2010-06-25 12:20:39 -04:00
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;;; ob-lob.el --- functions supporting the Library of Babel
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2009-06-12 20:26:28 -04:00
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2012-01-03 12:47:01 -05:00
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;; Copyright (C) 2009-2012 Free Software Foundation, Inc.
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2009-06-12 20:26:28 -04:00
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2011-08-24 14:55:11 -04:00
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;; Author: Eric Schulte
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;; Dan Davison
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2009-06-12 20:26:28 -04:00
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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2010-06-25 12:20:39 -04:00
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;; This file is part of GNU Emacs.
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2009-06-12 20:26:28 -04:00
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2010-06-25 12:20:39 -04:00
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;; GNU Emacs is free software: you can redistribute it and/or modify
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2009-06-12 20:26:28 -04:00
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;; it under the terms of the GNU General Public License as published by
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2010-06-25 12:20:39 -04:00
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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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2009-06-12 20:26:28 -04:00
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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 12:20:39 -04:00
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2009-06-12 20:26:28 -04:00
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;; You should have received a copy of the GNU General Public License
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2010-06-25 12:20:39 -04:00
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;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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2009-06-12 20:26:28 -04:00
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;;; Code:
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2011-06-26 20:13:14 -04:00
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(eval-when-compile
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(require 'cl))
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2010-06-11 19:02:42 -04:00
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(require 'ob)
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(require 'ob-table)
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2009-06-14 10:54:55 -04:00
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2011-11-15 10:38:41 -05:00
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(declare-function org-babel-in-example-or-verbatim "ob-exp" nil)
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2009-06-14 17:10:04 -04:00
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(defvar org-babel-library-of-babel nil
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2010-07-13 19:20:08 -04:00
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"Library of source-code blocks.
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This is an association list. Populate the library by adding
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files to `org-babel-lob-files'.")
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2009-06-14 17:10:04 -04:00
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(defcustom org-babel-lob-files '()
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2010-07-13 19:20:08 -04:00
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"Files used to populate the `org-babel-library-of-babel'.
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To add files to this list use the `org-babel-lob-ingest' command."
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2009-06-14 17:10:04 -04:00
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:group 'org-babel
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Add version tag "24.1" for options introduced since Emacs 23.4 (and <= 24.1)
* org-exp.el (org-export-kill-product-buffer-when-displayed)
(org-export-initial-scope, org-export-date-timestamp-format)
(org-export-with-tasks, org-export-email-info)
(org-export-table-remove-empty-lines): Add version tag.
* org-mobile.el (org-mobile-files-exclude-regexp)
(org-mobile-use-encryption, org-mobile-encryption-tempfile)
(org-mobile-encryption-password, org-mobile-agendas): Add
version tag.
* ob-plantuml.el (org-plantuml-jar-path): Add version tag.
* org.el (org-babel-load-languages, org-clone-delete-id)
(org-log-buffer-setup-hook)
(org-loop-over-headlines-in-active-region)
(org-use-sub-superscripts, org-startup-with-beamer-mode)
(org-startup-with-inline-images, org-ctrl-k-protect-subtree)
(org-catch-invisible-edits)
(org-link-search-must-match-exact-headline)
(org-confirm-shell-link-not-regexp)
(org-confirm-elisp-link-not-regexp, org-log-refile)
(org-refile-use-cache)
(org-refile-active-region-within-subtree)
(org-todo-repeat-to-state, org-get-priority-function)
(org-agenda-jump-prefer-future)
(org-read-date-force-compatible-dates)
(org-use-effective-time)
(org-complete-tags-always-offer-all-agenda-tags)
(org-properties-postprocess-alist)
(org-format-latex-signal-error)
(org-latex-to-mathml-jar-file)
(org-latex-to-mathml-convert-command)
(org-export-latex-default-packages-alist)
(org-hidden-keywords, org-pretty-entities)
(org-pretty-entities-include-sub-superscripts)
(org-src-fontify-natively, org-effort-durations)
(org-speed-command-hook): Add version tag.
* org-html.el (org-export-html-footnote-separator)
(org-export-html-mathjax-options)
(org-export-html-mathjax-template)
(org-export-html-headline-anchor-format)
(org-export-html-preamble-format)
(org-export-html-postamble-format)
(org-export-html-table-align-individual-fields)
(org-export-html-protect-char-alist, org-export-html-divs):
Add version tag.
* org-ctags.el (org-ctags-path-to-ctags)
(org-ctags-open-link-functions)
(org-ctags-new-topic-template): Add version tag.
* ob-exp.el (org-export-babel-evaluate): Add version tag.
* org-beamer.el (org-beamer-use-parts)
(org-beamer-frame-level, org-beamer-frame-default-options)
(org-beamer-column-view-format, org-beamer-themes)
(org-beamer-environments-extra, org-beamer-fragile-re)
(org-beamer-outline-frame-title)
(org-beamer-outline-frame-options): Add version tag.
* org-wl.el (org-wl-link-remove-filter)
(org-wl-shimbun-prefer-web-links)
(org-wl-nntp-prefer-web-links, org-wl-disable-folder-check)
(org-wl-namazu-default-index): Add version tag.
* org-clock.el (org-task-overrun-text)
(org-clocktable-defaults, org-clock-clocktable-formatter)
(org-clock-clocktable-language-setup)
(org-clock-report-include-clocking-task)
(org-clock-resolve-expert): Add version tag.
* ob-lob.el (org-babel-lob-files): Add version tag.
* org-freemind.el (org-freemind-node-css-style): Add version
tag.
* org-archive.el (org-archive-reversed-order)
(org-archive-subtree-add-inherited-tags): Add version tag.
* org-bibtex.el (org-bibtex-autogen-keys, org-bibtex-prefix)
(org-bibtex-treat-headline-as-title)
(org-bibtex-export-arbitrary-fields)
(org-bibtex-key-property, org-bibtex-tags)
(org-bibtex-tags-are-keywords, org-bibtex-no-export-tags)
(org-bibtex-type-property-name): Add version tag.
* org-timer.el (org-timer-default-timer): Add version tag.
* org-taskjuggler.el (org-export-taskjuggler-extension)
(org-export-taskjuggler-project-tag)
(org-export-taskjuggler-resource-tag)
(org-export-taskjuggler-target-version)
(org-export-taskjuggler-default-project-version)
(org-export-taskjuggler-default-project-duration)
(org-export-taskjuggler-default-reports)
(org-export-taskjuggler-default-global-properties): Add
version tag.
* org-habit.el (org-habit-today-glyph)
(org-habit-completed-glyph): Add version tag.
* org-list.el (org-alphabetical-lists)
(org-list-ending-method, org-list-end-regexp)
(org-list-automatic-rules, org-list-use-circular-motion)
(org-list-indent-offset): Add version tag.
* ob-picolisp.el (org-babel-picolisp-cmd): Add version tag.
* org-icalendar.el (org-icalendar-alarm-time)
(org-icalendar-combined-description)
(org-icalendar-honor-noexport-tag)
(org-icalendar-date-time-format): Add version tag.
* org-src.el (org-src-tab-acts-natively): Add version tag.
* org-exp-blocks.el (org-export-blocks-postblock-hook): Add
version tag.
* org-table.el (org-table-exit-follow-field-mode-when-leaving-table)
(org-table-fix-formulas-confirm)
(org-table-duration-custom-format)
(org-table-formula-field-format): Add version tag.
* org-publish.el (org-publish-sitemap-sort-files)
(org-publish-sitemap-sort-folders)
(org-publish-sitemap-sort-ignore-case)
(org-publish-sitemap-date-format)
(org-publish-sitemap-file-entry-format): Add version tag.
* ob-js.el (org-babel-js-cmd): Add version tag.
* org-docbook.el (org-export-docbook-footnote-separator)
(org-export-docbook-xslt-stylesheet): Add version tag.
* org-entities.el (org-entities-ascii-explanatory)
(org-entities-user): Add version tag.
* ob.el (org-confirm-babel-evaluate)
(org-babel-no-eval-on-ctrl-c-ctrl-c): Add version tag.
* ob-tangle.el (org-babel-tangle-lang-exts)
(org-babel-post-tangle-hook, org-babel-pre-tangle-hook)
(org-babel-tangle-body-hook)
(org-babel-tangle-comment-format-beg)
(org-babel-tangle-comment-format-end)
(org-babel-process-comment-text): Add version tag.
* org-gnus.el (org-gnus-nnimap-query-article-no-from-file):
Add version tag.
* org-crypt.el (org-crypt-disable-auto-save): Add version tag.
* org-inlinetask.el (org-inlinetask-default-state): Add
version tag.
* ob-scheme.el (org-babel-scheme-cmd): Add version tag.
* ob-lisp.el (org-babel-lisp-dir-fmt): Add version tag.
* org-attach.el (org-attach-store-link-p): Add version tag.
* org-capture.el (org-capture-templates)
(org-capture-before-finalize-hook)
(org-capture-after-finalize-hook): Add version tag.
* org-agenda.el (org-agenda-skip-deadline-prewarning-if-scheduled)
(org-agenda-time-leading-zero, org-agenda-follow-indirect)
(org-agenda-menu-two-column, org-agenda-menu-show-matcher)
(org-agenda-timegrid-use-ampm)
(org-agenda-remove-timeranges-from-blocks)
(org-agenda-inactive-leader, org-agenda-current-time-string)
(org-agenda-show-current-time-in-grid)
(org-agenda-search-view-force-full-words)
(org-agenda-search-view-always-boolean)
(org-agenda-clock-consistency-checks)
(org-agenda-include-deadlines)
(org-agenda-move-date-from-past-immediately-to-today)
(org-agenda-day-face-function)
(org-agenda-category-icon-alist)
(org-agenda-bulk-custom-functions)
(org-agenda-insert-diary-extract-time): Add version tag.
* org-latex.el (org-export-latex-inputenc-alist)
(org-export-latex-tag-markup)
(org-export-latex-timestamp-inactive-markup)
(org-export-latex-href-format)
(org-export-latex-hyperref-format)
(org-export-latex-footnote-separator)
(org-export-latex-quotes)
(org-export-latex-table-caption-above)
(org-export-latex-listings-w-names)
(org-export-latex-minted-langs)
(org-export-latex-listings-options)
(org-export-latex-minted-options)
(org-latex-default-figure-position, org-export-pdf-logfiles):
Add version tag.
* org-faces.el (org-faces-easy-properties)
(org-fontify-quote-and-verse-blocks, org-cycle-level-faces):
Add version tag.
* ob-ditaa.el (org-ditaa-jar-option): Add version tag.
Thanks to Glenn Morris for reporting this.
2012-02-13 09:49:28 -05:00
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:version "24.1"
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2009-06-14 17:10:04 -04:00
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:type 'list)
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2011-06-24 16:53:25 -04:00
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(defvar org-babel-default-lob-header-args '((:exports . "results"))
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"Default header arguments to use when exporting #+lob/call lines.")
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2010-06-23 14:24:33 -04:00
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;;;###autoload
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2009-06-14 17:10:04 -04:00
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(defun org-babel-lob-ingest (&optional file)
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2010-10-12 06:52:29 -04:00
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"Add all named source-blocks defined in FILE to
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`org-babel-library-of-babel'."
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2011-01-31 14:33:09 -05:00
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(interactive "fFile: ")
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2010-10-12 06:52:29 -04:00
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(let ((lob-ingest-count 0))
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(org-babel-map-src-blocks file
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2010-10-15 11:13:51 -04:00
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(let* ((info (org-babel-get-src-block-info 'light))
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2010-10-12 06:52:29 -04:00
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(source-name (nth 4 info)))
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(when source-name
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(setq source-name (intern source-name)
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org-babel-library-of-babel
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(cons (cons source-name info)
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(assq-delete-all source-name org-babel-library-of-babel))
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lob-ingest-count (1+ lob-ingest-count)))))
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(message "%d src block%s added to Library of Babel"
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2010-10-15 20:42:26 -04:00
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lob-ingest-count (if (> lob-ingest-count 1) "s" ""))
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lob-ingest-count))
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2009-06-14 17:10:04 -04:00
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2011-06-24 17:44:28 -04:00
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(defconst org-babel-block-lob-one-liner-regexp
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2010-07-20 14:40:57 -04:00
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(concat
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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 19:52:48 -04:00
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"^\\([ \t]*\\)#\\+call:[ \t]+\\([^\(\)\n]+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)"
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2011-06-24 17:44:28 -04:00
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"\(\\([^\n]*\\)\)\\(\\[.+\\]\\|\\)[ \t]*\\(\\([^\n]*\\)\\)?")
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"Regexp to match non-inline calls to predefined source block functions.")
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(defconst org-babel-inline-lob-one-liner-regexp
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(concat
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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 19:52:48 -04:00
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"\\([^\n]*\\)call_\\([^\(\)\n]+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)"
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2011-06-25 18:06:28 -04:00
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"\(\\([^\n]*\\)\)\\(\\[\\(.*?\\)\\]\\)?")
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2011-06-24 17:44:28 -04:00
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"Regexp to match inline calls to predefined source block functions.")
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(defconst org-babel-lob-one-liner-regexp
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(concat "\\(" org-babel-block-lob-one-liner-regexp
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"\\|" org-babel-inline-lob-one-liner-regexp "\\)")
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2010-07-13 19:20:08 -04:00
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"Regexp to match calls to predefined source block functions.")
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2009-06-14 17:10:04 -04:00
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2011-08-01 17:45:58 -04:00
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;; functions for executing lob one-liners
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2011-11-09 16:35:04 -05:00
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2010-06-23 14:24:33 -04:00
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;;;###autoload
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2009-06-14 10:54:55 -04:00
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(defun org-babel-lob-execute-maybe ()
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2010-07-13 19:20:08 -04:00
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"Execute a Library of Babel source block, if appropriate.
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Detect if this is context for a Library Of Babel source block and
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if so then run the appropriate source block from the Library."
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2009-06-14 10:54:55 -04:00
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(interactive)
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(let ((info (org-babel-lob-get-info)))
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2011-11-08 21:42:59 -05:00
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(if (and (nth 0 info) (not (org-babel-in-example-or-verbatim)))
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(progn (org-babel-lob-execute info) t)
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nil)))
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2009-06-14 10:54:55 -04:00
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2010-06-23 14:24:33 -04:00
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;;;###autoload
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2009-06-14 10:54:55 -04:00
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(defun org-babel-lob-get-info ()
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2010-08-19 09:31:19 -04:00
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"Return a Library of Babel function call as a string."
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2011-06-24 17:44:28 -04:00
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(flet ((nonempty (a b)
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(let ((it (match-string a)))
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(if (= (length it) 0) (match-string b) it))))
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(let ((case-fold-search t))
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(save-excursion
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(beginning-of-line 1)
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(when (looking-at org-babel-lob-one-liner-regexp)
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(append
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2012-01-04 10:20:04 -05:00
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(mapcar #'org-babel-clean-text-properties
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2010-07-20 14:40:57 -04:00
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(list
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2010-11-07 09:39:05 -05:00
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(format "%s%s(%s)%s"
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2011-06-24 17:44:28 -04:00
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(nonempty 3 12)
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(if (not (= 0 (length (nonempty 5 13))))
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(concat "[" (nonempty 5 13) "]") "")
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2011-06-25 17:25:18 -04:00
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(or (nonempty 7 16) "")
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2011-06-25 18:06:28 -04:00
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(or (nonempty 8 19) ""))
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(nonempty 9 18)))
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2011-06-25 20:56:40 -04:00
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(list (length (if (= (length (match-string 12)) 0)
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(match-string 2) (match-string 11))))))))))
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2012-01-04 10:20:04 -05:00
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2009-06-14 10:54:55 -04:00
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(defun org-babel-lob-execute (info)
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2010-06-11 20:12:15 -04:00
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"Execute the lob call specified by INFO."
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2010-10-16 14:14:20 -04:00
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(let ((params (org-babel-process-params
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2010-10-16 12:02:57 -04:00
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(org-babel-merge-params
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org-babel-default-header-args
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(org-babel-params-from-properties)
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(org-babel-parse-header-arguments
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(org-babel-clean-text-properties
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(concat ":var results="
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(mapconcat #'identity (butlast info) " "))))))))
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2010-06-10 17:36:08 -04:00
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(org-babel-execute-src-block
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2010-06-12 21:26:08 -04:00
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nil (list "emacs-lisp" "results" params nil nil (nth 2 info)))))
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2009-06-14 10:54:55 -04:00
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2010-06-11 19:02:42 -04:00
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(provide 'ob-lob)
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2010-06-25 12:20:39 -04:00
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2011-08-15 14:04:38 -04:00
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2010-06-25 12:20:39 -04:00
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2010-06-11 19:02:42 -04:00
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;;; ob-lob.el ends here
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