Merge branch 'master' of git@github.com:eschulte/rorg

litorgy/litorgy-R.el

@@ -1,105 +0,0 @@
-;;; litorgy-R.el --- litorgy functions for R code evaluation
-
-;; Copyright (C) 2009 Eric Schulte, Dan Davison, Austin F. Frank
-
-;; Author: Eric Schulte, Dan Davison, Austin F. Frank
-;; Keywords: literate programming, reproducible research
-;; Homepage: http://orgmode.org
-;; Version: 0.01
-
-;;; License:
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-
-;; Litorgy support for evaluating R code
-
-;;; Code:
-(require 'litorgy)
-
-(litorgy-add-interpreter "R")
-
-(defun litorgy-execute:R (body params)
-  "Execute a block of R code with litorgy.  This function is
-called by `litorgy-execute-src-block'."
-  (save-window-excursion
-    (let (results)
-      (message "executing R code block...")
-      (litorgy-initiate-R-buffer)
-      (mapc (lambda (line) (litorgy-R-input-command line)) (butlast (split-string body "[\r\n]")))
-      (litorgy-R-last-output))))
-
-;; Maybe the following be replaced with a method using `ess-execute',
-;; I went with the following functions because I wrote them and they
-;; are what I know
-;;
-;; (not the best reasons for making design decisions)
-
-(defvar litorgy-R-buffer nil
-  "Holds the buffer for the current R process")
-
-(defun litorgy-initiate-R-buffer ()
-  "If there is not a current R process then create one."
-  (unless (and (buffer-live-p litorgy-R-buffer) (get-buffer litorgy-R-buffer))
-    (save-excursion
-      (R)
-      (setf litorgy-R-buffer (current-buffer))
-      (litorgy-R-wait-for-output)
-      (litorgy-R-input-command ""))))
-
-(defun litorgy-R-command-to-string (command)
-  "Send a command to R, and return the results as a string."
-  (litorgy-R-input-command command)
-  (litorgy-R-last-output))
-
-(defun litorgy-R-input-command (command)
-  "Pass COMMAND to the R process running in `litorgy-R-buffer'."
-  (save-excursion
-    (save-match-data
-      (set-buffer litorgy-R-buffer)
-      (goto-char (process-mark (get-buffer-process (current-buffer))))
-      (insert command)
-      (comint-send-input)
-      (litorgy-R-wait-for-output))))
-
-(defun litorgy-R-wait-for-output ()
-  "Wait until output arrives"
-  (save-excursion
-    (save-match-data
-      (set-buffer litorgy-R-buffer)
-      (while (progn
-	       (goto-char comint-last-input-end)
-	       (not (re-search-forward comint-prompt-regexp nil t)))
-	(accept-process-output (get-buffer-process (current-buffer)))))))
-
-(defun litorgy-R-last-output ()
-  "Return the last R output as a string"
-  (save-excursion
-    (save-match-data
-      (set-buffer litorgy-R-buffer)
-      (goto-char (process-mark (get-buffer-process (current-buffer))))
-      (forward-line 0)
-      (let ((raw (buffer-substring comint-last-input-end (- (point) 1))))
-	(if (string-match "\n" raw)
-	    raw
-	  (and (string-match "\\[[[:digit:]+]\\] *\\(.*\\)$" raw)
-	       (message raw)
-	       (message (match-string 1 raw))
-	       (match-string 1 raw)))))))
-
-(provide 'litorgy-R)
-;;; litorgy-R.el ends here

litorgy/litorgy-lisp.el

@@ -0,0 +1,46 @@
+;;; litorgy-lisp.el --- litorgy functions for lisp code evaluation
+
+;; Copyright (C) 2009 Eric Schulte, Dan Davison, Austin F. Frank
+
+;; Author: Eric Schulte, Dan Davison, Austin F. Frank
+;; Keywords: literate programming, reproducible research
+;; Homepage: http://orgmode.org
+;; Version: 0.01
+
+;;; License:
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+
+;; Litorgy support for evaluating lisp code
+
+;;; Code:
+(require 'litorgy)
+
+(litorgy-add-interpreter "emacs-lisp")
+
+(defun litorgy-execute:emacs-lisp (body params)
+  "Execute a block of emacs-lisp code with litorgy.  This
+function is called by `litorgy-execute-src-block'."
+  (save-window-excursion
+    (let ((vars (litorgy-reference-variables params))
+          (print-level nil) (print-length nil) results)
+      (message "executing emacs-lisp code block...")
+      (format "%S" (eval (read body))))))
+
+(provide 'litorgy-lisp)
+;;; litorgy-lisp.el ends here

litorgy/litorgy-reference.el

@@ -0,0 +1,83 @@
+;;; litorgy-reference.el --- litorgical functions for referencing external data
+
+;; Copyright (C) 2009 Eric Schulte, Dan Davison, Austin F. Frank
+
+;; Author: Eric Schulte, Dan Davison, Austin F. Frank
+;; Keywords: literate programming, reproducible research
+;; Homepage: http://orgmode.org
+;; Version: 0.01
+
+;;; License:
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+
+;; Functions for referencing data from the header arguments of a
+;; litorgical block.  The syntax of such a reference should be
+;;
+;;   #+VAR: variable-name=file:resource-id
+;;
+;; - variable-name :: the name of the variable to which the value
+;;                    will be assigned
+;;                    
+;; - file :: path to the file containing the resource, or omitted if
+;;           resource is in the current file
+;;
+;; - resource-id :: the id or name of the resource, or 'previous' to
+;;                  grab the previous table, or 'next' to grab the
+;;                  next table
+;;
+;; So an example of a simple src block referencing table data in the
+;; same file would be
+;;
+;; #+var: table previous
+;; #+begin_src emacs-lisp
+;; (message table)
+;; #+end_src
+;;
+
+;;; Code:
+(require 'litorgy)
+
+(defun litorgy-reference-variables (params)
+  "Takes a parameter alist, and return an alist of variable
+names, and the string representation of the related value."
+  (mapcar #'litorgy-reference-parse
+   (delq nil (mapcar (lambda (pair) (if (= (car pair) :var) (cdr pair))) params))))
+
+(defun litorgy-reference-parse (reference)
+  "Parse a reference to an external resource returning a list
+with two elements.  The first element of the list will be the
+name of the variable, and the second will be an emacs-lisp
+representation of the value of the variable."
+  (save-excursion
+    (if (string-match "(.+)=(.+)" reference)
+      (let ((var (match-string 1 reference))
+            (ref (match-string 2 reference)))
+        (when (string-match "(.+):(.+)" reference)
+          (find-file (match-string 1 reference))
+          (setf ref (match-string 2 reference)))
+        ;; follow the reference in the current file
+        (case ref
+          ("previous"
+           )
+          ("next")
+          (t ))
+        ))))
+
+(provide 'litorgy-reference)
+;;; litorgy-reference.el ends here

litorgy/litorgy.el

@@ -93,8 +93,8 @@ lisp code use the `litorgy-add-interpreter' function."
 (defun litorgy-execute-src-block (&optional arg)
   "Execute the current source code block, and dump the results
 into the buffer immediately following the block.  Results are
-commented by `litorgy-make-region-example'.  With optional prefix
+commented by `org-toggle-fixed-width-section'.  With optional
-don't dump results into buffer."
+prefix don't dump results into buffer."
   (interactive "P")
   (let* ((info (litorgy-get-src-block-info))
          (lang (first info))
@@ -159,7 +159,10 @@ existing results currently located after the source block."
     (let ((beg (point))
           (end (progn (insert result)
                       (point))))
-      (litorgy-make-region-example beg end))))
+      (save-excursion
+        (set-mark beg)
+        (goto-char end)
+        (org-toggle-fixed-width-section nil)))))
 
 (defun litorgy-remove-result ()
   "Remove the result following the current source block"
@@ -175,20 +178,6 @@ existing results currently located after the source block."
                                    (forward-line -1)
                                    (point)))))
 
-(defun litorgy-make-region-example (beg end)
-  "Comment out region using the ': ' org example quote."
-  (interactive "*r")
-  (let ((size (abs (- (line-number-at-pos end)
-		      (line-number-at-pos beg)))))
-    (if (= size 0)
-	(let ((result (buffer-substring beg end)))
-	  (delete-region beg end)
-	  (insert (concat ": " result)))
-      (save-excursion
-	    (goto-char beg)
-	    (dotimes (n size)
-	      (move-beginning-of-line 1) (insert ": ") (forward-line 1))))))
-
 (defun litorgy-clean-text-properties (text)
   "Strip all properties from text return."
   (set-text-properties 0 (length text) nil text) text)

rorg.org

@@ -239,6 +239,11 @@ internal to the source-code evaluation process?
     formats for referencing data from source-code in such a way that it
     will be as source-code-language independent as possible.
     
+    Org tables already have a sophisticated reference system in place
+    that allows referencing table ranges in other files, as well as
+    specifying constants in the header arguments of a table.  This is
+    described in [[info:org:References]].
+
 **** Dan: thinking aloud re: referencing data from R
      Suppose in some R code, we want to reference data in an org
      table. I think that requires the use of 'header arguments', since