2010-06-25 16:20:39 +00:00
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;;; ob-table.el --- support for calling org-babel functions from tables
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2009-05-10 21:03:26 +00:00
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2015-01-01 22:26:41 +00:00
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;; Copyright (C) 2009-2015 Free Software Foundation, Inc.
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2009-05-10 21:03:26 +00:00
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;; Author: Eric Schulte
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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2010-06-25 16:20:39 +00:00
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;; This file is part of GNU Emacs.
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2009-05-10 21:03:26 +00:00
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2010-06-25 16:20:39 +00:00
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;; GNU Emacs is free software: you can redistribute it and/or modify
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2009-05-10 21:03:26 +00:00
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;; it under the terms of the GNU General Public License as published by
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2010-06-25 16:20:39 +00:00
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; GNU Emacs is distributed in the hope that it will be useful,
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2009-05-10 21:03:26 +00:00
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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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2010-06-25 16:20:39 +00:00
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2009-05-10 21:03:26 +00:00
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;; You should have received a copy of the GNU General Public License
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2010-06-25 16:20:39 +00:00
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;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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2009-05-10 21:03:26 +00:00
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;;; Commentary:
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;; Should allow calling functions from org-mode tables using the
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2014-01-12 11:02:25 +00:00
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;; function `org-sbe' as so...
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2010-06-25 16:20:39 +00:00
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2009-05-10 21:03:26 +00:00
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;; #+begin_src emacs-lisp :results silent
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2010-06-25 16:20:39 +00:00
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;; (defun fibbd (n) (if (< n 2) 1 (+ (fibbd (- n 1)) (fibbd (- n 2)))))
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2009-05-10 21:03:26 +00:00
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;; #+end_src
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2010-06-25 16:20:39 +00:00
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Standardized code block keywords
Nick Dokos <nicholas.dokos@hp.com> writes:
> Eric Schulte <schulte.eric@gmail.com> wrote:
>
>> The attached updated patch fixes a bug in the original.
>>
>
> Minor problem in applying:
>
> ,----
> | $ git apply ~/Mail/inbox/724
> | /home/nick/Mail/inbox/724:671: trailing whitespace.
> | #+name:
> | /home/nick/Mail/inbox/724:599: new blank line at EOF.
> | +
> | warning: 2 lines add whitespace errors.
> `----
The attached version fixes these issues, Thanks -- Eric
>From 0e43d59ee8d46a63f86780a502de726271bc39de Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Fri, 28 Oct 2011 10:44:21 -0600
Subject: [PATCH] removing code block, results and call-line synonyms -- BREAKING CHANGE
Following a round of on-list discussion many code block synonyms have
been removed, moving forward the following syntax is valid.
- call lines are specified with #+call:
- code blocks are named with #+name:
- results are named with #+name:, however results generated by a code
block may still be labeled with #+results:, and tables named with
#+tblname: will be considered to be named results
The following function may be used to update an existing Org-mode
buffer to the new syntax.
(defun update-org-buffer ()
"Update an Org-mode buffer to the new data, code block and call line syntax."
(interactive)
(save-excursion
(flet ((to-re (lst) (concat "^[ \t]*#\\+" (regexp-opt lst t)
"\\(\\[\\([[:alnum:]]+\\)\\]\\)?\\:[ \t]*"))
(update (re new)
(goto-char (point-min))
(while (re-search-forward re nil t)
(replace-match new nil nil nil 1))))
(let ((old-re (to-re '("RESULTS" "DATA" "SRCNAME" "SOURCE")))
(lob-re (to-re '("LOB")))
(case-fold-search t))
(update old-re "name")
(update lob-re "call")))))
Note: If an old version of Org-mode (e.g., the one shipped with Emacs)
is installed on your system many of the important variables will
be pre-defined with a defvar and *will not* have their values
automatically updated, these include the following.
- org-babel-data-names
- org-babel-result-regexp
- org-babel-src-block-regexp
- org-babel-src-name-regexp
- org-babel-src-name-w-name-regexp
It may be necessary to either remove the source code of older
versions of Org-mode, or to explicitly evaluate the ob.el file.
* lisp/ob-exp.el (org-exp-res/src-name-cleanup): Updated
Documentation.
* lisp/ob-lob.el (org-babel-block-lob-one-liner-regexp): Updated
regular expression.
(org-babel-inline-lob-one-liner-regexp): Updated regular expression.
* lisp/ob-ref.el (org-babel-ref-resolve): Notice when something that
looks like a data results may actually be a code block.
* lisp/ob-table.el: Updated documentation.
* lisp/ob.el (org-babel-src-name-regexp): Simplified regexp.
(org-babel-get-src-block-info): Updated match strings.
(org-babel-data-names): Simplified acceptable names.
(org-babel-find-named-block): Indentation.
(org-babel-find-named-result): Updated to not return a code block as
a result.
* lisp/org.el (org-fontify-meta-lines-and-blocks-1): Removing
references to old syntactic elements.
(org-additional-option-like-keywords): Removing references to old
syntactic elements.
* contrib/babel/library-of-babel.org: Updated to make use of the new
syntax.
* testing/examples/babel-dangerous.org: Updated to make use of the new
syntax.
* testing/examples/babel.org: Updated to make use of the new syntax.
* testing/examples/ob-awk-test.org: Updated to make use of the new
syntax.
* testing/examples/ob-fortran-test.org: Updated to make use of the new
syntax.
* testing/lisp/test-ob.el: Removed two bad tests which tested the
literal values of old regular expressions rather than their
behavior.
2011-10-28 23:52:48 +00:00
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;; #+name: fibbd
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2009-05-10 21:03:26 +00:00
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;; #+begin_src emacs-lisp :var n=2 :results silent
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;; (fibbd n)
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;; #+end_src
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2010-06-25 16:20:39 +00:00
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2009-05-10 21:03:26 +00:00
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;; | original | fibbd |
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;; |----------+--------|
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;; | 0 | |
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;; | 1 | |
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;; | 2 | |
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;; | 3 | |
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;; | 4 | |
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;; | 5 | |
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;; | 6 | |
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;; | 7 | |
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;; | 8 | |
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;; | 9 | |
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2014-09-30 09:53:36 +00:00
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;; #+TBLFM: $2='(org-sbe "fibbd" (n $1))
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;; NOTE: The quotation marks around the function name, 'fibbd' here,
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;; are optional.
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2009-05-10 21:03:26 +00:00
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;;; Code:
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2012-12-11 23:58:16 +00:00
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(require 'ob-core)
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2009-05-10 21:03:26 +00:00
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2009-05-24 20:38:01 +00:00
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(defun org-babel-table-truncate-at-newline (string)
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2010-07-13 23:20:08 +00:00
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"Replace newline character with ellipses.
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If STRING ends in a newline character, then remove the newline
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2010-06-12 00:12:15 +00:00
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character and replace it with ellipses."
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2010-11-14 15:50:47 +00:00
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(if (and (stringp string) (string-match "[\n\r]\\(.\\)?" string))
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(concat (substring string 0 (match-beginning 0))
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(if (match-string 1 string) "...")) string))
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2009-05-22 15:33:28 +00:00
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2014-01-12 11:02:25 +00:00
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(defmacro org-sbe (source-block &rest variables)
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2010-07-13 23:20:08 +00:00
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"Return the results of calling SOURCE-BLOCK with VARIABLES.
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2014-04-18 12:09:37 +00:00
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Each element of VARIABLES should be a list of two elements: the
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first element is the name of the variable and second element is a
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string of its value.
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So this `org-sbe' construct
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2009-05-10 21:03:26 +00:00
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2014-09-30 09:53:36 +00:00
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(org-sbe \"source-block\" (n $2) (m 3))
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2009-05-10 21:03:26 +00:00
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2014-04-18 12:09:37 +00:00
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is the equivalent of the following source code block:
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#+begin_src emacs-lisp :var results=source-block(n=val_at_col_2, m=3) :results silent
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results
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#+end_src
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2010-03-25 17:09:38 +00:00
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2014-09-30 09:53:36 +00:00
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NOTE: The quotation marks around the function name,
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'source-block', are optional.
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2014-04-18 12:09:37 +00:00
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NOTE: By default, string variable names are interpreted as
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2010-03-25 17:09:38 +00:00
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references to source-code blocks, to force interpretation of a
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2012-03-05 17:45:25 +00:00
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cell's value as a string, prefix the identifier a \"$\" (e.g.,
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\"$$2\" instead of \"$2\" or \"$@2$2\" instead of \"@2$2\").
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2011-10-07 18:16:33 +00:00
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2014-04-18 12:09:37 +00:00
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NOTE: It is also possible to pass header arguments to the code
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2011-10-07 18:16:33 +00:00
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block. In this case a table cell should hold the string value of
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the header argument which can then be passed before all variables
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as shown in the example below.
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| 1 | 2 | :file nothing.png | nothing.png |
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2015-09-21 04:24:12 +00:00
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#+TBLFM: @1$4=\\='(org-sbe test-sbe $3 (x $1) (y $2))"
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Backport changes from Emacs revs 115081 and 115082
2013-11-12 Stefan Monnier <monnier@iro.umontreal.ca>
Address some byte-compiler warnings.
* ob-abc.el (org-babel-expand-body:abc): Use dolist.
(org-babel-execute:abc): Fix regexp quoting.
* ob-calc.el (org--var-syms): Rename from `var-syms'.
* ob-lilypond.el (ly-compile-lilyfile): Remove redundant let-binding.
* ob-table.el (sbe): Move debug declaration.
* org-clock.el (org--msg-extra): Rename from `msg-extra'.
* org.el (org-version): Avoid var name starting with _.
(org-inhibit-startup, org-called-with-limited-levels)
(org-link-search-inhibit-query, org-time-was-given)
(org-end-time-was-given, org-def, org-defdecode, org-with-time):
* org-colview.el (org-agenda-overriding-columns-format):
* org-agenda.el (org-agenda-multi, org-depend-tag-blocked)
(org-agenda-show-log-scoped):
* ob-python.el (py-which-bufname, python-shell-buffer-name):
* ob-haskell.el (org-export-copy-to-kill-ring):
* ob-exp.el (org-link-search-inhibit-query):
* ob-R.el (ess-eval-visibly-p):
* ob-core.el (org-src-window-setup): Declare before use.
(org-babel-expand-noweb-references): Remove unused `blocks-in-buffer'.
* ox-odt.el (org-odt-hfy-face-to-css):
* org-src.el (org-src-associate-babel-session, org-src-get-lang-mode):
* org-bibtex.el (org-bibtex-get, org-bibtex-ask, org-bibtex)
(org-bibtex-check):
* ob-tangle.el (org-babel-tangle, org-babel-spec-to-string)
(org-babel-tangle-single-block, org-babel-tangle-comment-links):
* ob-table.el (sbe):
* ob-sqlite.el (org-babel-sqlite-expand-vars):
* ob-sql.el (org-babel-sql-expand-vars):
* ob-shen.el (org-babel-execute:shen):
* ob-sh.el (org-babel-execute:sh, org-babel-sh-evaluate):
* ob-scala.el (org-babel-scala-evaluate):
* ob-ruby.el (org-babel-ruby-table-or-string)
(org-babel-ruby-evaluate):
* ob-python.el (org-babel-python-table-or-string)
(org-babel-python-evaluate-external-process)
(org-babel-python-evaluate-session):
* ob-picolisp.el (org-babel-execute:picolisp):
* ob-perl.el (org-babel-perl-evaluate):
* ob-maxima.el (org-babel-execute:maxima):
* ob-lisp.el (org-babel-execute:lisp):
* ob-java.el (org-babel-execute:java):
* ob-io.el (org-babel-io-evaluate):
* ob-haskell.el (org-babel-execute:haskell):
* ob-fortran.el (org-babel-execute:fortran):
* ob-exp.el (org-babel-exp-code):
* ob-emacs-lisp.el (org-babel-execute:emacs-lisp):
* ob-ditaa.el (org-babel-execute:ditaa):
* ob-core.el (org-babel-execute-src-block, org-babel-sha1-hash)
(org-babel-parse-header-arguments, org-babel-reassemble-table)
(org-babel-goto-src-block-head, org-babel-mark-block)
(org-babel-expand-noweb-references, org-babel-script-escape)
(org-babel-process-file-name):
* ob-clojure.el (org-babel-execute:clojure):
* ob-calc.el (org-babel-execute:calc):
* ob-awk.el (org-babel-execute:awk):
* ob-abc.el (org-babel-execute:abc):
* ob-R.el (org-babel-expand-body:R):
* ob-C.el (org-babel-C-execute): Avoid deprecated ((lambda) ...).
2013-11-12 Glenn Morris <rgm@gnu.org>
* ox-html.el (org-html-scripts): Add 2013 to copyright years.
(org-html-infojs-template): Copyright holder to FSF.
2013-11-12 19:57:31 +00:00
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(declare (debug (form form)))
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2011-10-07 18:16:33 +00:00
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(let* ((header-args (if (stringp (car variables)) (car variables) ""))
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(variables (if (stringp (car variables)) (cdr variables) variables)))
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(let* (quote
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(variables
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(mapcar
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(lambda (var)
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;; ensure that all cells prefixed with $'s are strings
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(cons (car var)
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(delq nil (mapcar
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(lambda (el)
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(if (eq '$ el)
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2012-03-05 14:32:03 +00:00
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(prog1 nil (setq quote t))
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2013-07-14 22:20:49 +00:00
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(prog1
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(cond
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(quote (format "\"%s\"" el))
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((stringp el) (org-no-properties el))
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(t el))
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2011-10-07 18:16:33 +00:00
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(setq quote nil))))
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(cdr var)))))
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variables)))
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(unless (stringp source-block)
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(setq source-block (symbol-name source-block)))
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Backport changes from Emacs revs 115081 and 115082
2013-11-12 Stefan Monnier <monnier@iro.umontreal.ca>
Address some byte-compiler warnings.
* ob-abc.el (org-babel-expand-body:abc): Use dolist.
(org-babel-execute:abc): Fix regexp quoting.
* ob-calc.el (org--var-syms): Rename from `var-syms'.
* ob-lilypond.el (ly-compile-lilyfile): Remove redundant let-binding.
* ob-table.el (sbe): Move debug declaration.
* org-clock.el (org--msg-extra): Rename from `msg-extra'.
* org.el (org-version): Avoid var name starting with _.
(org-inhibit-startup, org-called-with-limited-levels)
(org-link-search-inhibit-query, org-time-was-given)
(org-end-time-was-given, org-def, org-defdecode, org-with-time):
* org-colview.el (org-agenda-overriding-columns-format):
* org-agenda.el (org-agenda-multi, org-depend-tag-blocked)
(org-agenda-show-log-scoped):
* ob-python.el (py-which-bufname, python-shell-buffer-name):
* ob-haskell.el (org-export-copy-to-kill-ring):
* ob-exp.el (org-link-search-inhibit-query):
* ob-R.el (ess-eval-visibly-p):
* ob-core.el (org-src-window-setup): Declare before use.
(org-babel-expand-noweb-references): Remove unused `blocks-in-buffer'.
* ox-odt.el (org-odt-hfy-face-to-css):
* org-src.el (org-src-associate-babel-session, org-src-get-lang-mode):
* org-bibtex.el (org-bibtex-get, org-bibtex-ask, org-bibtex)
(org-bibtex-check):
* ob-tangle.el (org-babel-tangle, org-babel-spec-to-string)
(org-babel-tangle-single-block, org-babel-tangle-comment-links):
* ob-table.el (sbe):
* ob-sqlite.el (org-babel-sqlite-expand-vars):
* ob-sql.el (org-babel-sql-expand-vars):
* ob-shen.el (org-babel-execute:shen):
* ob-sh.el (org-babel-execute:sh, org-babel-sh-evaluate):
* ob-scala.el (org-babel-scala-evaluate):
* ob-ruby.el (org-babel-ruby-table-or-string)
(org-babel-ruby-evaluate):
* ob-python.el (org-babel-python-table-or-string)
(org-babel-python-evaluate-external-process)
(org-babel-python-evaluate-session):
* ob-picolisp.el (org-babel-execute:picolisp):
* ob-perl.el (org-babel-perl-evaluate):
* ob-maxima.el (org-babel-execute:maxima):
* ob-lisp.el (org-babel-execute:lisp):
* ob-java.el (org-babel-execute:java):
* ob-io.el (org-babel-io-evaluate):
* ob-haskell.el (org-babel-execute:haskell):
* ob-fortran.el (org-babel-execute:fortran):
* ob-exp.el (org-babel-exp-code):
* ob-emacs-lisp.el (org-babel-execute:emacs-lisp):
* ob-ditaa.el (org-babel-execute:ditaa):
* ob-core.el (org-babel-execute-src-block, org-babel-sha1-hash)
(org-babel-parse-header-arguments, org-babel-reassemble-table)
(org-babel-goto-src-block-head, org-babel-mark-block)
(org-babel-expand-noweb-references, org-babel-script-escape)
(org-babel-process-file-name):
* ob-clojure.el (org-babel-execute:clojure):
* ob-calc.el (org-babel-execute:calc):
* ob-awk.el (org-babel-execute:awk):
* ob-abc.el (org-babel-execute:abc):
* ob-R.el (org-babel-expand-body:R):
* ob-C.el (org-babel-C-execute): Avoid deprecated ((lambda) ...).
2013-11-12 Glenn Morris <rgm@gnu.org>
* ox-html.el (org-html-scripts): Add 2013 to copyright years.
(org-html-infojs-template): Copyright holder to FSF.
2013-11-12 19:57:31 +00:00
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(let ((result
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(if (and source-block (> (length source-block) 0))
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(let ((params
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;; FIXME: Why `eval'?!?!?
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(eval `(org-babel-parse-header-arguments
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(concat
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":var results="
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,source-block
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"[" ,header-args "]"
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"("
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(mapconcat
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(lambda (var-spec)
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(if (> (length (cdr var-spec)) 1)
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(format "%S='%S"
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(car var-spec)
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(mapcar #'read (cdr var-spec)))
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(format "%S=%s"
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(car var-spec) (cadr var-spec))))
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',variables ", ")
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")")))))
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(org-babel-execute-src-block
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nil (list "emacs-lisp" "results" params)
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'((:results . "silent"))))
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"")))
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(org-babel-trim (if (stringp result) result (format "%S" result)))))))
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2009-05-10 21:03:26 +00:00
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2010-06-11 23:02:42 +00:00
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(provide 'ob-table)
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2010-06-25 16:20:39 +00:00
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2011-08-15 18:04:38 +00:00
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2010-06-25 16:20:39 +00:00
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2010-06-11 23:02:42 +00:00
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;;; ob-table.el ends here
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