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org-mode/lisp/ob-table.el

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;;; ob-table.el --- Support for Calling Babel Functions from Tables -*- lexical-binding: t; -*-
2022-01-01 20:10:55 +00:00
;; Copyright (C) 2009-2022 Free Software Foundation, Inc.
;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research
;; URL: https://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 <https://www.gnu.org/licenses/>.
;;; Commentary:
;; Should allow calling functions from Org tables using the function
;; `org-sbe' as so...
;; #+begin_src emacs-lisp :results silent
;; (defun fibbd (n) (if (< n 2) 1 (+ (fibbd (- n 1)) (fibbd (- n 2)))))
;; #+end_src
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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;; #+name: fibbd
;; #+begin_src emacs-lisp :var n=2 :results silent
;; (fibbd n)
;; #+end_src
;; | original | fibbd |
;; |----------+--------|
;; | 0 | |
;; | 1 | |
;; | 2 | |
;; | 3 | |
;; | 4 | |
;; | 5 | |
;; | 6 | |
;; | 7 | |
;; | 8 | |
;; | 9 | |
;; #+TBLFM: $2='(org-sbe "fibbd" (n $1))
;; NOTE: The quotation marks around the function name, 'fibbd' here,
;; are optional.
;;; Code:
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(require 'ob-core)
(require 'org-macs)
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(defun org-babel-table-truncate-at-newline (string)
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"Replace newline character with ellipses.
If STRING ends in a newline character, then remove the newline
character and replace it with ellipses."
(if (and (stringp string) (string-match "[\n\r]\\(.\\)?" string))
(concat (substring string 0 (match-beginning 0))
Tiny formatting fixes * lisp/ox.el (org-export-table-dimensions): * lisp/ox-texinfo.el (org-texinfo-template): * lisp/ox-md.el (org-md-link): * lisp/ox-icalendar.el (org-icalendar-use-UTC-date-time-p): * lisp/ox-ascii.el (org-ascii-fixed-width): * lisp/org.el (org-context): * lisp/org-table.el (org-table-eval-formula) (org-table-export): * lisp/org-refile.el: * lisp/org-plot.el (org-plot/gnuplot-to-grid-data): * lisp/org-num.el (org-num): * lisp/org-mouse.el (org-mouse-popup-global-menu) (org-mouse-context-menu): * lisp/org-macro.el (org-macro): * lisp/org-lint.el (org-lint): * lisp/org-keys.el (org-keys): * lisp/org-duration.el: * lisp/org-clock.el (org-clock-get-last-clock-out-time) (org-clock-update-mode-line, org-find-open-clocks): * lisp/org-agenda.el (org-diary) (org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item) (org-agenda-highlight-todo, org-cmp-alpha) (org-agenda-filter-by-category): * lisp/ol.el (org-link-expand-abbrev, ol): * lisp/ol-docview.el (ol-docview): * lisp/ol-bibtex.el (org-execute-file-search-in-bibtex) (org-bibtex, org-bibtex-read): * lisp/ol-bbdb.el (org-bbdb-anniversary-description): * lisp/ob-tangle.el (org-babel-tangle-jump-to-org): * lisp/ob-table.el (org-babel-table-truncate-at-newline): * lisp/ob-stan.el: * lisp/ob-sqlite.el (org-babel-sqlite-table-or-scalar): * lisp/ob-sql.el: * lisp/ob-shen.el: * lisp/ob-shell.el (org-babel-prep-session:shell) (org-babel-prep-session:shell): * lisp/ob-sed.el (org-babel-execute:sed) (org-babel-execute:sed): * lisp/ob-screen.el: * lisp/ob-sass.el: * lisp/ob-ruby.el (org-babel-prep-session:ruby) (org-babel-prep-session:ruby): * lisp/ob-ref.el (org-babel-ref-resolve, ob-ref): * lisp/ob-python.el (org-babel-prep-session:python) (org-babel-prep-session:python): * lisp/ob-plantuml.el: * lisp/ob-picolisp.el: * lisp/ob-perl.el: * lisp/ob-org.el: * lisp/ob-octave.el (org-babel-prep-session:octave) (org-babel-prep-session:octave) (org-babel-octave-evaluate-session): * lisp/ob-ocaml.el: * lisp/ob-mscgen.el (org-babel-execute:mscgen) (org-babel-execute:mscgen): * lisp/ob-maxima.el: (ob-maxima): * lisp/ob-matlab.el: * lisp/ob-makefile.el: * lisp/ob-lua.el (org-babel-prep-session:lua) (org-babel-prep-session:lua): * lisp/ob-lisp.el: * lisp/ob-ledger.el: * lisp/ob-latex.el (org-babel-expand-body:latex) (org-babel-expand-body:latex, ob-latex): * lisp/ob-js.el: * lisp/ob-java.el: * lisp/ob-io.el (org-babel-prep-session:io) (org-babel-prep-session:io): * lisp/ob-hledger.el: * lisp/ob-haskell.el: * lisp/ob-groovy.el (org-babel-groovy-wrapper-method) (org-babel-groovy-evaluate): * lisp/ob-gnuplot.el: * lisp/ob-fortran.el (org-babel-expand-body:fortran) (org-babel-expand-body:fortran): * lisp/ob-forth.el (org-babel-forth-session-execute): * lisp/ob-exp.el (ob-exp): * lisp/ob-eval.el: * lisp/ob-emacs-lisp.el: * lisp/ob-ebnf.el: * lisp/ob-dot.el: * lisp/ob-ditaa.el: * lisp/ob-css.el: * lisp/ob-core.el (org-babel-put-rownames): * lisp/ob-coq.el: * lisp/ob-comint.el: * lisp/ob-calc.el: * lisp/ob-awk.el: * lisp/ob-asymptote.el: * lisp/ob-abc.el: * lisp/ob-R.el (org-babel-prep-session:R): Formatting fixes.
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(when (match-string 1 string) "..."))
string))
(defmacro org-sbe (source-block &rest variables)
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"Return the results of calling SOURCE-BLOCK with VARIABLES.
Each element of VARIABLES should be a list of two elements: the
first element is the name of the variable and second element is a
string of its value.
So this `org-sbe' construct
(org-sbe \"source-block\" (n $2) (m 3))
is the equivalent of the following source code block:
#+begin_src emacs-lisp :var results=source-block(n=val_at_col_2, m=3) \\
:results silent
results
#+end_src
NOTE: The quotation marks around the function name,
`source-block', are optional.
NOTE: By default, string variable names are interpreted as
references to source-code blocks, to force interpretation of a
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cell's value as a string, prefix the identifier a \"$\" (e.g.,
\"$$2\" instead of \"$2\" or \"$@2$2\" instead of \"@2$2\").
NOTE: It is also possible to pass header arguments to the code
block. In this case a table cell should hold the string value of
the header argument which can then be passed before all variables
as shown in the example below.
| 1 | 2 | :file nothing.png | nothing.png |
#+TBLFM: @1$4=\\='(org-sbe test-sbe $3 (x $1) (y $2))"
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.
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(declare (debug (form form)))
(let* ((header-args (if (stringp (car variables)) (car variables) ""))
(variables (if (stringp (car variables)) (cdr variables) variables)))
(let* (quote
(variables
(mapcar
(lambda (var)
;; ensure that all cells prefixed with $'s are strings
(cons (car var)
(delq nil (mapcar
(lambda (el)
(if (eq '$ el)
(prog1 nil (setq quote t))
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(prog1
(cond
(quote (format "\"%s\"" el))
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((stringp el) (org-no-properties el))
(t el))
(setq quote nil))))
(cdr var)))))
variables)))
(unless (stringp source-block)
(setq source-block (symbol-name source-block)))
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.
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(let ((result
(if (and source-block (> (length source-block) 0))
(let ((params
;; FIXME: Why `eval'?!?!?
(eval `(org-babel-parse-header-arguments
(concat
":var results="
,source-block
"[" ,header-args "]"
"("
(mapconcat
(lambda (var-spec)
(if (> (length (cdr var-spec)) 1)
(format "%S='%S"
(car var-spec)
(mapcar #'read (cdr var-spec)))
(format "%S=%s"
(car var-spec) (cadr var-spec))))
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.
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',variables ", ")
")")))))
(org-babel-execute-src-block
nil (list "emacs-lisp" "results" params)
'((:results . "silent"))))
"")))
(org-trim (if (stringp result) result (format "%S" result)))))))
(provide 'ob-table)
;;; ob-table.el ends here