org-mode/lisp/ob-lob.el

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;;; ob-lob.el --- functions supporting the Library of Babel
;; Copyright (C) 2009-2012 Free Software Foundation, Inc.
;; Author: Eric Schulte
;; Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; This file is part of GNU Emacs.
;; GNU Emacs 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 of the License, or
;; (at your option) any later version.
;; GNU Emacs 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. If not, see <http://www.gnu.org/licenses/>.
;;; Code:
(eval-when-compile
(require 'cl))
(require 'ob)
(require 'ob-table)
(declare-function org-babel-in-example-or-verbatim "ob-exp" nil)
(defvar org-babel-library-of-babel nil
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"Library of source-code blocks.
This is an association list. Populate the library by adding
files to `org-babel-lob-files'.")
(defcustom org-babel-lob-files '()
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"Files used to populate the `org-babel-library-of-babel'.
To add files to this list use the `org-babel-lob-ingest' command."
:group 'org-babel
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.
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:version "24.1"
:type 'list)
(defvar org-babel-default-lob-header-args '((:exports . "results"))
"Default header arguments to use when exporting #+lob/call lines.")
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;;;###autoload
(defun org-babel-lob-ingest (&optional file)
"Add all named source-blocks defined in FILE to
`org-babel-library-of-babel'."
(interactive "fFile: ")
(let ((lob-ingest-count 0))
(org-babel-map-src-blocks file
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(let* ((info (org-babel-get-src-block-info 'light))
(source-name (nth 4 info)))
(when source-name
(setq source-name (intern source-name)
org-babel-library-of-babel
(cons (cons source-name info)
(assq-delete-all source-name org-babel-library-of-babel))
lob-ingest-count (1+ lob-ingest-count)))))
(message "%d src block%s added to Library of Babel"
lob-ingest-count (if (> lob-ingest-count 1) "s" ""))
lob-ingest-count))
(defconst org-babel-block-lob-one-liner-regexp
(concat
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.
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"^\\([ \t]*\\)#\\+call:[ \t]+\\([^\(\)\n]+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)"
"\(\\([^\n]*\\)\)\\(\\[.+\\]\\|\\)[ \t]*\\(\\([^\n]*\\)\\)?")
"Regexp to match non-inline calls to predefined source block functions.")
(defconst org-babel-inline-lob-one-liner-regexp
(concat
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.
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"\\([^\n]*\\)call_\\([^\(\)\n]+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)"
"\(\\([^\n]*\\)\)\\(\\[\\(.*?\\)\\]\\)?")
"Regexp to match inline calls to predefined source block functions.")
(defconst org-babel-lob-one-liner-regexp
(concat "\\(" org-babel-block-lob-one-liner-regexp
"\\|" org-babel-inline-lob-one-liner-regexp "\\)")
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"Regexp to match calls to predefined source block functions.")
;; functions for executing lob one-liners
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;;;###autoload
(defun org-babel-lob-execute-maybe ()
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"Execute a Library of Babel source block, if appropriate.
Detect if this is context for a Library Of Babel source block and
if so then run the appropriate source block from the Library."
(interactive)
(let ((info (org-babel-lob-get-info)))
(if (and (nth 0 info) (not (org-babel-in-example-or-verbatim)))
(progn (org-babel-lob-execute info) t)
nil)))
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;;;###autoload
(defun org-babel-lob-get-info ()
"Return a Library of Babel function call as a string."
(flet ((nonempty (a b)
(let ((it (match-string a)))
(if (= (length it) 0) (match-string b) it))))
(let ((case-fold-search t))
(save-excursion
(beginning-of-line 1)
(when (looking-at org-babel-lob-one-liner-regexp)
(append
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(mapcar #'org-babel-clean-text-properties
(list
(format "%s%s(%s)%s"
(nonempty 3 12)
(if (not (= 0 (length (nonempty 5 13))))
(concat "[" (nonempty 5 13) "]") "")
(or (nonempty 7 16) "")
(or (nonempty 8 19) ""))
(nonempty 9 18)))
(list (length (if (= (length (match-string 12)) 0)
(match-string 2) (match-string 11))))))))))
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(defun org-babel-lob-execute (info)
"Execute the lob call specified by INFO."
(let ((params (org-babel-process-params
(org-babel-merge-params
org-babel-default-header-args
(org-babel-params-from-properties)
(org-babel-parse-header-arguments
(org-babel-clean-text-properties
(concat ":var results="
(mapconcat #'identity (butlast info) " "))))))))
(org-babel-execute-src-block
nil (list "emacs-lisp" "results" params nil nil (nth 2 info)))))
(provide 'ob-lob)
;;; ob-lob.el ends here