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Merge branch 'master' of git@github.com:eschulte/rorg
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Dan Davison
commit
080a1634d7
@ -1,105 +0,0 @@
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;;; litorgy-R.el --- litorgy functions for R code evaluation
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;; Copyright (C) 2009 Eric Schulte, Dan Davison, Austin F. Frank
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;; Author: Eric Schulte, Dan Davison, Austin F. Frank
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;;; License:
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation; either version 3, or (at your option)
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;; any later version.
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;;
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;; Litorgy support for evaluating R code
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;;; Code:
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(require 'litorgy)
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(litorgy-add-interpreter "R")
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(defun litorgy-execute:R (body params)
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"Execute a block of R code with litorgy. This function is
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called by `litorgy-execute-src-block'."
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(save-window-excursion
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(let (results)
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(message "executing R code block...")
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(litorgy-initiate-R-buffer)
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(mapc (lambda (line) (litorgy-R-input-command line)) (butlast (split-string body "[\r\n]")))
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(litorgy-R-last-output))))
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;; Maybe the following be replaced with a method using `ess-execute',
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;; I went with the following functions because I wrote them and they
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;; are what I know
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;;
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;; (not the best reasons for making design decisions)
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(defvar litorgy-R-buffer nil
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"Holds the buffer for the current R process")
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(defun litorgy-initiate-R-buffer ()
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"If there is not a current R process then create one."
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(unless (and (buffer-live-p litorgy-R-buffer) (get-buffer litorgy-R-buffer))
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(save-excursion
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(R)
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(setf litorgy-R-buffer (current-buffer))
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(litorgy-R-wait-for-output)
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(litorgy-R-input-command ""))))
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(defun litorgy-R-command-to-string (command)
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"Send a command to R, and return the results as a string."
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(litorgy-R-input-command command)
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(litorgy-R-last-output))
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(defun litorgy-R-input-command (command)
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"Pass COMMAND to the R process running in `litorgy-R-buffer'."
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(save-excursion
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(save-match-data
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(set-buffer litorgy-R-buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert command)
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(comint-send-input)
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(litorgy-R-wait-for-output))))
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(defun litorgy-R-wait-for-output ()
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"Wait until output arrives"
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(save-excursion
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(save-match-data
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(set-buffer litorgy-R-buffer)
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(while (progn
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(goto-char comint-last-input-end)
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(not (re-search-forward comint-prompt-regexp nil t)))
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(accept-process-output (get-buffer-process (current-buffer)))))))
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(defun litorgy-R-last-output ()
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"Return the last R output as a string"
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(save-excursion
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(save-match-data
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(set-buffer litorgy-R-buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(forward-line 0)
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(let ((raw (buffer-substring comint-last-input-end (- (point) 1))))
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(if (string-match "\n" raw)
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raw
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(and (string-match "\\[[[:digit:]+]\\] *\\(.*\\)$" raw)
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(message raw)
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(message (match-string 1 raw))
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(match-string 1 raw)))))))
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(provide 'litorgy-R)
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;;; litorgy-R.el ends here
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46
litorgy/litorgy-lisp.el
Normal file
46
litorgy/litorgy-lisp.el
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;;; litorgy-lisp.el --- litorgy functions for lisp code evaluation
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;; Copyright (C) 2009 Eric Schulte, Dan Davison, Austin F. Frank
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;; Author: Eric Schulte, Dan Davison, Austin F. Frank
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;;; License:
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation; either version 3, or (at your option)
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;; any later version.
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;;
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;; Litorgy support for evaluating lisp code
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;;; Code:
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(require 'litorgy)
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(litorgy-add-interpreter "emacs-lisp")
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(defun litorgy-execute:emacs-lisp (body params)
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"Execute a block of emacs-lisp code with litorgy. This
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function is called by `litorgy-execute-src-block'."
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(save-window-excursion
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(let ((vars (litorgy-reference-variables params))
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(print-level nil) (print-length nil) results)
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(message "executing emacs-lisp code block...")
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(format "%S" (eval (read body))))))
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(provide 'litorgy-lisp)
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;;; litorgy-lisp.el ends here
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83
litorgy/litorgy-reference.el
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83
litorgy/litorgy-reference.el
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@ -0,0 +1,83 @@
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;;; litorgy-reference.el --- litorgical functions for referencing external data
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;; Copyright (C) 2009 Eric Schulte, Dan Davison, Austin F. Frank
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;; Author: Eric Schulte, Dan Davison, Austin F. Frank
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;;; License:
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation; either version 3, or (at your option)
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;; any later version.
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;;
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;; Functions for referencing data from the header arguments of a
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;; litorgical block. The syntax of such a reference should be
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;;
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;; #+VAR: variable-name=file:resource-id
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;;
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;; - variable-name :: the name of the variable to which the value
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;; will be assigned
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;;
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;; - file :: path to the file containing the resource, or omitted if
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;; resource is in the current file
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;;
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;; - resource-id :: the id or name of the resource, or 'previous' to
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;; grab the previous table, or 'next' to grab the
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;; next table
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;;
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;; So an example of a simple src block referencing table data in the
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;; same file would be
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;;
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;; #+var: table previous
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;; #+begin_src emacs-lisp
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;; (message table)
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;; #+end_src
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;;
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;;; Code:
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(require 'litorgy)
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(defun litorgy-reference-variables (params)
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"Takes a parameter alist, and return an alist of variable
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names, and the string representation of the related value."
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(mapcar #'litorgy-reference-parse
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(delq nil (mapcar (lambda (pair) (if (= (car pair) :var) (cdr pair))) params))))
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(defun litorgy-reference-parse (reference)
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"Parse a reference to an external resource returning a list
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with two elements. The first element of the list will be the
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name of the variable, and the second will be an emacs-lisp
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representation of the value of the variable."
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(save-excursion
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(if (string-match "(.+)=(.+)" reference)
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(let ((var (match-string 1 reference))
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(ref (match-string 2 reference)))
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(when (string-match "(.+):(.+)" reference)
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(find-file (match-string 1 reference))
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(setf ref (match-string 2 reference)))
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;; follow the reference in the current file
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(case ref
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("previous"
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)
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("next")
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(t ))
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))))
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(provide 'litorgy-reference)
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;;; litorgy-reference.el ends here
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@ -93,8 +93,8 @@ lisp code use the `litorgy-add-interpreter' function."
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(defun litorgy-execute-src-block (&optional arg)
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"Execute the current source code block, and dump the results
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into the buffer immediately following the block. Results are
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commented by `litorgy-make-region-example'. With optional prefix
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don't dump results into buffer."
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commented by `org-toggle-fixed-width-section'. With optional
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prefix don't dump results into buffer."
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(interactive "P")
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(let* ((info (litorgy-get-src-block-info))
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(lang (first info))
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@ -159,7 +159,10 @@ existing results currently located after the source block."
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(let ((beg (point))
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(end (progn (insert result)
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(point))))
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(litorgy-make-region-example beg end))))
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(save-excursion
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(set-mark beg)
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(goto-char end)
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(org-toggle-fixed-width-section nil)))))
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(defun litorgy-remove-result ()
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"Remove the result following the current source block"
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@ -175,20 +178,6 @@ existing results currently located after the source block."
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(forward-line -1)
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(point)))))
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(defun litorgy-make-region-example (beg end)
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"Comment out region using the ': ' org example quote."
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(interactive "*r")
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(let ((size (abs (- (line-number-at-pos end)
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(line-number-at-pos beg)))))
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(if (= size 0)
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(let ((result (buffer-substring beg end)))
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(delete-region beg end)
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(insert (concat ": " result)))
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(save-excursion
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(goto-char beg)
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(dotimes (n size)
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(move-beginning-of-line 1) (insert ": ") (forward-line 1))))))
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(defun litorgy-clean-text-properties (text)
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"Strip all properties from text return."
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(set-text-properties 0 (length text) nil text) text)
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5
rorg.org
5
rorg.org
@ -238,6 +238,11 @@ internal to the source-code evaluation process?
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need to look more closely at that and we should try to come up with a
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formats for referencing data from source-code in such a way that it
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will be as source-code-language independent as possible.
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Org tables already have a sophisticated reference system in place
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that allows referencing table ranges in other files, as well as
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specifying constants in the header arguments of a table. This is
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described in [[info:org:References]].
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**** Dan: thinking aloud re: referencing data from R
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Suppose in some R code, we want to reference data in an org
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