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

contrib/babel/library-of-babel.org

@@ -35,6 +35,32 @@
   The raw Org-mode text of this file can be downloaded at
   [[repofile:contrib/babel/library-of-babel.org][library-of-babel.org]]
 
+* File I/O
+** reading and writing files
+Read the contents of the file at =path= into a string.
+#+srcname: read
+#+begin_src emacs-lisp :var path=""
+  (with-temp-filebuffer path
+    (buffer-substring (point-min) (point-max)))
+#+end_src
+
+Read the lines of the file at =path= into a list.
+#+srcname: read-lines
+#+begin_src emacs-lisp :var path=""
+  (split-string
+   (with-temp-filebuffer path
+     (buffer-substring (point-min) (point-max))))
+#+end_src
+
+Write =data= to a file at =path=.  If =data= is a list, then write it
+as a table in traditional Org-mode table syntax.
+#+srcname: write
+#+begin_src emacs-lisp :var data="" :var path=""
+  (with-temp-file path
+    (org-babel-insert-result data))
+  nil
+#+end_src
+
 * Plotting code
 
 ** R

contrib/babel/lisp/langs/org-babel-ruby.el

@@ -65,13 +65,15 @@ called by `org-babel-execute-src-block'."
          (result-params (third processed-params))
          (result-type (fourth processed-params))
          (full-body (org-babel-expand-body:ruby
-                     body params processed-params)) ;; then the source block body
+                     body params processed-params))
          (result (org-babel-ruby-evaluate session full-body result-type)))
     (or (cdr (assoc :file params))
         (org-babel-reassemble-table
          result
-         (org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
-         (org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params)))))))
+         (org-babel-pick-name (nth 4 processed-params)
+			      (cdr (assoc :colnames params)))
+         (org-babel-pick-name (nth 5 processed-params)
+			      (cdr (assoc :rownames params)))))))
 
 (defun org-babel-prep-session:ruby (session params)
   "Prepare SESSION according to the header arguments specified in PARAMS."
@@ -129,9 +131,10 @@ Emacs-lisp table, otherwise return the results as a string."
   "If there is not a current inferior-process-buffer in SESSION
 then create.  Return the initialized session."
   (unless (string= session "none")
-    (let ((session-buffer (save-window-excursion (run-ruby nil session) (current-buffer))))
+    (let ((session-buffer (save-window-excursion
+			    (run-ruby nil session) (current-buffer))))
       (if (org-babel-comint-buffer-livep session-buffer)
-          session-buffer
+	  (progn (sit-for .25) session-buffer)
         (sit-for .5)
         (org-babel-ruby-initiate-session session)))))
 
@@ -175,24 +178,30 @@ last statement in BODY, as elisp."
            (with-temp-buffer
              (insert body)
              ;; (message "buffer=%s" (buffer-string)) ;; debugging
-             (org-babel-shell-command-on-region (point-min) (point-max) "ruby" 'current-buffer 'replace)
+             (org-babel-shell-command-on-region
+	      (point-min) (point-max) "ruby" 'current-buffer 'replace)
              (buffer-string)))
           (value
-           (let* ((tmp-file (make-temp-file "ruby-functional-results")) exit-code
+           (let* ((tmp-file (make-temp-file "ruby-functional-results"))
+		  exit-code
 		  (stderr
 		   (with-temp-buffer
 		     (insert (format (if (member "pp" result-params)
 					 org-babel-ruby-pp-wrapper-method
-				       org-babel-ruby-wrapper-method) body tmp-file))
-		     ;; (message "buffer=%s" (buffer-string)) ;; debugging
+				       org-babel-ruby-wrapper-method)
+				     body tmp-file))
 		     (setq exit-code
-			   (org-babel-shell-command-on-region (point-min) (point-max) "ruby" nil 'replace (current-buffer)))
+			   (org-babel-shell-command-on-region
+			    (point-min) (point-max) "ruby"
+			    nil 'replace (current-buffer)))
 		     (buffer-string))))
 	     (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
              (let ((raw (with-temp-buffer
-			  (insert-file-contents (org-babel-maybe-remote-file tmp-file))
+			  (insert-file-contents
+			   (org-babel-maybe-remote-file tmp-file))
 			  (buffer-string))))
-               (if (or (member "code" result-params) (member "pp" result-params))
+               (if (or (member "code" result-params)
+		       (member "pp" result-params))
                    raw
                  (org-babel-ruby-table-or-string raw)))))))
     ;; comint session evaluation
@@ -203,11 +212,13 @@ last statement in BODY, as elisp."
                             org-babel-ruby-pp-last-value-eval
                           org-babel-ruby-last-value-eval)
                    org-babel-ruby-eoe-indicator) "\n"))
-           (raw (org-babel-comint-with-output buffer org-babel-ruby-eoe-indicator t
+           (raw (org-babel-comint-with-output
+		    buffer org-babel-ruby-eoe-indicator t
                   (insert full-body) (comint-send-input nil t)))
-           (results (cdr (member org-babel-ruby-eoe-indicator
-                                 (reverse (mapcar #'org-babel-ruby-read-string
-                                                  (mapcar #'org-babel-trim raw)))))))
+           (results (cdr (member
+			  org-babel-ruby-eoe-indicator
+			  (reverse (mapcar #'org-babel-ruby-read-string
+					   (mapcar #'org-babel-trim raw)))))))
       (case result-type
         (output (mapconcat #'identity (reverse (cdr results)) "\n"))
         (value

contrib/babel/lisp/org-babel-comint.el

@@ -52,38 +52,53 @@ body inside the protection of `save-window-excursion' and
        (set-buffer ,buffer)
        ,@body)))
 
-(defmacro org-babel-comint-with-output (buffer eoe-indicator remove-echo &rest body)
+(defmacro org-babel-comint-with-output
+  (buffer eoe-indicator remove-echo &rest body)
   "Evaluate BODY in BUFFER, wait until EOE-INDICATOR appears in
 output, then return all process output.  This ensures that the
 filter is removed in case of an error or user `keyboard-quit'
 during execution of body."
   (declare (indent 3))
   `(org-babel-comint-in-buffer ,buffer
-     (let ((string-buffer ""))
+     (let ((string-buffer "") dangling-text)
        (flet ((my-filt (text) (setq string-buffer (concat string-buffer text))))
          ;; setup filter
          (add-hook 'comint-output-filter-functions 'my-filt)
          (unwind-protect
              (progn
-               ;; pass FULL-BODY to process
+               ;; got located, and save dangling text
                (goto-char (process-mark (get-buffer-process (current-buffer))))
+	       (let ((start (point))
+		     (end (point-max)))
+		 (setq dangling-text (buffer-substring start end))
+		 (delete-region start end))
+	       ;; pass FULL-BODY to process
                ,@body
                ;; wait for end-of-evaluation indicator
                (while (progn
                         (goto-char comint-last-input-end)
                         (not (save-excursion
-			       (and (re-search-forward comint-prompt-regexp nil t)
-				    (re-search-forward (regexp-quote ,eoe-indicator) nil t)))))
+			       (and (re-search-forward
+				     comint-prompt-regexp nil t)
+				    (re-search-forward
+				     (regexp-quote ,eoe-indicator) nil t)))))
                  (accept-process-output (get-buffer-process (current-buffer)))
-                 ;; ;; thought this would allow async background running, but I was wrong...
-                 ;; (run-with-timer .5 .5 'accept-process-output (get-buffer-process (current-buffer)))
-                 ))
+                 ;; thought the following this would allow async
+                 ;; background running, but I was wrong...
+                 ;; (run-with-timer .5 .5 'accept-process-output
+		 ;; 		 (get-buffer-process (current-buffer)))
+                 )
+	       ;; replace cut dangling text
+	       (goto-char (process-mark (get-buffer-process (current-buffer))))
+	       (insert dangling-text))
            ;; remove filter
            (remove-hook 'comint-output-filter-functions 'my-filt)))
        ;; remove echo'd FULL-BODY from input
        (if (and ,remove-echo
 		(string-match
-		 (replace-regexp-in-string "\n" "\r\n" (regexp-quote ,full-body)) string-buffer))
+		 (replace-regexp-in-string
+		  "\n" "[\r\n]+" (regexp-quote ,full-body))
+		 string-buffer))
            (setq raw (substring string-buffer (match-end 0))))
        (split-string string-buffer comint-prompt-regexp))))
 

contrib/babel/lisp/org-babel-exp.el

@@ -121,18 +121,25 @@ options are taken from `org-babel-default-header-args'."
 (defun org-babel-exp-do-export (info type)
   "Return a string containing the exported content of the current
 code block respecting the value of the :exports header argument."
-  (case (intern (or (cdr (assoc :exports (third info))) "code"))
-    ('none "")
-    ('code (org-babel-exp-code info type))
-    ('results (org-babel-exp-results info type))
-    ('both (concat (org-babel-exp-code info type)
-                   "\n\n"
-                   (org-babel-exp-results info type)))))
+  (flet ((silently () (let ((session (cdr (assoc :session (third info)))))
+			(when (and session
+				   (not (equal "none" session))
+				   (not (assoc :noeval (third info))))
+			  (org-babel-exp-results info type 'silent))))
+	 (clean () (org-babel-remove-result info)))
+    (case (intern (or (cdr (assoc :exports (third info))) "code"))
+      ('none (silently) (clean) "")
+      ('code (silently) (clean) (org-babel-exp-code info type))
+      ('results (org-babel-exp-results info type))
+      ('both (concat (org-babel-exp-code info type)
+		     "\n\n"
+		     (org-babel-exp-results info type))))))
 
 (defun org-babel-exp-code (info type)
   "Return the code the current code block in a manner suitable
 for exportation by org-mode.  This function is called by
-`org-babel-exp-do-export'."
+`org-babel-exp-do-export'.  The code block will not be
+evaluated."
   (let ((lang (first info))
         (body (second info))
         (switches (fourth info))
@@ -165,10 +172,12 @@ for exportation by org-mode.  This function is called by
 		   call-line))
           ((t (format ": %s\n" call-line)))))))))
 
-(defun org-babel-exp-results (info type)
+(defun org-babel-exp-results (info type &optional silent)
   "Return the results of the current code block in a manner
 suitable for exportation by org-mode.  This function is called by
-`org-babel-exp-do-export'."
+`org-babel-exp-do-export'.  The code block will be evaluated.
+Optional argument SILENT can be used to inhibit insertion of
+results into the buffer."
   (let ((lang (first info))
 	(body (second info))
 	(params
@@ -189,28 +198,31 @@ suitable for exportation by org-mode.  This function is called by
         (let ((raw (org-babel-execute-src-block
                     nil info '((:results . "silent"))))
               (result-params (split-string (cdr (assoc :results params)))))
-          (cond ;; respect the value of the :results header argument
-           ((member "file" result-params)
-            (org-babel-result-to-file raw))
-           ((or (member "raw" result-params) (member "org" result-params))
-            (format "%s" raw))
-           ((member "code" result-params)
-            (format "src_%s{%s}" lang raw))
-           (t
-            (if (stringp raw)
-		(if (= 0 (length raw)) "=(no results)="
-		  (format "=%s=" raw))
-	      (format "=%S=" raw))))))
+          (unless silent
+	    (cond ;; respect the value of the :results header argument
+	     ((member "file" result-params)
+	      (org-babel-result-to-file raw))
+	     ((or (member "raw" result-params) (member "org" result-params))
+	      (format "%s" raw))
+	     ((member "code" result-params)
+	      (format "src_%s{%s}" lang raw))
+	     (t
+	      (if (stringp raw)
+		  (if (= 0 (length raw)) "=(no results)="
+		    (format "=%s=" raw))
+		(format "=%S=" raw)))))))
       ('block
           (org-babel-execute-src-block
-           nil nil (org-babel-merge-params params '((:results . "replace"))))
+           nil nil (org-babel-merge-params
+		    params `((:results . ,(if silent "silent" "replace")))))
         "")
       ('lob
        (save-excursion
 	 (re-search-backward org-babel-lob-one-liner-regexp nil t)
 	 (org-babel-execute-src-block
-	  nil (list lang body (org-babel-merge-params
-			       params '((:results . "replace"))))) "")))))
+	  nil (list lang body
+		    (org-babel-merge-params
+		     params `((:results . ,(if silent "silent" "replace")))))) "")))))
 
 (provide 'org-babel-exp)
 ;;; org-babel-exp.el ends here

contrib/babel/lisp/org-babel-tangle.el

@@ -255,7 +255,8 @@ form
 					 "no")
                               (fifth spec)))))
       (insert-comment (format "[[%s][%s]]" (org-link-escape link) source-name))
-      (insert (format "\n%s\n" (org-babel-chomp body)))
+      (insert (format "\n%s\n" (replace-regexp-in-string
+				"^," "" (org-babel-chomp body))))
       (insert-comment (format "%s ends here" source-name)))))
 
 (provide 'org-babel-tangle)

contrib/babel/lisp/org-babel.el

@@ -46,7 +46,9 @@ then run `org-babel-execute-src-block'."
 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)))
+    (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
@@ -75,7 +77,9 @@ to `org-open-at-point'."
 then run `org-babel-load-in-session'."
   (interactive)
   (let ((info (org-babel-get-src-block-info)))
-    (if info (progn (org-babel-load-in-session current-prefix-arg info) t) nil)))
+    (if info
+	(progn (org-babel-load-in-session current-prefix-arg info) t)
+      nil)))
 
 (add-hook 'org-metaup-hook 'org-babel-load-in-session-maybe)
 
@@ -89,7 +93,8 @@ then run `org-babel-pop-to-session'."
 (add-hook 'org-metadown-hook 'org-babel-pop-to-session-maybe)
 
 (defconst org-babel-header-arg-names
-  '(cache cmdline colnames dir exports file noweb results session tangle var)
+  '(cache cmdline colnames dir exports file noweb results
+	  session tangle var noeval)
   "Common header arguments used by org-babel.  Note that
 individual languages may define their own language specific
 header arguments as well.")
@@ -384,10 +389,11 @@ the current buffer."
   "Call `org-babel-execute-src-block' on every source block in
 the current subtree."
   (interactive "P")
-  (save-excursion
-    (org-narrow-to-subtree)
-    (org-babel-execute-buffer)
-    (widen)))
+  (save-restriction
+    (save-excursion
+      (org-narrow-to-subtree)
+      (org-babel-execute-buffer)
+      (widen))))
 
 (defun org-babel-get-src-block-info (&optional header-vars-only)
   "Get information of the current source block.
@@ -965,7 +971,7 @@ code ---- the results are extracted in the syntax of the source
 					  (listp (cdr (car result)))))
 				 result (list result))
 			     '(:fmt (lambda (cell) (format "%s" cell)))) "\n"))
-	    (goto-char beg) (org-cycle))
+	    (goto-char beg) (org-table-align))
 	   ((member "file" result-params)
 	    (insert result))
 	   ((member "html" result-params)