org-babel-haskell.el
index 571ca1961..8ec169395 100644
--- a/contrib/babel/lisp/langs/org-babel-haskell.el
+++ b/contrib/babel/lisp/langs/org-babel-haskell.el
@@ -75,9 +75,11 @@
                    #'org-babel-haskell-read-string
                    (cdr (member org-babel-haskell-eoe
                                 (reverse (mapcar #'org-babel-trim raw)))))))
-    (case result-type
-      (output (mapconcat #'identity (reverse (cdr results)) "\n"))
-      (value (org-babel-haskell-table-or-string (car results))))))
+    (org-babel-reassemble-table
+     (case result-type
+       (output (mapconcat #'identity (reverse (cdr results)) "\n"))
+       (value (org-babel-haskell-table-or-string (car results))))
+     (nth 4 processed-params) (nth 5 processed-params))))
 
 (defun org-babel-haskell-read-string (string)
   "Strip \\\"s from around haskell string"
diff --git a/contrib/babel/lisp/langs/org-babel-ocaml.el b/contrib/babel/lisp/langs/org-babel-ocaml.el
index d596e3a84..c28fb9d22 100644
--- a/contrib/babel/lisp/langs/org-babel-ocaml.el
+++ b/contrib/babel/lisp/langs/org-babel-ocaml.el
@@ -63,7 +63,9 @@
                 (comint-send-input nil t)
                 (insert org-babel-ocaml-eoe-indicator)
                 (comint-send-input nil t))))
-    (org-babel-ocaml-parse-output (org-babel-trim (car raw)))))
+    (org-babel-reassemble-table
+     (org-babel-ocaml-parse-output (org-babel-trim (car raw)))
+     (nth 4 processed-params) (nth 5 processed-params))))
 
 (defun org-babel-prep-session:ocaml (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-octave.el b/contrib/babel/lisp/langs/org-babel-octave.el
index 48d81f94d..7508b966d 100644
--- a/contrib/babel/lisp/langs/org-babel-octave.el
+++ b/contrib/babel/lisp/langs/org-babel-octave.el
@@ -62,7 +62,9 @@
 				     (org-babel-octave-var-to-octave (cdr pair))))
 			   vars "\n") "\n" body "\n"))
 	 (result (org-babel-octave-evaluate session augmented-body result-type matlabp)))
-    (or out-file result)))
+    (or out-file
+        (org-babel-reassemble-table
+         result (nth 4 processed-params) (nth 5 processed-params)))))
 
 (defun org-babel-octave-var-to-octave (var)
   "Convert an emacs-lisp variable into an octave variable.
diff --git a/contrib/babel/lisp/langs/org-babel-oz.el b/contrib/babel/lisp/langs/org-babel-oz.el
index 1a3e8d327..4b9812bad 100644
--- a/contrib/babel/lisp/langs/org-babel-oz.el
+++ b/contrib/babel/lisp/langs/org-babel-oz.el
@@ -233,7 +233,8 @@ called by `org-babel-execute-src-block' via multiple-value-bind."
 ;; 	(session-buffer (org-babel-oz-initiate-session session))
 ;; 	(session (org-babel-prep-session:oz session params))
 	)
-    ;; actually execute the source-code block 
+    ;; actually execute the source-code block
+    (org-babel-reassemble-table
      (case result-type
        (output
 	(progn 
@@ -245,7 +246,7 @@ called by `org-babel-execute-src-block' via multiple-value-bind."
 	  (oz-send-string-expression full-body (if wait-time
 						   wait-time
 						 1)))))
-    ))
+     (nth 4 processed-params) (nth 5 processed-params))))
 
 ;; This function should be used to assign any variables in params in
 ;; the context of the session environment.
diff --git a/contrib/babel/lisp/langs/org-babel-perl.el b/contrib/babel/lisp/langs/org-babel-perl.el
index 0162bbb21..5e94111a6 100644
--- a/contrib/babel/lisp/langs/org-babel-perl.el
+++ b/contrib/babel/lisp/langs/org-babel-perl.el
@@ -52,7 +52,9 @@ called by `org-babel-execute-src-block'."
 			       (org-babel-perl-var-to-perl (cdr pair))))
 		     vars "\n") "\n" (org-babel-trim body) "\n")) ;; then the source block body
 	(session (org-babel-perl-initiate-session session)))
-    (org-babel-perl-evaluate session full-body result-type)))
+    (org-babel-reassemble-table
+     (org-babel-perl-evaluate session full-body result-type)
+     (nth 4 processed-params) (nth 5 processed-params))))
 
 (defun org-babel-prep-session:perl (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-python.el b/contrib/babel/lisp/langs/org-babel-python.el
index fd2b0ed65..b69807d01 100644
--- a/contrib/babel/lisp/langs/org-babel-python.el
+++ b/contrib/babel/lisp/langs/org-babel-python.el
@@ -54,7 +54,9 @@ called by `org-babel-execute-src-block'."
                       vars "\n") "\n" (org-babel-trim body) "\n")) ;; then the source block body
          
          (result (org-babel-python-evaluate session full-body result-type)))
-    (or (cdr (assoc :file params)) result)))
+    (or (cdr (assoc :file params))
+        (org-babel-reassemble-table
+         result (nth 4 processed-params) (nth 5 processed-params)))))
 
 (defun org-babel-prep-session:python (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-ruby.el b/contrib/babel/lisp/langs/org-babel-ruby.el
index 0a6b6d13c..8af8aece4 100644
--- a/contrib/babel/lisp/langs/org-babel-ruby.el
+++ b/contrib/babel/lisp/langs/org-babel-ruby.el
@@ -63,7 +63,9 @@ called by `org-babel-execute-src-block'."
 			       (org-babel-ruby-var-to-ruby (cdr pair))))
 		     vars "\n") "\n" body "\n")) ;; then the source block body
          (result (org-babel-ruby-evaluate session full-body result-type)))
-    (or (cdr (assoc :file params)) result)))
+    (or (cdr (assoc :file params))
+        (org-babel-reassemble-table
+         result (nth 4 processed-params) (nth 5 processed-params)))))
 
 (defun org-babel-prep-session:ruby (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-sh.el b/contrib/babel/lisp/langs/org-babel-sh.el
index f6d1fec61..711362e3c 100644
--- a/contrib/babel/lisp/langs/org-babel-sh.el
+++ b/contrib/babel/lisp/langs/org-babel-sh.el
@@ -56,7 +56,9 @@ function is called by `org-babel-execute-src-block'."
                                 (car pair)
                                 (org-babel-sh-var-to-sh (cdr pair) sep)))
                       vars "\n") "\n" body "\n\n"))) ;; then the source block body
-    (org-babel-sh-evaluate session full-body result-type)))
+    (org-babel-reassemble-table
+     (org-babel-sh-evaluate session full-body result-type)
+     (nth 4 processed-params) (nth 5 processed-params))))
 
 (defun org-babel-prep-session:sh (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-sql.el b/contrib/babel/lisp/langs/org-babel-sql.el
index fd26c6f0e..327502458 100644
--- a/contrib/babel/lisp/langs/org-babel-sql.el
+++ b/contrib/babel/lisp/langs/org-babel-sql.el
@@ -70,7 +70,10 @@ called by `org-babel-execute-src-block'."
     (shell-command command)
     (with-temp-buffer
       (org-table-import out-file nil)
-      (org-table-to-lisp))))
+      (org-babel-reassemble-table
+       (org-table-to-lisp)
+       (nth 4 processed-params) (nth 5 processed-params)))))
+
 
 (defun org-babel-prep-session:sql (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."

From b9aa92ba2180124f4c6b386469273db0c20dd130 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Mon, 19 Apr 2010 23:33:47 -0600
Subject: [PATCH 04/46] org-babel: splitting `org-babel-pick-name' into it's
 own function

  also renaming org-babel-manicure-tables to org-babel-disassemble-tables
---
 contrib/babel/lisp/langs/org-babel-C.el       |  3 +-
 contrib/babel/lisp/langs/org-babel-clojure.el |  3 +-
 .../babel/lisp/langs/org-babel-emacs-lisp.el  |  3 +-
 contrib/babel/lisp/langs/org-babel-haskell.el |  3 +-
 contrib/babel/lisp/langs/org-babel-ocaml.el   |  3 +-
 contrib/babel/lisp/langs/org-babel-octave.el  |  4 +-
 contrib/babel/lisp/langs/org-babel-oz.el      |  3 +-
 contrib/babel/lisp/langs/org-babel-perl.el    |  3 +-
 contrib/babel/lisp/langs/org-babel-python.el  |  4 +-
 contrib/babel/lisp/langs/org-babel-ruby.el    |  4 +-
 contrib/babel/lisp/langs/org-babel-sh.el      |  3 +-
 contrib/babel/lisp/langs/org-babel-sql.el     |  3 +-
 contrib/babel/lisp/org-babel.el               | 64 ++++++++++---------
 13 files changed, 60 insertions(+), 43 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-C.el b/contrib/babel/lisp/langs/org-babel-C.el
index fe6f359c3..69ce9d7a4 100644
--- a/contrib/babel/lisp/langs/org-babel-C.el
+++ b/contrib/babel/lisp/langs/org-babel-C.el
@@ -125,7 +125,8 @@ called by `org-babel-execute-src-block'."
               (concat tmp-bin-file (if cmdline (concat " " cmdline) ""))
               (current-buffer) 'replace)
              (buffer-string))))
-         (nth 4 processed-params) (nth 5 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))))
       (progn
         (with-current-buffer error-buf
           (goto-char (point-max))
diff --git a/contrib/babel/lisp/langs/org-babel-clojure.el b/contrib/babel/lisp/langs/org-babel-clojure.el
index d23fecc60..b3bc77806 100644
--- a/contrib/babel/lisp/langs/org-babel-clojure.el
+++ b/contrib/babel/lisp/langs/org-babel-clojure.el
@@ -271,6 +271,7 @@ last statement in BODY, as elisp."
          (session (org-babel-clojure-initiate-session (first processed-params))))
     (org-babel-reassemble-table
      (org-babel-clojure-evaluate session body (fourth processed-params))
-     (nth 4 processed-params) (nth 5 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))))))
 
 (provide 'org-babel-clojure)
diff --git a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
index 67fad7cea..b1a4acd14 100644
--- a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
+++ b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
@@ -55,7 +55,8 @@
                                        (member "pp" result-params))
                                    (concat "(pp " body ")") body)
                                ")"))))
-       (nth 4 processed-params) (nth 5 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)))))))
 
 (provide 'org-babel-emacs-lisp)
 ;;; org-babel-emacs-lisp.el ends here
diff --git a/contrib/babel/lisp/langs/org-babel-haskell.el b/contrib/babel/lisp/langs/org-babel-haskell.el
index 8ec169395..d593bb1f4 100644
--- a/contrib/babel/lisp/langs/org-babel-haskell.el
+++ b/contrib/babel/lisp/langs/org-babel-haskell.el
@@ -79,7 +79,8 @@
      (case result-type
        (output (mapconcat #'identity (reverse (cdr results)) "\n"))
        (value (org-babel-haskell-table-or-string (car results))))
-     (nth 4 processed-params) (nth 5 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))))))
 
 (defun org-babel-haskell-read-string (string)
   "Strip \\\"s from around haskell string"
diff --git a/contrib/babel/lisp/langs/org-babel-ocaml.el b/contrib/babel/lisp/langs/org-babel-ocaml.el
index c28fb9d22..107de0c7f 100644
--- a/contrib/babel/lisp/langs/org-babel-ocaml.el
+++ b/contrib/babel/lisp/langs/org-babel-ocaml.el
@@ -65,7 +65,8 @@
                 (comint-send-input nil t))))
     (org-babel-reassemble-table
      (org-babel-ocaml-parse-output (org-babel-trim (car raw)))
-     (nth 4 processed-params) (nth 5 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))))))
 
 (defun org-babel-prep-session:ocaml (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-octave.el b/contrib/babel/lisp/langs/org-babel-octave.el
index 7508b966d..740e156be 100644
--- a/contrib/babel/lisp/langs/org-babel-octave.el
+++ b/contrib/babel/lisp/langs/org-babel-octave.el
@@ -64,7 +64,9 @@
 	 (result (org-babel-octave-evaluate session augmented-body result-type matlabp)))
     (or out-file
         (org-babel-reassemble-table
-         result (nth 4 processed-params) (nth 5 processed-params)))))
+         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)))))))
 
 (defun org-babel-octave-var-to-octave (var)
   "Convert an emacs-lisp variable into an octave variable.
diff --git a/contrib/babel/lisp/langs/org-babel-oz.el b/contrib/babel/lisp/langs/org-babel-oz.el
index 4b9812bad..ca0b576d0 100644
--- a/contrib/babel/lisp/langs/org-babel-oz.el
+++ b/contrib/babel/lisp/langs/org-babel-oz.el
@@ -246,7 +246,8 @@ called by `org-babel-execute-src-block' via multiple-value-bind."
 	  (oz-send-string-expression full-body (if wait-time
 						   wait-time
 						 1)))))
-     (nth 4 processed-params) (nth 5 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))))))
 
 ;; This function should be used to assign any variables in params in
 ;; the context of the session environment.
diff --git a/contrib/babel/lisp/langs/org-babel-perl.el b/contrib/babel/lisp/langs/org-babel-perl.el
index 5e94111a6..23d893cee 100644
--- a/contrib/babel/lisp/langs/org-babel-perl.el
+++ b/contrib/babel/lisp/langs/org-babel-perl.el
@@ -54,7 +54,8 @@ called by `org-babel-execute-src-block'."
 	(session (org-babel-perl-initiate-session session)))
     (org-babel-reassemble-table
      (org-babel-perl-evaluate session full-body result-type)
-     (nth 4 processed-params) (nth 5 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))))))
 
 (defun org-babel-prep-session:perl (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-python.el b/contrib/babel/lisp/langs/org-babel-python.el
index b69807d01..07a7abf37 100644
--- a/contrib/babel/lisp/langs/org-babel-python.el
+++ b/contrib/babel/lisp/langs/org-babel-python.el
@@ -56,7 +56,9 @@ called by `org-babel-execute-src-block'."
          (result (org-babel-python-evaluate session full-body result-type)))
     (or (cdr (assoc :file params))
         (org-babel-reassemble-table
-         result (nth 4 processed-params) (nth 5 processed-params)))))
+         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)))))))
 
 (defun org-babel-prep-session:python (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-ruby.el b/contrib/babel/lisp/langs/org-babel-ruby.el
index 8af8aece4..f35bddac7 100644
--- a/contrib/babel/lisp/langs/org-babel-ruby.el
+++ b/contrib/babel/lisp/langs/org-babel-ruby.el
@@ -65,7 +65,9 @@ called by `org-babel-execute-src-block'."
          (result (org-babel-ruby-evaluate session full-body result-type)))
     (or (cdr (assoc :file params))
         (org-babel-reassemble-table
-         result (nth 4 processed-params) (nth 5 processed-params)))))
+         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)))))))
 
 (defun org-babel-prep-session:ruby (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-sh.el b/contrib/babel/lisp/langs/org-babel-sh.el
index 711362e3c..aed73d1e3 100644
--- a/contrib/babel/lisp/langs/org-babel-sh.el
+++ b/contrib/babel/lisp/langs/org-babel-sh.el
@@ -58,7 +58,8 @@ function is called by `org-babel-execute-src-block'."
                       vars "\n") "\n" body "\n\n"))) ;; then the source block body
     (org-babel-reassemble-table
      (org-babel-sh-evaluate session full-body result-type)
-     (nth 4 processed-params) (nth 5 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))))))
 
 (defun org-babel-prep-session:sh (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
diff --git a/contrib/babel/lisp/langs/org-babel-sql.el b/contrib/babel/lisp/langs/org-babel-sql.el
index 327502458..da746f257 100644
--- a/contrib/babel/lisp/langs/org-babel-sql.el
+++ b/contrib/babel/lisp/langs/org-babel-sql.el
@@ -72,7 +72,8 @@ called by `org-babel-execute-src-block'."
       (org-table-import out-file nil)
       (org-babel-reassemble-table
        (org-table-to-lisp)
-       (nth 4 processed-params) (nth 5 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)))))))
 
 
 (defun org-babel-prep-session:sql (session params)
diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index 9987b8690..791f360fd 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -607,7 +607,7 @@ may be specified in the properties of the current outline entry."
 
 Return a list (session vars result-params result-type colnames rownames)."
   (let* ((session (cdr (assoc :session params)))
-         (vars-and-names (org-babel-manicure-tables
+         (vars-and-names (org-babel-disassemble-tables
                           (org-babel-ref-variables params)
                           (cdr (assoc :hlines params))
                           (cdr (assoc :colnames params))
@@ -664,39 +664,41 @@ Return a list (session vars result-params result-type colnames rownames)."
                   row)) table)
     table))
 
-(defun org-babel-manicure-tables (vars hlines colnames rownames)
+(defun org-babel-pick-name (names selector)
+  "Select one out of an alist of row or column names."
+  (when names
+    (if (and selector (symbolp selector) (not (equal t selector)))
+        (cdr (assoc selector names))
+      (if (integerp selector)
+          (nth (- selector 1) names)
+        (cdr (car (last names)))))))
+
+(defun org-babel-disassemble-tables (vars hlines colnames rownames)
   "Process the variables in VARS according to the HLINES,
 ROWNAMES and COLNAMES header arguments.  Return a list consisting
 of the vars, cnames and rnames."
-  (flet ((pick (names sel)
-           (when names
-             (if (and sel (symbolp sel) (not (equal t sel)))
-                 (cdr (assoc sel names))
-               (if (integerp sel)
-                   (nth (- sel 1) names)
-                 (cdr (car (last names))))))))
-    (let (cnames rnames)
-      (list
-       (mapcar
-        (lambda (var)
-          (when (listp (cdr var))
-            (when (and (not (equal colnames "no"))
-                       (or colnames (and (equal (second (cdr var)) 'hline)
-                                         (not (member 'hline (cddr (cdr var)))))))
-              (let ((both (org-babel-get-colnames (cdr var))))
-                (setq cnames (cons (cons (car var) (cdr both))
-                                   cnames))
-                (setq var (cons (car var) (car both)))))
-            (when (and rownames (not (equal rownames "no")))
-              (let ((both (org-babel-get-rownames (cdr var))))
-                (setq rnames (cons (cons (car var) (cdr both))
-                                   rnames))
-                (setq var (cons (car var) (car both)))))
-            (when (and hlines (not (equal hlines "yes")))
-              (setq var (cons (car var) (org-babel-del-hlines (cdr var))))))
-          var)
-        vars)
-       (pick cnames colnames) (pick rnames rownames)))))
+  (let (cnames rnames)
+    (list
+     (mapcar
+      (lambda (var)
+        (when (listp (cdr var))
+          (when (and (not (equal colnames "no"))
+                     (or colnames (and (equal (second (cdr var)) 'hline)
+                                       (not (member 'hline (cddr (cdr var)))))))
+            (let ((both (org-babel-get-colnames (cdr var))))
+              (setq cnames (cons (cons (car var) (cdr both))
+                                 cnames))
+              (setq var (cons (car var) (car both)))))
+          (when (and rownames (not (equal rownames "no")))
+            (let ((both (org-babel-get-rownames (cdr var))))
+              (setq rnames (cons (cons (car var) (cdr both))
+                                 rnames))
+              (setq var (cons (car var) (car both)))))
+          (when (and hlines (not (equal hlines "yes")))
+            (setq var (cons (car var) (org-babel-del-hlines (cdr var))))))
+        var)
+      vars)
+     cnames rnames)))
 
 (defun org-babel-reassemble-table (table colnames rownames)
   "Given a TABLE and set of COLNAMES and ROWNAMES add the names

From d5dd160b232b0f15c7aa1acbcf381a275e453f60 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Mon, 19 Apr 2010 17:20:54 -0400
Subject: [PATCH 05/46] babel: bug fix in org-babel-get-colnames

---
 contrib/babel/lisp/org-babel.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index 791f360fd..5462e3e3a 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -632,7 +632,7 @@ Return a list (session vars result-params result-type colnames rownames)."
         column names"
   (if (equal 'hline (second table))
       (cons (cddr table) (car table))
-    table))
+    (list table)))
 
 (defun org-babel-get-rownames (table)
   "Return a cons cell, the `car' of which contains the TABLE less

From bd3c85ed60592d5cbd891fc7c348d3319d76e651 Mon Sep 17 00:00:00 2001
From: Julien Barnier <julien@nozav.org>
Date: Fri, 9 Apr 2010 20:32:37 -0400
Subject: [PATCH 06/46] babel: add :rownames header arg for R

---
 contrib/babel/lisp/langs/org-babel-R.el | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-R.el b/contrib/babel/lisp/langs/org-babel-R.el
index b571558fb..4a6959370 100644
--- a/contrib/babel/lisp/langs/org-babel-R.el
+++ b/contrib/babel/lisp/langs/org-babel-R.el
@@ -46,6 +46,8 @@ called by `org-babel-execute-src-block'."
            (vars (second processed-params))
 	   (column-names-p (and (cdr (assoc :colnames params))
 				(string= "yes" (cdr (assoc :colnames params)))))
+	   (row-names-p (and (cdr (assoc :rownames params))
+				(string= "yes" (cdr (assoc :rownames params)))))
 	   (out-file (cdr (assoc :file params)))
 	   (augmented-body
 	    (concat
@@ -53,7 +55,7 @@ called by `org-babel-execute-src-block'."
 	     (mapconcat ;; define any variables
 	      (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars "\n")
 	     "\n" body "\n" (if out-file "dev.off()\n" "")))
-	   (result (org-babel-R-evaluate session augmented-body result-type column-names-p)))
+	   (result (org-babel-R-evaluate session augmented-body result-type column-names-p row-names-p)))
       (or out-file result))))
 
 (defun org-babel-prep-session:R (session params)
@@ -140,9 +142,9 @@ called by `org-babel-execute-src-block'."
 (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=FALSE, col.names=%s, quote=FALSE)")
+write.table(main(), 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)
+(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
@@ -160,7 +162,7 @@ last statement in BODY, as elisp."
 		(stderr
 		 (with-temp-buffer
 		   (insert (format org-babel-R-wrapper-method
-				   body tmp-file (if column-names-p "TRUE" "FALSE")))
+				   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))))
@@ -175,7 +177,7 @@ last statement in BODY, as elisp."
 	      (case result-type
 		(value
 		 (mapconcat #'org-babel-chomp (list body
-						    (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)" tmp-file (if column-names-p "TRUE" "FALSE"))
+						    (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"))))

From c777e729fbc9fb4bcccbf553ab217f5947a2b589 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Mon, 19 Apr 2010 17:25:43 -0400
Subject: [PATCH 07/46] babel: bring R row- and col-names into line with others

---
 contrib/babel/lisp/langs/org-babel-R.el | 29 +++++++++++++++++--------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-R.el b/contrib/babel/lisp/langs/org-babel-R.el
index 4a6959370..e7188d9b4 100644
--- a/contrib/babel/lisp/langs/org-babel-R.el
+++ b/contrib/babel/lisp/langs/org-babel-R.el
@@ -43,19 +43,24 @@ called by `org-babel-execute-src-block'."
     (let* ((processed-params (org-babel-process-params params))
            (result-type (fourth processed-params))
            (session (org-babel-R-initiate-session (first processed-params) params))
-           (vars (second processed-params))
-	   (column-names-p (and (cdr (assoc :colnames params))
+           (vars (mapcar (lambda (i) (cons (car (nth i (second processed-params)))
+					   (org-babel-reassemble-table
+					    (cdr (nth i (second processed-params)))
+					    (cdr (nth i (fifth processed-params)))
+					    (cdr (nth i (sixth processed-params))))))
+			 (number-sequence 0 (1- (length (second processed-params))))))
+	   (colnames-p (and (cdr (assoc :colnames params))
 				(string= "yes" (cdr (assoc :colnames params)))))
-	   (row-names-p (and (cdr (assoc :rownames params))
+	   (rownames-p (and (cdr (assoc :rownames params))
 				(string= "yes" (cdr (assoc :rownames params)))))
 	   (out-file (cdr (assoc :file params)))
 	   (augmented-body
 	    (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))) vars "\n")
+	      (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair) colnames-p rownames-p)) vars "\n")
 	     "\n" body "\n" (if out-file "dev.off()\n" "")))
-	   (result (org-babel-R-evaluate session augmented-body result-type column-names-p row-names-p)))
+	   (result (org-babel-R-evaluate session augmented-body result-type colnames-p rownames-p)))
       (or out-file result))))
 
 (defun org-babel-prep-session:R (session params)
@@ -64,7 +69,11 @@ called by `org-babel-execute-src-block'."
 	 (vars (org-babel-ref-variables params))
 	 (var-lines
 	  (mapcar
-	   (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars)))
+	   (lambda (pair) (org-babel-R-assign-elisp
+			   (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)
               (move-end-of-line 1) (insert var) (comint-send-input nil t)
@@ -88,7 +97,7 @@ called by `org-babel-execute-src-block'."
       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
     (format "%S" s)))
 
-(defun org-babel-R-assign-elisp (name value)
+(defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
   "Construct R code assigning the elisp VALUE to a variable named NAME."
   (if (listp value)
       (let ((transition-file (make-temp-file "org-babel-R-import")))
@@ -97,8 +106,10 @@ called by `org-babel-execute-src-block'."
         (with-temp-file (org-babel-maybe-remote-file transition-file)
           (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
           (insert "\n"))
-        (format "%s <- read.table(\"%s\", header=%s, sep=\"\\t\", as.is=TRUE)"
-                name transition-file (if (eq (second value) 'hline) "TRUE" "FALSE")))
+        (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)"
+                name transition-file
+		(if (and (eq (second value) 'hline) colnames-p) "TRUE" "FALSE")
+		(if rownames-p "1" "NULL")))
     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 
 (defun org-babel-R-initiate-session (session params)

From 788779e16c385268e80212c950ed424d9eae0653 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Mon, 19 Apr 2010 17:30:38 -0400
Subject: [PATCH 08/46] babel: typo in org-babel-get-rownames

---
 contrib/babel/lisp/org-babel.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index 5462e3e3a..e8b15909f 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -646,7 +646,7 @@ Return a list (session vars result-params result-type colnames rownames)."
                                      (setq row '())
                                      (dotimes (n width) (setq row (cons 'hline row)))
                                      row))
-                                 tab))))
+                                 table))))
       (cons (mapcar (lambda (row) (if (equal (car row) 'hline) 'hline row))
                     (trans (cdr table)))
             (remove 'hline (car table))))))

From 2fe12b99f44799b473a1c8e1db2b05a981179091 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Mon, 19 Apr 2010 23:40:58 -0600
Subject: [PATCH 09/46] babel: adding new function `org-babel-expand-src-block'

  org-babel-expand-body:lang function needs to be implemented by every
  language, and is used to expand the body of a code block for
  execution or tangling
---
 contrib/babel/lisp/org-babel-tangle.el | 19 +++++++++++----
 contrib/babel/lisp/org-babel.el        | 32 +++++++++++++++++++++++++-
 2 files changed, 45 insertions(+), 6 deletions(-)

diff --git a/contrib/babel/lisp/org-babel-tangle.el b/contrib/babel/lisp/org-babel-tangle.el
index e77f0a353..b66d66ee6 100644
--- a/contrib/babel/lisp/org-babel-tangle.el
+++ b/contrib/babel/lisp/org-babel-tangle.el
@@ -177,17 +177,26 @@ code blocks by language."
                                       (format "block-%d" block-counter))))
              (src-lang (first info))
              (params (third info))
-	     (body (if (equal "no" (cdr (assoc :noweb params)))
-		       (second info)
-		     (org-babel-expand-noweb-references info)))
-             (spec (list link source-name params body (third (cdr (assoc src-lang org-babel-tangle-langs)))))
              by-lang)
         (unless (string= (cdr (assoc :tangle params)) "no") ;; maybe skip
           (unless (and lang (not (string= lang src-lang))) ;; maybe limit by language
             ;; add the spec for this block to blocks under it's language
             (setq by-lang (cdr (assoc src-lang blocks)))
             (setq blocks (delq (assoc src-lang blocks) blocks))
-            (setq blocks (cons (cons src-lang (cons spec by-lang)) blocks))))))
+            (setq blocks
+                  (cons
+                   (cons src-lang
+                         (cons (list link source-name params
+                                     (funcall
+                                      (intern
+                                       (concat "org-babel-expand-body:" src-lang))
+                                      (if (and (cdr (assoc :noweb params))
+                                               (string= "yes" (cdr (assoc :noweb params))))
+                                          (org-babel-expand-noweb-references info) (second info))
+                                      params)
+                                     (third (cdr (assoc
+                                                  src-lang org-babel-tangle-langs))))
+                               by-lang)) blocks))))))
     ;; ensure blocks in the correct order
     (setq blocks
           (mapcar (lambda (by-lang) (cons (car by-lang) (reverse (cdr by-lang)))) blocks))
diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index e8b15909f..02c668083 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -41,6 +41,13 @@ then run `org-babel-execute-src-block'."
 
 (add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-execute-src-block-maybe)
 
+(defun org-babel-expand-src-block-maybe ()
+  "Detect if this is context for a org-babel src-block and if so
+then run `org-babel-expand-src-block'."
+  (interactive)
+  (let ((info (org-babel-get-src-block-info)))
+    (if info (progn (org-babel-expand-src-block current-prefix-arg info) t) nil)))
+
 (defadvice org-edit-special (around org-babel-prep-session-for-edit activate)
   "Prepare the current source block's session according to it's
 header arguments before editing in an org-src buffer.  This
@@ -255,6 +262,29 @@ block."
             result))
       (setq call-process-region 'call-process-region-original))))
 
+(defun org-babel-expand-src-block (&optional arg info params)
+  "Expand the current source code block according to it's header
+arguments, and pop open the results in a preview buffer."
+  (interactive)
+  ;; (message "supplied params=%S" params) ;; debugging
+  (let* ((info (or info (org-babel-get-src-block-info)))
+         (lang (first info))
+	 (params (setf (third info)
+                       (sort (org-babel-merge-params (third info) params)
+                             (lambda (el1 el2) (string< (symbol-name (car el1))
+                                                   (symbol-name (car el2)))))))
+         (body (setf (second info)
+		     (if (and (cdr (assoc :noweb params))
+                              (string= "yes" (cdr (assoc :noweb params))))
+			 (org-babel-expand-noweb-references info) (second info))))
+         (cmd (intern (concat "org-babel-expand-body:" lang)))
+         (expanded (funcall cmd body params))
+         (buf (get-buffer-create "*Org-Babel Code Body Preview*")))
+    (with-current-buffer buf
+      (insert expanded)
+      (funcall (intern (concat lang "-mode"))))
+    (pop-to-buffer buf)))
+
 (defun org-babel-load-in-session (&optional arg info)
   "Load the body of the current source-code block.  Evaluate the
 header arguments for the source block before entering the
@@ -533,7 +563,7 @@ with C-c C-c."
          (goto-char (match-beginning 0))
          (save-match-data ,@body)
          (goto-char (match-end 0))))
-     (unless visited-p (kill-buffer (file-name-nondirectory file)))))
+     (unless visited-p (kill-buffer (file-name-nondirectory ,file)))))
 
 (defun org-babel-params-from-properties ()
   "Return an association list of any source block params which

From 8c8c96972e09a7019531df6faa63843ebefc7623 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Tue, 20 Apr 2010 00:07:46 -0600
Subject: [PATCH 10/46] org-babel-expand-body:emacs-lisp

---
 .../babel/lisp/langs/org-babel-emacs-lisp.el  | 33 +++++++++++--------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
index b1a4acd14..858b3dbe7 100644
--- a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
+++ b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
@@ -39,24 +39,31 @@
   '((:hlines . "no") (:colnames . "no"))
   "Default arguments to use when evaluating an emacs-lisp source block.")
 
+(defun org-babel-expand-body:emacs-lisp (body params &optional processed-params)
+  (let* ((processed-params (or processed-params (org-babel-process-params params)))
+         (vars (second processed-params))
+         (processed-params (org-babel-process-params params))
+         (result-params (third processed-params))
+         (print-level nil) (print-length nil)
+         (body (concat "(let ("
+                       (mapconcat
+                        (lambda (var) (format "%S" (print `(,(car var) ',(cdr var)))))
+                        vars "\n      ")
+                       ")\n"
+                       (if (or (member "code" result-params)
+                               (member "pp" result-params))
+                           (concat "(pp " body ")") body) ")")))
+    body))
+
 (defun org-babel-execute:emacs-lisp (body params)
   "Execute a block of emacs-lisp code with org-babel."
   (message "executing emacs-lisp code block...")
   (save-window-excursion
-    (let* ((processed-params (org-babel-process-params params))
-           (result-params (third processed-params))
-           (vars (second processed-params))
-           (print-level nil) (print-length nil))
+    (let ((processed-params (org-babel-process-params params)))
       (org-babel-reassemble-table
-       (eval `(let ,(mapcar (lambda (var) `(,(car var) ',(cdr var)))
-                            vars)
-                ,(read (concat "(progn "
-                               (if (or (member "code" result-params)
-                                       (member "pp" result-params))
-                                   (concat "(pp " body ")") body)
-                               ")"))))
-     (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
-     (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params)))))))
+       (eval (read (org-babel-expand-body:emacs-lisp body 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 'org-babel-emacs-lisp)
 ;;; org-babel-emacs-lisp.el ends here

From 34eed9b48dbdde7b1bfa14b7b6ee13786dccf09a Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sun, 11 Apr 2010 14:29:02 -0600
Subject: [PATCH 11/46] org-babel-expand-body:c, org-babel-expand-body:c++

---
 contrib/babel/lisp/langs/org-babel-C.el | 65 +++++++++++++++----------
 1 file changed, 40 insertions(+), 25 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-C.el b/contrib/babel/lisp/langs/org-babel-C.el
index 69ce9d7a4..0c4f5d63c 100644
--- a/contrib/babel/lisp/langs/org-babel-C.el
+++ b/contrib/babel/lisp/langs/org-babel-C.el
@@ -58,17 +58,26 @@
 called by `org-babel-execute-src-block'."
   (let ((c-variant 'cpp)) (org-babel-C-execute body params)))
 
+(defun org-babel-expand-body:c++ (body params &optional processed-params)
+  "Expand a block of C++ code with org-babel according to it's
+header arguments (calls `org-babel-C-expand')."
+  (let ((c-variant 'cpp)) (org-babel-C-expand body params)))
+
 (defun org-babel-execute:C (body params)
   "Execute a block of C code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
   (let ((c-variant 'c)) (org-babel-C-execute body params)))
 
+(defun org-babel-expand-body:c (body params &optional processed-params)
+  "Expand a block of C code with org-babel according to it's
+header arguments (calls `org-babel-C-expand')."
+  (let ((c-variant 'c)) (org-babel-C-expand body params)))
+
 (defun org-babel-C-execute (body params)
   "This should only be called by `org-babel-execute:C' or
 `org-babel-execute:c++'."
   (message "executing C source code block")
-  (let* ((processed-params (org-babel-process-params params))
-         (tmp-src-file (make-temp-file "org-babel-C-src" nil
+  (let* ((tmp-src-file (make-temp-file "org-babel-C-src" nil
                                        (case c-variant
                                          ('c ".c")
                                          ('cpp ".cpp"))))
@@ -76,29 +85,7 @@ called by `org-babel-execute-src-block'."
          (tmp-out-file (make-temp-file "org-babel-C-out"))
          (cmdline (cdr (assoc :cmdline params)))
          (flags (cdr (assoc :flags params)))
-         (vars (second processed-params))
-         (main-p (not (string= (cdr (assoc :main params)) "no")))
-         (includes (or (cdr (assoc :includes params))
-                       (org-entry-get nil "includes" t)))
-         (defines (org-babel-read
-                   (or (cdr (assoc :defines params))
-                       (org-entry-get nil "defines" t))))
-         (full-body (mapconcat 'identity
-                     (list
-                      ;; includes
-                      (mapconcat
-                       (lambda (inc) (format "#include %s" inc))
-                       (if (listp includes) includes (list includes)) "\n")
-                      ;; defines
-                      (mapconcat
-                       (lambda (inc) (format "#define %s" inc))
-                       (if (listp defines) defines (list defines)) "\n")
-                      ;; variables
-                      (mapconcat 'org-babel-C-var-to-C vars "\n")
-                      ;; body
-                      "\n" (if main-p
-                               (org-babel-C-ensure-main-wrap body)
-                             body) "\n") "\n"))
+         (full-body (org-babel-C-expand body params))
          (error-buf (get-buffer-create "*Org-Babel Error Output*"))
          (compile
           (progn
@@ -134,6 +121,34 @@ called by `org-babel-execute-src-block'."
           (goto-char (point-min)))
         (display-buffer error-buf) nil))))
 
+(defun org-babel-C-expand (body params &optional processed-params)
+  "Expand a block of C or C++ code with org-babel according to
+it's header arguments."
+  (let ((vars (second (or processed-params
+                          (org-babel-process-params params))))
+        (main-p (not (string= (cdr (assoc :main params)) "no")))
+        (includes (or (cdr (assoc :includes params))
+                      (org-entry-get nil "includes" t)))
+        (defines (org-babel-read
+                  (or (cdr (assoc :defines params))
+                      (org-entry-get nil "defines" t)))))
+    (mapconcat 'identity
+               (list
+                ;; includes
+                (mapconcat
+                 (lambda (inc) (format "#include %s" inc))
+                 (if (listp includes) includes (list includes)) "\n")
+                ;; defines
+                (mapconcat
+                 (lambda (inc) (format "#define %s" inc))
+                 (if (listp defines) defines (list defines)) "\n")
+                ;; variables
+                (mapconcat 'org-babel-C-var-to-C vars "\n")
+                ;; body
+                "\n" (if main-p
+                         (org-babel-C-ensure-main-wrap body)
+                       body) "\n") "\n")))
+
 (defun org-babel-C-ensure-main-wrap (body)
   "Wrap body in a \"main\" function call if none exists."
   (if (string-match "^[ \t]*[intvod]+[ \t]*main[ \t]*(.*)" body)

From 4ba08f9b5bcbdf54671cf226de6e480813dcdafa Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sun, 11 Apr 2010 14:29:19 -0600
Subject: [PATCH 12/46] org-babel-expand-body:asymptote

---
 contrib/babel/lisp/langs/org-babel-asymptote.el | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/contrib/babel/lisp/langs/org-babel-asymptote.el b/contrib/babel/lisp/langs/org-babel-asymptote.el
index 8af97b02f..59ca29153 100644
--- a/contrib/babel/lisp/langs/org-babel-asymptote.el
+++ b/contrib/babel/lisp/langs/org-babel-asymptote.el
@@ -56,6 +56,8 @@
 (defvar org-babel-default-header-args:asymptote '((:results . "file") (:exports . "results"))
   "Default arguments to use when evaluating a asymptote source block.")
 
+(defun org-babel-expand-body:asymptote (body params &optional processed-params) body)
+
 (defun org-babel-execute:asymptote (body params)
   "Execute a block of Asymptote code with org-babel.  This function is
 called by `org-babel-execute-src-block'."

From 6d61edd1ea42ef931ec4d7c091af55dda1f13696 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sun, 11 Apr 2010 14:29:24 -0600
Subject: [PATCH 13/46] org-babel-expand-body:clojure

---
 contrib/babel/lisp/langs/org-babel-clojure.el | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-clojure.el b/contrib/babel/lisp/langs/org-babel-clojure.el
index b3bc77806..ffd07ec82 100644
--- a/contrib/babel/lisp/langs/org-babel-clojure.el
+++ b/contrib/babel/lisp/langs/org-babel-clojure.el
@@ -263,11 +263,14 @@ last statement in BODY, as elisp."
       (org-babel-clojure-evaluate-session buffer body result-type)
     (org-babel-clojure-evaluate-external-process buffer body result-type)))
 
+(defun org-babel-expand-body:clojure (body params &optional processed-params)
+  (org-babel-clojure-build-full-form
+   body (second (or processed-params (org-babel-process-params params)))))
+
 (defun org-babel-execute:clojure (body params)
   "Execute a block of Clojure code with org-babel."
   (let* ((processed-params (org-babel-process-params params))
-         (vars (second processed-params))
-         (body (org-babel-clojure-build-full-form body vars))
+         (body (org-babel-expand-body:clojure body params processed-params))
          (session (org-babel-clojure-initiate-session (first processed-params))))
     (org-babel-reassemble-table
      (org-babel-clojure-evaluate session body (fourth processed-params))

From b805089eb82366a3b1a6df28c56f76125d94d235 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sun, 11 Apr 2010 14:29:28 -0600
Subject: [PATCH 14/46] org-babel-expand-body:css

---
 contrib/babel/lisp/langs/org-babel-css.el | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/contrib/babel/lisp/langs/org-babel-css.el b/contrib/babel/lisp/langs/org-babel-css.el
index 96c9fdcb6..4b5331d5b 100644
--- a/contrib/babel/lisp/langs/org-babel-css.el
+++ b/contrib/babel/lisp/langs/org-babel-css.el
@@ -36,6 +36,8 @@
 
 (add-to-list 'org-babel-tangle-langs '("css" "css" nil t))
 
+(defun org-babel-expand-body:css (body params &optional processed-params) body)
+
 (defun org-babel-execute:css (body params)
   "Execute a block of CSS code with org-babel.  This function is
 called by `org-babel-execute-src-block'."

From 4d862912b22893ff385c4fab772cf2ad972f755f Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sun, 11 Apr 2010 14:29:32 -0600
Subject: [PATCH 15/46] org-babel-expand-body:ditaa

---
 contrib/babel/lisp/langs/org-babel-ditaa.el | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/contrib/babel/lisp/langs/org-babel-ditaa.el b/contrib/babel/lisp/langs/org-babel-ditaa.el
index cc57584c4..b85f836b2 100644
--- a/contrib/babel/lisp/langs/org-babel-ditaa.el
+++ b/contrib/babel/lisp/langs/org-babel-ditaa.el
@@ -49,6 +49,8 @@
   '((:results . "file") (:exports . "results"))
   "Default arguments to use when evaluating a ditaa source block.")
 
+(defun org-babel-expand-body:ditaa (body params &optional processed-params) body)
+
 (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'."

From 01918dffc45413602188a07068e5dfbaf6ef8e44 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Sun, 11 Apr 2010 14:29:36 -0600
Subject: [PATCH 16/46] org-babel-expand-body:dot

---
 contrib/babel/lisp/langs/org-babel-dot.el | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/contrib/babel/lisp/langs/org-babel-dot.el b/contrib/babel/lisp/langs/org-babel-dot.el
index 5f6c34896..30798f9c7 100644
--- a/contrib/babel/lisp/langs/org-babel-dot.el
+++ b/contrib/babel/lisp/langs/org-babel-dot.el
@@ -50,6 +50,8 @@
 (defvar org-babel-default-header-args:dot '((:results . "file") (:exports . "results"))
   "Default arguments to use when evaluating a dot source block.")
 
+(defun org-babel-expand-body:dot (body params &optional processed-params) body)
+
 (defun org-babel-execute:dot (body params)
   "Execute a block of Dot code with org-babel.  This function is
 called by `org-babel-execute-src-block'."

From 58c8ddd5c6e6525651b3efdecc57455adb641ae7 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 22:57:13 -0600
Subject: [PATCH 17/46] org-babel-expand-body:gnuplot

---
 contrib/babel/lisp/langs/org-babel-gnuplot.el | 51 ++++++++++---------
 1 file changed, 28 insertions(+), 23 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-gnuplot.el b/contrib/babel/lisp/langs/org-babel-gnuplot.el
index 6d1922c58..101eda397 100644
--- a/contrib/babel/lisp/langs/org-babel-gnuplot.el
+++ b/contrib/babel/lisp/langs/org-babel-gnuplot.el
@@ -68,13 +68,9 @@ variable names and the value to be used in the gnuplot code."
         (cdr pair))))
    (org-babel-ref-variables params)))
 
-(defun org-babel-execute:gnuplot (body params)
-  "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")
+(defun org-babel-expand-body:gnuplot (body params &optional processed-params)
   (save-window-excursion
     (let* ((vars (org-babel-gnuplot-process-vars params))
-           (session (cdr (assoc :session params)))
            (out-file (cdr (assoc :file params)))
            (term (or (cdr (assoc :term params))
                      (when out-file (file-name-extension out-file))))
@@ -87,7 +83,6 @@ called by `org-babel-execute-src-block'."
            (timefmt (plist-get params :timefmt))
            (time-ind (or (plist-get params :timeind)
                          (when timefmt 1)))
-           (result-type (cdr (assoc :results params)))
            output)
       (flet ((add-to-body (text)
                           (setq body (concat text "\n" body))))
@@ -126,23 +121,33 @@ called by `org-babel-execute-src-block'."
         (mapc (lambda (pair)
                 (setq body (replace-regexp-in-string
                             (format "\\$%s" (car pair)) (cdr pair) body)))
-              vars)
-        ;; evaluate the code body with gnuplot
-        (if (string= session "none")
-            (let ((script-file (make-temp-file "org-babel-gnuplot-script")))
-              (with-temp-file script-file
-                (insert (concat body "\n")))
-              (message "gnuplot \"%s\"" script-file)
-              (setq output
-                    (shell-command-to-string (format "gnuplot \"%s\"" script-file)))
-              (message output))
-          (with-temp-buffer
-            (insert (concat body "\n"))
-            (gnuplot-mode)
-            (gnuplot-send-buffer-to-gnuplot)))
-        (if (member "output" (split-string result-type))
-            output
-          out-file)))))
+              vars))
+      body)))
+
+(defun org-babel-execute:gnuplot (body params)
+  "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")
+  (let ((session (cdr (assoc :session params)))
+        (result-type (cdr (assoc :results params)))
+        (body (org-babel-expand-body:gnuplot body params)))
+    (save-window-excursion
+      ;; evaluate the code body with gnuplot
+      (if (string= session "none")
+          (let ((script-file (make-temp-file "org-babel-gnuplot-script")))
+            (with-temp-file script-file
+              (insert (concat body "\n")))
+            (message "gnuplot \"%s\"" script-file)
+            (setq output
+                  (shell-command-to-string (format "gnuplot \"%s\"" script-file)))
+            (message output))
+        (with-temp-buffer
+          (insert (concat body "\n"))
+          (gnuplot-mode)
+          (gnuplot-send-buffer-to-gnuplot)))
+      (if (member "output" (split-string result-type))
+          output
+        out-file))))
 
 (defun org-babel-prep-session:gnuplot (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."

From dd500005ef6ca6d99863ac8fed23d0699a4172a6 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:00:14 -0600
Subject: [PATCH 18/46] org-babel-expand-body:haskell

---
 contrib/babel/lisp/langs/org-babel-haskell.el | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-haskell.el b/contrib/babel/lisp/langs/org-babel-haskell.el
index d593bb1f4..9b6785745 100644
--- a/contrib/babel/lisp/langs/org-babel-haskell.el
+++ b/contrib/babel/lisp/langs/org-babel-haskell.el
@@ -54,6 +54,13 @@
 
 (defvar org-babel-haskell-eoe "\"org-babel-haskell-eoe\"")
 
+(defun org-babel-expand-body:haskell (body params &optional processed-params)
+  (let (vars (second (or processed-params (org-babel-process-params params))))
+    (concat
+     (mapconcat
+      (lambda (pair) (format "let %s = %s;" (car pair) (cdr pair)))
+      vars "\n") "\n" body "\n")))
+
 (defun org-babel-execute:haskell (body params)
   "Execute a block of Haskell code with org-babel."
   (message "executing haskell source code block")
@@ -61,10 +68,7 @@
          (session (first processed-params))
          (vars (second processed-params))
          (result-type (fourth processed-params))
-         (full-body (concat
-                     (mapconcat
-                      (lambda (pair) (format "let %s = %s;" (car pair) (cdr pair)))
-                      vars "\n") "\n" body "\n"))
+         (full-body (org-babel-expand-body:haskell body params processed-params))
          (session (org-babel-prep-session:haskell session params))
          (raw (org-babel-comint-with-output session org-babel-haskell-eoe t
                 (insert (org-babel-trim full-body))

From 7bd0712ac2e517a5f8c138a70026e5ee0d3dea6e Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:03:07 -0600
Subject: [PATCH 19/46] org-babel-expand-body:latex

---
 contrib/babel/lisp/langs/org-babel-latex.el | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-latex.el b/contrib/babel/lisp/langs/org-babel-latex.el
index 14bace1c3..5b8723c53 100644
--- a/contrib/babel/lisp/langs/org-babel-latex.el
+++ b/contrib/babel/lisp/langs/org-babel-latex.el
@@ -43,10 +43,7 @@
   '((:results . "latex") (:exports . "results"))
   "Default arguments to use when evaluating a latex source block.")
 
-(defun org-babel-execute:latex (body params)
-  "Execute a block of Latex code with org-babel.  This function is
-called by `org-babel-execute-src-block'."
-  (message "executing Latex source code block")
+(defun org-babel-expand-body:latex (body params &optional processed-params)
   (mapc (lambda (pair) ;; replace variables
           (setq body
                 (replace-regexp-in-string
@@ -54,6 +51,13 @@ called by `org-babel-execute-src-block'."
                  (if (stringp (cdr pair))
                      (cdr pair) (format "%S" (cdr pair)))
                  body))) (second (org-babel-process-params params)))
+  body)
+
+(defun org-babel-execute:latex (body params)
+  "Execute a block of Latex code with org-babel.  This function is
+called by `org-babel-execute-src-block'."
+  (message "executing Latex source code block")
+  (setq body (org-babel-expand-body:latex body params))
   (if (cdr (assoc :file params))
       (let ((out-file (cdr (assoc :file params)))
             (tex-file (make-temp-file "org-babel-latex" nil ".tex"))

From e07aced1785e30e744e059f8e49d09a7c7c68c35 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:04:30 -0600
Subject: [PATCH 20/46] org-babel-expand-body:matlab

---
 contrib/babel/lisp/langs/org-babel-matlab.el | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/contrib/babel/lisp/langs/org-babel-matlab.el b/contrib/babel/lisp/langs/org-babel-matlab.el
index eceb3f2f1..d40496e9d 100644
--- a/contrib/babel/lisp/langs/org-babel-matlab.el
+++ b/contrib/babel/lisp/langs/org-babel-matlab.el
@@ -48,6 +48,8 @@
 (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) body)
+
 (defun org-babel-execute:matlab (body params)
   "Execute a block of matlab code with org-babel."
   (org-babel-execute:octave body params 'matlab))

From 8e9f4eec88155ac9126f5bb43557a7043e586d13 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:06:14 -0600
Subject: [PATCH 21/46] org-babel-expand-body:ocaml

---
 contrib/babel/lisp/langs/org-babel-ocaml.el | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-ocaml.el b/contrib/babel/lisp/langs/org-babel-ocaml.el
index 107de0c7f..27f6ea117 100644
--- a/contrib/babel/lisp/langs/org-babel-ocaml.el
+++ b/contrib/babel/lisp/langs/org-babel-ocaml.el
@@ -48,15 +48,19 @@
 (defvar org-babel-ocaml-eoe-indicator "\"org-babel-ocaml-eoe\";;")
 (defvar org-babel-ocaml-eoe-output "org-babel-ocaml-eoe")
 
+(defun org-babel-expand-body:ocaml (body params &optional processed-params)
+  (let ((vars (second (or processed-params (org-babel-process-params params)))))
+    (concat
+     (mapconcat
+      (lambda (pair) (format "let %s = %s;" (car pair) (cdr pair)))
+      vars "\n") "\n" body "\n")))
+
 (defun org-babel-execute:ocaml (body params)
   "Execute a block of Ocaml code with org-babel."
   (message "executing ocaml source code block")
   (let* ((processed-params (org-babel-process-params params))
          (vars (second processed-params))
-         (full-body (concat
-                     (mapconcat
-                      (lambda (pair) (format "let %s = %s;" (car pair) (cdr pair)))
-                      vars "\n") "\n" body "\n"))
+         (full-body (org-babel-expand-body:ocaml body params processed-params))
          (session (org-babel-prep-session:ocaml session params))
          (raw (org-babel-comint-with-output session org-babel-ocaml-eoe-output t
                 (insert (concat (org-babel-chomp full-body) " ;;"))

From 2759b6621db495a8f64aa9d713b3e36028b41f64 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:07:57 -0600
Subject: [PATCH 22/46] org-babel-expand-body:octave

---
 contrib/babel/lisp/langs/org-babel-octave.el | 22 ++++++++++++--------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-octave.el b/contrib/babel/lisp/langs/org-babel-octave.el
index 740e156be..72183a155 100644
--- a/contrib/babel/lisp/langs/org-babel-octave.el
+++ b/contrib/babel/lisp/langs/org-babel-octave.el
@@ -41,6 +41,18 @@
 (defvar org-babel-octave-shell-command "octave -q"
   "Shell command to use to run octave as an external process.")
 
+(defun org-babel-expand-body:octave (org-babel-process-params params)
+  (let ((vars (second (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"
+                (car pair)
+                (org-babel-octave-var-to-octave (cdr pair))))
+      vars "\n") "\n" body "\n")))
+
 (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")))
@@ -52,15 +64,7 @@
          (result-params (third processed-params))
          (result-type (fourth processed-params))
 	 (out-file (cdr (assoc :file params)))
-	 (augmented-body (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"
-				     (car pair)
-				     (org-babel-octave-var-to-octave (cdr pair))))
-			   vars "\n") "\n" body "\n"))
+	 (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

From 41663b0ce483ea6e9a635726c5fff30055cca14c Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:09:57 -0600
Subject: [PATCH 23/46] org-babel-expand-body:oz

---
 contrib/babel/lisp/langs/org-babel-oz.el | 33 +++++++++++++-----------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-oz.el b/contrib/babel/lisp/langs/org-babel-oz.el
index ca0b576d0..d11e9a036 100644
--- a/contrib/babel/lisp/langs/org-babel-oz.el
+++ b/contrib/babel/lisp/langs/org-babel-oz.el
@@ -204,6 +204,23 @@ StartOzServer.oz is located.")
 	    (setq org-babel-oz-collected-result nil))))
     result))
 
+(defun org-babel-expand-body:oz (body params &optional processed-params)
+  (let ((vars (second (or processed-params (org-babel-process-params params))))))
+  (if vars
+      ;; only add var declarations if any variables are there
+      (concat
+       ;; prepend code to define all arguments passed to the code block
+       "local\n"
+       (mapconcat
+        (lambda (pair)
+          (format "%s=%s"
+                  (car pair)
+                  (org-babel-oz-var-to-oz (cdr pair))))
+        vars "\n") "\n" 
+        "in\n"
+        body 
+        "end\n")
+    body))
 
 (defun org-babel-execute:oz (body params)
   "Execute a block of Oz code with org-babel.  This function is
@@ -213,21 +230,7 @@ called by `org-babel-execute-src-block' via multiple-value-bind."
 	(vars (second processed-params))
 ;; 	(result-params (third processed-params))
 	(result-type (fourth processed-params))
-	(full-body (if vars
-		       ;; only add var declarations if any variables are there
-		     (concat
-		      ;; prepend code to define all arguments passed to the code block
-		      "local\n"
-		      (mapconcat
-		       (lambda (pair)
-			 (format "%s=%s"
-				 (car pair)
-				 (org-babel-oz-var-to-oz (cdr pair))))
-		       vars "\n") "\n" 
-		       "in\n"
-		       body 
-		       "end\n")
-		     body))
+	(full-body (org-babel-expand-body:oz body params processed-params))
 	(wait-time (plist-get params :wait-time))
         ;; set the session if the session variable is non-nil
 ;; 	(session-buffer (org-babel-oz-initiate-session session))

From 598dc1ad677f9fcf45e9c961d5e1950764da839a Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:12:02 -0600
Subject: [PATCH 24/46] org-babel-expand-body:perl

---
 contrib/babel/lisp/langs/org-babel-perl.el | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-perl.el b/contrib/babel/lisp/langs/org-babel-perl.el
index 23d893cee..ac1438573 100644
--- a/contrib/babel/lisp/langs/org-babel-perl.el
+++ b/contrib/babel/lisp/langs/org-babel-perl.el
@@ -35,6 +35,16 @@
 
 (add-to-list 'org-babel-tangle-langs '("perl" "pl" "#!/usr/bin/env perl"))
 
+(defun org-babel-expand-body:perl (body params &optional processed-params)
+  (let ((vars (second (or processed-params (org-babel-process-params params)))))
+    (concat
+     (mapconcat ;; define any variables
+      (lambda (pair)
+        (format "$%s=%s;"
+                (car pair)
+                (org-babel-perl-var-to-perl (cdr pair))))
+      vars "\n") "\n" (org-babel-trim body) "\n")))
+
 (defun org-babel-execute:perl (body params)
   "Execute a block of Perl code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
@@ -44,13 +54,8 @@ called by `org-babel-execute-src-block'."
          (vars (second processed-params))
          (result-params (third processed-params))
          (result-type (fourth processed-params))
-         (full-body (concat
-		    (mapconcat ;; define any variables
-		     (lambda (pair)
-		       (format "$%s=%s;"
-			       (car pair)
-			       (org-babel-perl-var-to-perl (cdr pair))))
-		     vars "\n") "\n" (org-babel-trim body) "\n")) ;; then the source block body
+         (full-body (org-babel-expand-body:perl
+                     body params processed-params)) ;; then the source block body
 	(session (org-babel-perl-initiate-session session)))
     (org-babel-reassemble-table
      (org-babel-perl-evaluate session full-body result-type)

From 1bcafa5d9f1df510ea82b41f65d136fd974f0979 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:14:10 -0600
Subject: [PATCH 25/46] org-babel-expand-body:python

---
 contrib/babel/lisp/langs/org-babel-python.el | 21 +++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-python.el b/contrib/babel/lisp/langs/org-babel-python.el
index 07a7abf37..17a90b8fc 100644
--- a/contrib/babel/lisp/langs/org-babel-python.el
+++ b/contrib/babel/lisp/langs/org-babel-python.el
@@ -36,23 +36,26 @@
 
 (add-to-list 'org-babel-tangle-langs '("python" "py" "#!/usr/bin/env python"))
 
+(defun org-babel-expand-body:python (body params &optional processed-params)
+  (let (vars (second (or processed-params (org-babel-process-params params))))
+    (concat
+     (mapconcat ;; define any variables
+      (lambda (pair)
+        (format "%s=%s"
+                (car pair)
+                (org-babel-python-var-to-python (cdr pair))))
+      vars "\n") "\n" (org-babel-trim body) "\n")))
+
 (defun org-babel-execute:python (body params)
   "Execute a block of Python code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
   (message "executing Python source code block")
   (let* ((processed-params (org-babel-process-params params))
          (session (org-babel-python-initiate-session (first processed-params)))
-         (vars (second processed-params))
          (result-params (third processed-params))
          (result-type (fourth processed-params))
-         (full-body (concat
-                     (mapconcat ;; define any variables
-                      (lambda (pair)
-                        (format "%s=%s"
-                                (car pair)
-                                (org-babel-python-var-to-python (cdr pair))))
-                      vars "\n") "\n" (org-babel-trim body) "\n")) ;; then the source block body
-         
+         (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)))
     (or (cdr (assoc :file params))
         (org-babel-reassemble-table

From 394031eb384c48b87b383bff367e6cbf04f694d9 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:15:47 -0600
Subject: [PATCH 26/46] org-babel-expand-body:ruby

---
 contrib/babel/lisp/langs/org-babel-ruby.el | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-ruby.el b/contrib/babel/lisp/langs/org-babel-ruby.el
index f35bddac7..4919850cb 100644
--- a/contrib/babel/lisp/langs/org-babel-ruby.el
+++ b/contrib/babel/lisp/langs/org-babel-ruby.el
@@ -46,22 +46,26 @@
 
 (add-to-list 'org-babel-tangle-langs '("ruby" "rb" "#!/usr/bin/env ruby"))
 
+(defun org-babel-expand-body:ruby (body params &optional processed-params)
+  (let ((vars (second (or processed-params (org-babel-process-params params)))))
+    (concat
+     (mapconcat ;; define any variables
+      (lambda (pair)
+        (format "%s=%s"
+                (car pair)
+                (org-babel-ruby-var-to-ruby (cdr pair))))
+      vars "\n") "\n" body "\n")))
+
 (defun org-babel-execute:ruby (body params)
   "Execute a block of Ruby code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
   (message "executing Ruby source code block")
   (let* ((processed-params (org-babel-process-params params))
          (session (org-babel-ruby-initiate-session (first processed-params)))
-         (vars (second processed-params))
          (result-params (third processed-params))
          (result-type (fourth processed-params))
-         (full-body (concat
-		    (mapconcat ;; define any variables
-		     (lambda (pair)
-		       (format "%s=%s"
-			       (car pair)
-			       (org-babel-ruby-var-to-ruby (cdr pair))))
-		     vars "\n") "\n" body "\n")) ;; then the source block body
+         (full-body (org-babel-expand-body:ruby
+                     body params processed-params)) ;; then the source block body
          (result (org-babel-ruby-evaluate session full-body result-type)))
     (or (cdr (assoc :file params))
         (org-babel-reassemble-table

From 35434e1389c30e500648b6bffc9d04409e7bbd70 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:18:13 -0600
Subject: [PATCH 27/46] org-babel-expand-body:sass

---
 contrib/babel/lisp/langs/org-babel-sass.el | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/langs/org-babel-sass.el b/contrib/babel/lisp/langs/org-babel-sass.el
index d20e91da8..37b1ec99b 100644
--- a/contrib/babel/lisp/langs/org-babel-sass.el
+++ b/contrib/babel/lisp/langs/org-babel-sass.el
@@ -48,6 +48,8 @@
 
 (add-to-list 'org-babel-tangle-langs '("sass" "sass"))
 
+(defun org-babel-expand-body:sass (body params &optional processed-params) body)
+
 (defun org-babel-execute:sass (body params)
   "Execute a block of Sass code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
@@ -58,7 +60,8 @@ called by `org-babel-execute-src-block'."
          (cmdline (cdr (assoc :cmdline params)))
          (in-file (make-temp-file "org-babel-sass-in"))
          (cmd (concat "sass " (or cmdline "") in-file " " out-file)))
-    (with-temp-file in-file (insert body)) (shell-command cmd)
+    (with-temp-file in-file
+      (insert (org-babel-expand-body:sass body))) (shell-command cmd)
     (or file (with-temp-buffer (insert-file-contents out-file) (buffer-string)))))
 
 (defun org-babel-prep-session:sass (session params)

From e6c979f0d74ee7e095401b622c50d2ed56674a8b Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:17:39 -0600
Subject: [PATCH 28/46] org-babel-expand-body:screen

---
 contrib/babel/lisp/langs/org-babel-screen.el | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/langs/org-babel-screen.el b/contrib/babel/lisp/langs/org-babel-screen.el
index 1529ac0d4..98b9d011a 100644
--- a/contrib/babel/lisp/langs/org-babel-screen.el
+++ b/contrib/babel/lisp/langs/org-babel-screen.el
@@ -50,6 +50,8 @@ In case you want to use a different screen than one selected by your $PATH")
   '((:results . "silent") (:session . "default") (:cmd . "sh") (:terminal . "xterm"))
   "Default arguments to use when running screen source blocks.")
 
+(defun org-babel-expand-body:screen (body params &optional processed-params) body)
+
 (defun org-babel-execute:screen (body params)
   "Send a block of code via screen to a terminal using org-babel.
 \"default\" session is be used when none is specified."
@@ -59,7 +61,8 @@ In case you want to use a different screen than one selected by your $PATH")
            (session (first processed-params))
            (socket (org-babel-screen-session-socketname session)))
       (unless socket (org-babel-prep-session:screen session params))
-      (org-babel-screen-session-execute-string session body))))
+      (org-babel-screen-session-execute-string
+       session (org-babel-expand-body:screen body)))))
 
 (defun org-babel-prep-session:screen (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."

From 1fdc012e3d50279c469acfc3b1851147f11449ee Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Mon, 19 Apr 2010 23:47:43 -0600
Subject: [PATCH 29/46] org-babel-expand-body:sh

---
 contrib/babel/lisp/langs/org-babel-sh.el | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-sh.el b/contrib/babel/lisp/langs/org-babel-sh.el
index aed73d1e3..c39d55649 100644
--- a/contrib/babel/lisp/langs/org-babel-sh.el
+++ b/contrib/babel/lisp/langs/org-babel-sh.el
@@ -40,22 +40,26 @@
   "Command used to invoke a shell.  This will be passed to
   `shell-command-on-region'")
 
+(defun org-babel-expand-body:sh (body params &optional processed-params)
+  (let ((vars (second (or processed-params (org-babel-process-params params))))
+        (sep (cdr (assoc :separator params))))
+    (concat
+   (mapconcat ;; define any variables
+    (lambda (pair)
+      (format "%s=%s"
+              (car pair)
+              (org-babel-sh-var-to-sh (cdr pair) sep)))
+    vars "\n") "\n" body "\n\n")))
+
 (defun org-babel-execute:sh (body params)
   "Execute a block of Shell commands with org-babel.  This
 function is called by `org-babel-execute-src-block'."
   (message "executing Shell source code block")
   (let* ((processed-params (org-babel-process-params params))
          (session (org-babel-sh-initiate-session (first processed-params)))
-         (vars (second processed-params))
          (result-type (fourth processed-params))
-         (sep (cdr (assoc :separator params)))
-         (full-body (concat
-                     (mapconcat ;; define any variables
-                      (lambda (pair)
-                        (format "%s=%s"
-                                (car pair)
-                                (org-babel-sh-var-to-sh (cdr pair) sep)))
-                      vars "\n") "\n" body "\n\n"))) ;; then the source block body
+         (full-body (org-babel-expand-body:sh
+                     body params processed-params))) ;; then the source block body
     (org-babel-reassemble-table
      (org-babel-sh-evaluate session full-body result-type)
      (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))

From 0734bf96ba24c44be088bfdbb7f04c5fd80e0588 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:21:56 -0600
Subject: [PATCH 30/46] org-babel-expand-body:sql

---
 contrib/babel/lisp/langs/org-babel-sql.el | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/langs/org-babel-sql.el b/contrib/babel/lisp/langs/org-babel-sql.el
index da746f257..b995e4856 100644
--- a/contrib/babel/lisp/langs/org-babel-sql.el
+++ b/contrib/babel/lisp/langs/org-babel-sql.el
@@ -51,6 +51,8 @@
 
 (add-to-list 'org-babel-tangle-langs '("sql" "sql"))
 
+(defun org-babel-expand-body:sql (body params &optional processed-params) body)
+
 (defun org-babel-execute:sql (body params)
   "Execute a block of Sql code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
@@ -65,7 +67,8 @@ called by `org-babel-execute-src-block'."
                     ('mysql (format "mysql %s -e \"source %s\" > %s"
                                     (or cmdline "") in-file out-file))
                     (t (error "no support for the %s sql engine")))))
-    (with-temp-file in-file (insert body))
+    (with-temp-file in-file
+      (insert (org-babel-expand-body:sql body params)))
     (message command)
     (shell-command command)
     (with-temp-buffer

From 9ff31a51100911b35afbf798e982c6657a096268 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 15 Apr 2010 23:35:50 -0600
Subject: [PATCH 31/46] babel: bound `org-babel-expand-src-block' to (C-c M-b
 p)

---
 contrib/babel/lisp/org-babel-keys.el | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/org-babel-keys.el b/contrib/babel/lisp/org-babel-keys.el
index 14083e1eb..a1ddbae22 100644
--- a/contrib/babel/lisp/org-babel-keys.el
+++ b/contrib/babel/lisp/org-babel-keys.el
@@ -48,7 +48,8 @@ interactive babel functions which are assigned key bindings.")
     ("h" . org-babel-sha1-hash)
     ("g" . org-babel-goto-named-source-block)
     ("l" . org-babel-lob-ingest)
-    ("z" . org-babel-switch-to-session))
+    ("z" . org-babel-switch-to-session)
+    ("p" . org-babel-expand-src-block))
   "Org-babel keybindings.  This list associates interactive
 org-babel functions with keys.  Each element of this list will
 add an entry to the `org-mode-map' using the letter key which is

From 0917218da5c8675b77660ff25e683880ce729abb Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Tue, 20 Apr 2010 00:18:03 -0600
Subject: [PATCH 32/46] babel: fixed bug in org-babel-expand-body:python

---
 contrib/babel/lisp/langs/org-babel-python.el | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-python.el b/contrib/babel/lisp/langs/org-babel-python.el
index 17a90b8fc..8f1049a92 100644
--- a/contrib/babel/lisp/langs/org-babel-python.el
+++ b/contrib/babel/lisp/langs/org-babel-python.el
@@ -37,14 +37,14 @@
 (add-to-list 'org-babel-tangle-langs '("python" "py" "#!/usr/bin/env python"))
 
 (defun org-babel-expand-body:python (body params &optional processed-params)
-  (let (vars (second (or processed-params (org-babel-process-params params))))
-    (concat
-     (mapconcat ;; define any variables
-      (lambda (pair)
-        (format "%s=%s"
-                (car pair)
-                (org-babel-python-var-to-python (cdr pair))))
-      vars "\n") "\n" (org-babel-trim body) "\n")))
+  (concat
+   (mapconcat ;; define any variables
+    (lambda (pair)
+      (format "%s=%s"
+              (car pair)
+              (org-babel-python-var-to-python (cdr pair))))
+    (second (or processed-params (org-babel-process-params params))) "\n")
+   "\n" (org-babel-trim body) "\n"))
 
 (defun org-babel-execute:python (body params)
   "Execute a block of Python code with org-babel.  This function is

From 8872454566445e7714865ff052a44913503080b2 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Tue, 20 Apr 2010 12:16:21 -0400
Subject: [PATCH 33/46] org-babel-expand-body:R

---
 contrib/babel/lisp/langs/org-babel-R.el | 35 ++++++++++++++-----------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-R.el b/contrib/babel/lisp/langs/org-babel-R.el
index e7188d9b4..ae6b6cbfd 100644
--- a/contrib/babel/lisp/langs/org-babel-R.el
+++ b/contrib/babel/lisp/langs/org-babel-R.el
@@ -35,6 +35,22 @@
 
 (add-to-list 'org-babel-tangle-langs '("R" "R" "#!/usr/bin/env Rscript"))
 
+(defun org-babel-expand-body:R (body params &optional processed-params)
+  (let* ((processed-params (or processed-params
+                               (org-babel-process-params params)))
+	 (vars (mapcar (lambda (i) (cons (car (nth i (second processed-params)))
+					 (org-babel-reassemble-table
+					  (cdr (nth i (second processed-params)))
+					  (cdr (nth i (fifth processed-params)))
+					  (cdr (nth i (sixth processed-params))))))
+		       (number-sequence 0 (1- (length (second 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))) vars "\n")
+     "\n" body "\n" (if out-file "dev.off()\n" ""))))
+
 (defun org-babel-execute:R (body params)
   "Execute a block of R code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
@@ -43,24 +59,13 @@ called by `org-babel-execute-src-block'."
     (let* ((processed-params (org-babel-process-params params))
            (result-type (fourth processed-params))
            (session (org-babel-R-initiate-session (first processed-params) params))
-           (vars (mapcar (lambda (i) (cons (car (nth i (second processed-params)))
-					   (org-babel-reassemble-table
-					    (cdr (nth i (second processed-params)))
-					    (cdr (nth i (fifth processed-params)))
-					    (cdr (nth i (sixth processed-params))))))
-			 (number-sequence 0 (1- (length (second processed-params))))))
 	   (colnames-p (and (cdr (assoc :colnames params))
-				(string= "yes" (cdr (assoc :colnames params)))))
+			    (string= "yes" (cdr (assoc :colnames params)))))
 	   (rownames-p (and (cdr (assoc :rownames params))
-				(string= "yes" (cdr (assoc :rownames params)))))
+			    (string= "yes" (cdr (assoc :rownames params)))))
 	   (out-file (cdr (assoc :file params)))
-	   (augmented-body
-	    (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) colnames-p rownames-p)) vars "\n")
-	     "\n" body "\n" (if out-file "dev.off()\n" "")))
-	   (result (org-babel-R-evaluate session augmented-body result-type colnames-p rownames-p)))
+	   (full-body (org-babel-expand-body:R body params processed-params))
+	   (result (org-babel-R-evaluate session full-body result-type column-names-p)))
       (or out-file result))))
 
 (defun org-babel-prep-session:R (session params)

From 7decdec3b2ffded56d7056021308b99f17617512 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Tue, 20 Apr 2010 12:17:48 -0400
Subject: [PATCH 34/46] babel: erase previous contents of preview buffer

---
 contrib/babel/lisp/org-babel.el | 1 +
 1 file changed, 1 insertion(+)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index 02c668083..fd6086cc2 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -281,6 +281,7 @@ arguments, and pop open the results in a preview buffer."
          (expanded (funcall cmd body params))
          (buf (get-buffer-create "*Org-Babel Code Body Preview*")))
     (with-current-buffer buf
+      (erase-buffer)
       (insert expanded)
       (funcall (intern (concat lang "-mode"))))
     (pop-to-buffer buf)))

From 626cb079e434a7a9497499eb1c68fe01001a1f3d Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Tue, 20 Apr 2010 11:06:17 -0600
Subject: [PATCH 35/46] babel: fixed bug in org-babel-expand-body:sass

---
 contrib/babel/lisp/langs/org-babel-sass.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/langs/org-babel-sass.el b/contrib/babel/lisp/langs/org-babel-sass.el
index 37b1ec99b..4bf5b9944 100644
--- a/contrib/babel/lisp/langs/org-babel-sass.el
+++ b/contrib/babel/lisp/langs/org-babel-sass.el
@@ -61,7 +61,7 @@ called by `org-babel-execute-src-block'."
          (in-file (make-temp-file "org-babel-sass-in"))
          (cmd (concat "sass " (or cmdline "") in-file " " out-file)))
     (with-temp-file in-file
-      (insert (org-babel-expand-body:sass body))) (shell-command cmd)
+      (insert (org-babel-expand-body:sass body params))) (shell-command cmd)
     (or file (with-temp-buffer (insert-file-contents out-file) (buffer-string)))))
 
 (defun org-babel-prep-session:sass (session params)

From 03f13106fba9b51676a9392cbd1ea0858c162921 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Tue, 20 Apr 2010 20:43:35 -0600
Subject: [PATCH 36/46] babel: adding org-babel-expand-body:generic for
 languages w/o body expansion support

---
 contrib/babel/lisp/org-babel.el | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index fd6086cc2..58b4290eb 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -262,6 +262,12 @@ block."
             result))
       (setq call-process-region 'call-process-region-original))))
 
+(defun org-babel-expand-body:generic (body params &optional processed-params)
+  "Expand a block of code with org-babel according to it's header
+arguments.  This generic implementation of body expansion is
+called for languages which have not defined their own specific
+org-babel-expand-body:lang function." body)
+
 (defun org-babel-expand-src-block (&optional arg info params)
   "Expand the current source code block according to it's header
 arguments, and pop open the results in a preview buffer."
@@ -278,7 +284,8 @@ arguments, and pop open the results in a preview buffer."
                               (string= "yes" (cdr (assoc :noweb params))))
 			 (org-babel-expand-noweb-references info) (second info))))
          (cmd (intern (concat "org-babel-expand-body:" lang)))
-         (expanded (funcall cmd body params))
+         (expanded (funcall (if (fboundp cmd) cmd 'org-babel-expand-body:generic)
+                            body params))
          (buf (get-buffer-create "*Org-Babel Code Body Preview*")))
     (with-current-buffer buf
       (erase-buffer)

From 32c7ae42c365da3125617651606291ba547f57bf Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Tue, 20 Apr 2010 20:55:30 -0600
Subject: [PATCH 37/46] babel: remove superfluous newlines from tangled C code
 bodies

---
 contrib/babel/lisp/langs/org-babel-C.el | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-C.el b/contrib/babel/lisp/langs/org-babel-C.el
index 0c4f5d63c..0bddc69fd 100644
--- a/contrib/babel/lisp/langs/org-babel-C.el
+++ b/contrib/babel/lisp/langs/org-babel-C.el
@@ -145,9 +145,9 @@ it's header arguments."
                 ;; variables
                 (mapconcat 'org-babel-C-var-to-C vars "\n")
                 ;; body
-                "\n" (if main-p
-                         (org-babel-C-ensure-main-wrap body)
-                       body) "\n") "\n")))
+                (if main-p
+                    (org-babel-C-ensure-main-wrap body)
+                  body) "\n") "\n")))
 
 (defun org-babel-C-ensure-main-wrap (body)
   "Wrap body in a \"main\" function call if none exists."

From 9fdd058669aa0d07ab8f5909c93d1d24957f5ae4 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Tue, 20 Apr 2010 18:25:09 -0400
Subject: [PATCH 38/46] org-babel-expand-body:R

---
 contrib/babel/lisp/langs/org-babel-R.el | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-R.el b/contrib/babel/lisp/langs/org-babel-R.el
index ae6b6cbfd..220e44c46 100644
--- a/contrib/babel/lisp/langs/org-babel-R.el
+++ b/contrib/babel/lisp/langs/org-babel-R.el
@@ -48,7 +48,11 @@
     (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))) vars "\n")
+      (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" ""))))
 
 (defun org-babel-execute:R (body params)
@@ -59,13 +63,11 @@ called by `org-babel-execute-src-block'."
     (let* ((processed-params (org-babel-process-params params))
            (result-type (fourth processed-params))
            (session (org-babel-R-initiate-session (first processed-params) params))
-	   (colnames-p (and (cdr (assoc :colnames params))
-			    (string= "yes" (cdr (assoc :colnames params)))))
-	   (rownames-p (and (cdr (assoc :rownames params))
-			    (string= "yes" (cdr (assoc :rownames params)))))
+	   (colnames-p (equal "yes" (cdr (assoc :colnames params))))
+	   (rownames-p (equal "yes" (cdr (assoc :rownames params))))
 	   (out-file (cdr (assoc :file params)))
 	   (full-body (org-babel-expand-body:R body params processed-params))
-	   (result (org-babel-R-evaluate session full-body result-type column-names-p)))
+	   (result (org-babel-R-evaluate session full-body result-type colnames-p rownames-p)))
       (or out-file result))))
 
 (defun org-babel-prep-session:R (session params)

From d0dde7c6d523d69b66c36fc849faf69aa46e364d Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Tue, 20 Apr 2010 18:27:33 -0400
Subject: [PATCH 39/46] babel: flip default values of :hlines header arg

---
 contrib/babel/lisp/langs/org-babel-emacs-lisp.el | 2 +-
 contrib/babel/lisp/org-babel.el                  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
index 858b3dbe7..073ee3daf 100644
--- a/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
+++ b/contrib/babel/lisp/langs/org-babel-emacs-lisp.el
@@ -36,7 +36,7 @@
 (add-to-list 'org-babel-tangle-langs '("emacs-lisp" "el"))
 
 (defvar org-babel-default-header-args:emacs-lisp
-  '((:hlines . "no") (:colnames . "no"))
+  '((:hlines . "yes") (:colnames . "no"))
   "Default arguments to use when evaluating an emacs-lisp source block.")
 
 (defun org-babel-expand-body:emacs-lisp (body params &optional processed-params)
diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index 58b4290eb..0c3fc6452 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -96,7 +96,7 @@ header arguments as well.")
 
 (defvar org-babel-default-header-args
   '((:session . "none") (:results . "replace") (:exports . "code")
-    (:cache . "no") (:noweb . "no") (:hlines . "yes"))
+    (:cache . "no") (:noweb . "no") (:hlines . "no"))
   "Default arguments to use when evaluating a source block.")
 
 (defvar org-babel-default-inline-header-args

From 59251c8d0840d07befc438e9ddbd63b2abbc2670 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Wed, 21 Apr 2010 14:38:38 -0600
Subject: [PATCH 40/46] babel: fixed bug in org-babel-execute:gnuplot related
 to body-expand changes

---
 contrib/babel/lisp/langs/org-babel-gnuplot.el | 1 +
 1 file changed, 1 insertion(+)

diff --git a/contrib/babel/lisp/langs/org-babel-gnuplot.el b/contrib/babel/lisp/langs/org-babel-gnuplot.el
index 101eda397..04d216947 100644
--- a/contrib/babel/lisp/langs/org-babel-gnuplot.el
+++ b/contrib/babel/lisp/langs/org-babel-gnuplot.el
@@ -130,6 +130,7 @@ called by `org-babel-execute-src-block'."
   (message "executing Gnuplot source code block")
   (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)))
     (save-window-excursion
       ;; evaluate the code body with gnuplot

From 9124e9055d82df816bbf27158cb204e664a90713 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 22 Apr 2010 19:33:01 -0600
Subject: [PATCH 41/46] fixed bug in org-babel-execute:C

---
 contrib/babel/lisp/langs/org-babel-C.el | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-C.el b/contrib/babel/lisp/langs/org-babel-C.el
index 0bddc69fd..8e94812a4 100644
--- a/contrib/babel/lisp/langs/org-babel-C.el
+++ b/contrib/babel/lisp/langs/org-babel-C.el
@@ -61,7 +61,7 @@ called by `org-babel-execute-src-block'."
 (defun org-babel-expand-body:c++ (body params &optional processed-params)
   "Expand a block of C++ code with org-babel according to it's
 header arguments (calls `org-babel-C-expand')."
-  (let ((c-variant 'cpp)) (org-babel-C-expand body params)))
+  (let ((c-variant 'cpp)) (org-babel-C-expand body params processed-params)))
 
 (defun org-babel-execute:C (body params)
   "Execute a block of C code with org-babel.  This function is
@@ -71,13 +71,14 @@ called by `org-babel-execute-src-block'."
 (defun org-babel-expand-body:c (body params &optional processed-params)
   "Expand a block of C code with org-babel according to it's
 header arguments (calls `org-babel-C-expand')."
-  (let ((c-variant 'c)) (org-babel-C-expand body params)))
+  (let ((c-variant 'c)) (org-babel-C-expand body params processed-params)))
 
 (defun org-babel-C-execute (body params)
   "This should only be called by `org-babel-execute:C' or
 `org-babel-execute:c++'."
   (message "executing C source code block")
-  (let* ((tmp-src-file (make-temp-file "org-babel-C-src" nil
+  (let* ((processed-params (org-babel-process-params params))
+         (tmp-src-file (make-temp-file "org-babel-C-src" nil
                                        (case c-variant
                                          ('c ".c")
                                          ('cpp ".cpp"))))

From 2f71d79e5eac579ccc88cee96aecbeca9c33f957 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 22 Apr 2010 19:39:12 -0600
Subject: [PATCH 42/46] org-babel-c: now using org-babel-read on
 outline-property parameters

---
 contrib/babel/lisp/langs/org-babel-C.el | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/contrib/babel/lisp/langs/org-babel-C.el b/contrib/babel/lisp/langs/org-babel-C.el
index 8e94812a4..13e6fcacd 100644
--- a/contrib/babel/lisp/langs/org-babel-C.el
+++ b/contrib/babel/lisp/langs/org-babel-C.el
@@ -129,10 +129,10 @@ it's header arguments."
                           (org-babel-process-params params))))
         (main-p (not (string= (cdr (assoc :main params)) "no")))
         (includes (or (cdr (assoc :includes params))
-                      (org-entry-get nil "includes" t)))
+                      (org-babel-read (org-entry-get nil "includes" t))))
         (defines (org-babel-read
                   (or (cdr (assoc :defines params))
-                      (org-entry-get nil "defines" t)))))
+                      (org-babel-read (org-entry-get nil "defines" t))))))
     (mapconcat 'identity
                (list
                 ;; includes

From d1b8b347fec1a3843354fa8f8e8733f329e9d4c2 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Thu, 22 Apr 2010 17:37:35 -0400
Subject: [PATCH 43/46] Allow org-src edit buffer to be used in read-only mode

org-edit-src-code gains extra optional arguments `code' and
`edit-buffer-name'. If `code' is supplied, then this code forms the
contents of the edit buffer, which is made read-only. In this case,
the mechanisms for writing back to the org buffer on save are
disabled.

Optional argument `edit-buffer-name' allows a name for the edit buffer
to be supplied.
---
 lisp/ChangeLog  |   5 ++
 lisp/org-src.el | 132 ++++++++++++++++++++++++++----------------------
 2 files changed, 76 insertions(+), 61 deletions(-)

diff --git a/lisp/ChangeLog b/lisp/ChangeLog
index 713139469..b8a2f4834 100755
--- a/lisp/ChangeLog
+++ b/lisp/ChangeLog
@@ -51,6 +51,11 @@
 	(org-export-html-close-lists-maybe): Allow to splice raw HTML into
 	and out of lists.
 
+2010-04-22  Dan Davison  <davison@stats.ox.ac.uk>
+
+	* org-src.el (org-edit-src-code): Allow the org-src edit buffer to
+	be used in a read-only mode.
+
 2010-04-21  Carsten Dominik  <carsten.dominik@gmail.com>
 
 	* org-src.el (org-edit-src-find-region-and-lang): Test for
diff --git a/lisp/org-src.el b/lisp/org-src.el
index 8eab12aaf..6a865bbe8 100644
--- a/lisp/org-src.el
+++ b/lisp/org-src.el
@@ -187,7 +187,7 @@ This minor mode is turned on in two situations:
 There is a mode hook, and keybindings for `org-edit-src-exit' and
 `org-edit-src-save'")
 
-(defun org-edit-src-code (&optional context)
+(defun org-edit-src-code (&optional context code edit-buffer-name)
   "Edit the source code example at point.
 The example is copied to a separate buffer, and that buffer is switched
 to the correct language mode.  When done, exit with \\[org-edit-src-exit].
@@ -207,12 +207,13 @@ the edited version. Optional argument CONTEXT is used by
 	(beg (make-marker))
 	(end (make-marker))
 	(preserve-indentation org-src-preserve-indentation)
-	block-nindent total-nindent ovl lang lang-f single lfmt code begline buffer)
+	block-nindent total-nindent ovl lang lang-f single lfmt begline buffer)
     (if (not info)
 	nil
       (setq beg (move-marker beg (nth 0 info))
 	    end (move-marker end (nth 1 info))
-	    code (buffer-substring-no-properties beg end)
+	    allow-write-back-p (null code)
+	    code (or code (buffer-substring-no-properties beg end))
 	    lang (or (cdr (assoc (nth 2 info) org-src-lang-modes))
                      (nth 2 info))
 	    lang (if (symbolp lang) (symbol-name lang) lang)
@@ -241,16 +242,17 @@ the edited version. Optional argument CONTEXT is used by
 		(delete-overlay org-edit-src-overlay)))
 	  (kill-buffer buffer))
 	(setq buffer (generate-new-buffer
-		      (org-src-construct-edit-buffer-name (buffer-name) lang)))
+		      (or edit-buffer-name
+			  (org-src-construct-edit-buffer-name (buffer-name) lang))))
 	(setq ovl (make-overlay beg end))
 	(overlay-put ovl 'edit-buffer buffer)
 	(overlay-put ovl 'help-echo "Click with mouse-1 to switch to buffer editing this segment")
 	(overlay-put ovl 'face 'secondary-selection)
 	(overlay-put ovl
-			 'keymap
-			 (let ((map (make-sparse-keymap)))
-			   (define-key map [mouse-1] 'org-edit-src-continue)
-			   map))
+		     'keymap
+		     (let ((map (make-sparse-keymap)))
+		       (define-key map [mouse-1] 'org-edit-src-continue)
+		       map))
 	(overlay-put ovl :read-only "Leave me alone")
 	(org-src-switch-to-buffer buffer 'edit)
 	(if (eq single 'macro-definition)
@@ -264,6 +266,7 @@ the edited version. Optional argument CONTEXT is used by
 	  (funcall lang-f))
 	(set (make-local-variable 'org-edit-src-force-single-line) single)
 	(set (make-local-variable 'org-edit-src-from-org-mode) org-mode-p)
+	(set (make-local-variable 'org-edit-src-allow-write-back-p) allow-write-back-p)
 	(set (make-local-variable 'org-src-preserve-indentation) preserve-indentation)
 	(when lfmt
 	  (set (make-local-variable 'org-coderef-label-format) lfmt))
@@ -406,7 +409,7 @@ the fragment in the Org-mode buffer."
 	 ((eq org-edit-fixed-width-region-mode 'artist-mode)
 	  (fundamental-mode)
 	  (artist-mode 1))
-       (t (funcall org-edit-fixed-width-region-mode)))
+	 (t (funcall org-edit-fixed-width-region-mode)))
 	(set (make-local-variable 'org-edit-src-force-single-line) nil)
 	(set (make-local-variable 'org-edit-src-from-org-mode) org-mode-p)
 	(set (make-local-variable 'org-edit-src-picture) t)
@@ -529,7 +532,7 @@ the language, a switch telling if the content should be in a single line."
 (defun org-edit-src-exit (&optional context)
   "Exit special edit and protect problematic lines."
   (interactive)
-  (unless org-edit-src-from-org-mode
+  (unless (org-bound-and-true-p org-edit-src-from-org-mode)
     (error "This is not a sub-editing buffer, something is wrong..."))
   (widen)
   (let* ((beg org-edit-src-beg-marker)
@@ -541,57 +544,61 @@ the language, a switch telling if the content should be in a single line."
 	 (total-nindent (+ (or org-edit-src-block-indentation 0)
 			   org-edit-src-content-indentation))
 	 (preserve-indentation org-src-preserve-indentation)
+	 (allow-write-back-p (org-bound-and-true-p org-edit-src-allow-write-back-p))
 	 (delta 0) code line col indent)
-    (unless preserve-indentation (untabify (point-min) (point-max)))
-    (save-excursion
-      (goto-char (point-min))
-      (if (looking-at "[ \t\n]*\n") (replace-match ""))
-      (unless macro
-	(if (re-search-forward "\n[ \t\n]*\\'" nil t) (replace-match ""))))
+    (when allow-write-back-p
+      (unless preserve-indentation (untabify (point-min) (point-max)))
+      (save-excursion
+	(goto-char (point-min))
+	(if (looking-at "[ \t\n]*\n") (replace-match ""))
+	(unless macro
+	  (if (re-search-forward "\n[ \t\n]*\\'" nil t) (replace-match "")))))
     (setq line (if (org-bound-and-true-p org-edit-src-force-single-line)
 		   1
 		 (org-current-line))
 	  col (current-column))
-    (when single
-      (goto-char (point-min))
-      (if (re-search-forward "\\s-+\\'" nil t) (replace-match ""))
-      (goto-char (point-min))
-      (let ((cnt 0))
-	(while (re-search-forward "\n" nil t)
-	  (setq cnt (1+ cnt))
-	  (replace-match (if macro "\\n" " ") t t))
-	(when (and macro (> cnt 0))
-	  (goto-char (point-max)) (insert "\\n")))
-      (goto-char (point-min))
-      (if (looking-at "\\s-*") (replace-match " ")))
-    (when (org-bound-and-true-p org-edit-src-from-org-mode)
-      (goto-char (point-min))
-      (while (re-search-forward
-	      (if (org-mode-p) "^\\(.\\)" "^\\([*]\\|[ \t]*#\\+\\)") nil t)
-	(if (eq (org-current-line) line) (setq delta (1+ delta)))
-	(replace-match ",\\1")))
-    (when (org-bound-and-true-p org-edit-src-picture)
-      (setq preserve-indentation nil)
-      (untabify (point-min) (point-max))
-      (goto-char (point-min))
-      (while (re-search-forward "^" nil t)
-	(replace-match ": ")))
-    (unless (or single preserve-indentation (= total-nindent 0))
-      (setq indent (make-string total-nindent ?\ ))
-      (goto-char (point-min))
-      (while (re-search-forward "^" nil t)
-	(replace-match indent)))
-    (if (org-bound-and-true-p org-edit-src-picture)
-	(setq total-nindent (+ total-nindent 2)))
-    (setq code (buffer-string))
-    (set-buffer-modified-p nil)
+    (when allow-write-back-p
+      (when single
+	(goto-char (point-min))
+	(if (re-search-forward "\\s-+\\'" nil t) (replace-match ""))
+	(goto-char (point-min))
+	(let ((cnt 0))
+	  (while (re-search-forward "\n" nil t)
+	    (setq cnt (1+ cnt))
+	    (replace-match (if macro "\\n" " ") t t))
+	  (when (and macro (> cnt 0))
+	    (goto-char (point-max)) (insert "\\n")))
+	(goto-char (point-min))
+	(if (looking-at "\\s-*") (replace-match " ")))
+      (when (org-bound-and-true-p org-edit-src-from-org-mode)
+	(goto-char (point-min))
+	(while (re-search-forward
+		(if (org-mode-p) "^\\(.\\)" "^\\([*]\\|[ \t]*#\\+\\)") nil t)
+	  (if (eq (org-current-line) line) (setq delta (1+ delta)))
+	  (replace-match ",\\1")))
+      (when (org-bound-and-true-p org-edit-src-picture)
+	(setq preserve-indentation nil)
+	(untabify (point-min) (point-max))
+	(goto-char (point-min))
+	(while (re-search-forward "^" nil t)
+	  (replace-match ": ")))
+      (unless (or single preserve-indentation (= total-nindent 0))
+	(setq indent (make-string total-nindent ?\ ))
+	(goto-char (point-min))
+	(while (re-search-forward "^" nil t)
+	  (replace-match indent)))
+      (if (org-bound-and-true-p org-edit-src-picture)
+	  (setq total-nindent (+ total-nindent 2)))
+      (setq code (buffer-string))
+      (set-buffer-modified-p nil))
     (org-src-switch-to-buffer (marker-buffer beg) (or context 'exit))
     (kill-buffer buffer)
     (goto-char beg)
-    (delete-region beg end)
-    (insert code)
-    (goto-char beg)
-    (if single (just-one-space))
+    (when allow-write-back-p
+      (delete-region beg end)
+      (insert code)
+      (goto-char beg)
+      (if single (just-one-space)))
     (if (memq t (mapcar (lambda (overlay)
 			  (eq (overlay-get overlay 'invisible)
 			      'org-hide-block))
@@ -625,15 +632,18 @@ the language, a switch telling if the content should be in a single line."
     (message (or msg ""))))
 
 (defun org-src-mode-configure-edit-buffer ()
-  (when org-edit-src-from-org-mode
-    (setq buffer-offer-save t)
-    (setq buffer-file-name
-	  (concat (buffer-file-name (marker-buffer org-edit-src-beg-marker))
-		  "[" (buffer-name) "]"))
-    (set (if (featurep 'xemacs) 'write-contents-hooks 'write-contents-functions)
-	 '(org-edit-src-save))
+  (when (org-bound-and-true-p org-edit-src-from-org-mode)
     (org-add-hook 'kill-buffer-hook
-		  '(lambda () (delete-overlay org-edit-src-overlay)) nil 'local)))
+		  '(lambda () (delete-overlay org-edit-src-overlay)) nil 'local)
+    (if (org-bound-and-true-p org-edit-src-allow-write-back-p)
+	(progn
+	  (setq buffer-offer-save t)
+	  (setq buffer-file-name
+		(concat (buffer-file-name (marker-buffer org-edit-src-beg-marker))
+			"[" (buffer-name) "]"))
+	  (set (if (featurep 'xemacs) 'write-contents-hooks 'write-contents-functions)
+	       '(org-edit-src-save)))
+      (setq buffer-read-only t))))
 
 (org-add-hook 'org-src-mode-hook 'org-src-mode-configure-edit-buffer)
 

From b8c4bb27ba6ef83350f80f49b398b1a3c3336017 Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Wed, 21 Apr 2010 11:41:03 -0400
Subject: [PATCH 44/46] babel: Use org-src edit buffer for expanded body
 preview

---
 contrib/babel/lisp/org-babel.el | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index 0c3fc6452..eeeb213db 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -285,13 +285,9 @@ arguments, and pop open the results in a preview buffer."
 			 (org-babel-expand-noweb-references info) (second info))))
          (cmd (intern (concat "org-babel-expand-body:" lang)))
          (expanded (funcall (if (fboundp cmd) cmd 'org-babel-expand-body:generic)
-                            body params))
-         (buf (get-buffer-create "*Org-Babel Code Body Preview*")))
-    (with-current-buffer buf
-      (erase-buffer)
-      (insert expanded)
-      (funcall (intern (concat lang "-mode"))))
-    (pop-to-buffer buf)))
+                            body params)))
+    (org-edit-src-code
+     nil expanded (concat "*Org-Babel Preview " (buffer-name) "[ " lang " ]*"))))
 
 (defun org-babel-load-in-session (&optional arg info)
   "Load the body of the current source-code block.  Evaluate the

From 02e557745fa735561698191bf44ca8ec5168d80b Mon Sep 17 00:00:00 2001
From: Dan Davison <davison@stats.ox.ac.uk>
Date: Thu, 22 Apr 2010 18:16:13 -0400
Subject: [PATCH 45/46] org-src: different message in read-only mode

---
 lisp/ChangeLog  | 1 +
 lisp/org-src.el | 8 +++++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/lisp/ChangeLog b/lisp/ChangeLog
index b8a2f4834..45a44257c 100755
--- a/lisp/ChangeLog
+++ b/lisp/ChangeLog
@@ -55,6 +55,7 @@
 
 	* org-src.el (org-edit-src-code): Allow the org-src edit buffer to
 	be used in a read-only mode.
+	(org-edit-src-code): Different message in read-only mode
 
 2010-04-21  Carsten Dominik  <carsten.dominik@gmail.com>
 
diff --git a/lisp/org-src.el b/lisp/org-src.el
index 6a865bbe8..2c067ff34 100644
--- a/lisp/org-src.el
+++ b/lisp/org-src.el
@@ -200,19 +200,21 @@ the edited version. Optional argument CONTEXT is used by
   (let ((line (org-current-line))
 	(col (current-column))
 	(case-fold-search t)
-	(msg (substitute-command-keys
-	      "Edit, then exit with C-c ' (C-c and single quote)"))
 	(info (org-edit-src-find-region-and-lang))
 	(org-mode-p (eq major-mode 'org-mode))
 	(beg (make-marker))
 	(end (make-marker))
 	(preserve-indentation org-src-preserve-indentation)
-	block-nindent total-nindent ovl lang lang-f single lfmt begline buffer)
+	block-nindent total-nindent ovl lang lang-f single lfmt begline buffer msg)
     (if (not info)
 	nil
       (setq beg (move-marker beg (nth 0 info))
 	    end (move-marker end (nth 1 info))
 	    allow-write-back-p (null code)
+	    msg (if allow-write-back-p
+		    (substitute-command-keys
+		     "Edit, then exit with C-c ' (C-c and single quote)")
+		  "Exit with C-c ' (C-c and single quote)")
 	    code (or code (buffer-substring-no-properties beg end))
 	    lang (or (cdr (assoc (nth 2 info) org-src-lang-modes))
                      (nth 2 info))

From c12e18b6cf2341ca4ca6fcdf1d9c878ef6ee97bc Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Fri, 23 Apr 2010 11:54:31 -0600
Subject: [PATCH 46/46] babel: org-babel-reassemble-table checks for matching
 table/name dimensions

---
 contrib/babel/lisp/org-babel.el | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/contrib/babel/lisp/org-babel.el b/contrib/babel/lisp/org-babel.el
index eeeb213db..5ad484f40 100644
--- a/contrib/babel/lisp/org-babel.el
+++ b/contrib/babel/lisp/org-babel.el
@@ -739,8 +739,11 @@ of the vars, cnames and rnames."
 to the table for reinsertion to org-mode."
   (if (listp table)
       ((lambda (table)
-         (if colnames (org-babel-put-colnames table colnames) table))
-       (if rownames (org-babel-put-rownames table rownames) table))
+         (if (and colnames (listp (car table)) (= (length (car table))
+                                                  (length colnames)))
+             (org-babel-put-colnames table colnames) table))
+       (if (and rownames (= (length table) (length rownames)))
+           (org-babel-put-rownames table rownames) table))
     table))
 
 (defun org-babel-where-is-src-block-head ()