org-mode/lisp/org-babel.el

472 lines
19 KiB
EmacsLisp
Raw Normal View History

2009-05-24 17:10:03 -04:00
;;; org-babel.el --- facilitating communication between programming languages and people
;; Copyright (C) 2009 Eric Schulte, Dan Davison
;; Author: Eric Schulte, Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; Version: 0.01
;;; License:
;; This program 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, or (at your option)
;; any later version.
;;
;; This program 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; see the file COPYING. If not, write to the
;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301, USA.
;;; Commentary:
2009-06-02 19:26:57 -04:00
;; See org-babel.org in the parent directory for more information
;;; Code:
(require 'org)
2009-05-24 16:38:01 -04:00
(defun org-babel-execute-src-block-maybe ()
"Detect if this is context for a org-babel src-block and if so
then run `org-babel-execute-src-block'."
(interactive)
2009-05-24 16:38:01 -04:00
(let ((info (org-babel-get-src-block-info)))
(if info (progn (org-babel-execute-src-block current-prefix-arg info) t) nil)))
2009-05-24 16:38:01 -04:00
(add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-execute-src-block-maybe)
(defun org-babel-pop-to-session-maybe ()
"Detect if this is context for a org-babel src-block and if so
then run `org-babel-pop-to-session'."
(interactive)
(let ((info (org-babel-get-src-block-info)))
(if info (progn (org-babel-pop-to-session current-prefix-arg info) t) nil)))
(add-hook 'org-metadown-hook 'org-babel-pop-to-session-maybe)
2009-06-15 12:28:01 -04:00
(defvar org-babel-default-header-args '((:session . "none"))
"Default arguments to use when evaluating a source block.")
2009-05-24 16:38:01 -04:00
(defvar org-babel-default-inline-header-args '((:results . "silent") (:exports . "results"))
"Default arguments to use when evaluating an inline source block.")
2009-05-24 16:38:01 -04:00
(defvar org-babel-src-block-regexp nil
"Regexp used to test when inside of a org-babel src-block")
2009-05-24 16:38:01 -04:00
(defvar org-babel-inline-src-block-regexp nil
"Regexp used to test when on an inline org-babel src-block")
(defun org-babel-named-src-block-regexp-for-name (name)
"Regexp used to match named src block."
(concat "#\\+srcname:[ \t]*" (regexp-quote name) "[ \t\n]*"
org-babel-src-block-regexp))
2009-05-24 16:38:01 -04:00
(defun org-babel-set-interpreters (var value)
(set-default var value)
2009-05-24 16:38:01 -04:00
(setq org-babel-src-block-regexp
(concat "#\\+begin_src \\("
(mapconcat 'regexp-quote value "\\|")
"\\)[ \t]*"
"\\([ \t]+\\([^\n]+\\)\\)?\n" ;; match header arguments
"\\([^\000]+?\\)#\\+end_src"))
2009-05-24 16:38:01 -04:00
(setq org-babel-inline-src-block-regexp
(concat "src_\\("
(mapconcat 'regexp-quote value "\\|")
"\\)"
"\\(\\|\\[\\(.*\\)\\]\\)"
"{\\([^\n]+\\)}")))
2009-05-24 16:38:01 -04:00
(defun org-babel-add-interpreter (interpreter)
"Add INTERPRETER to `org-babel-interpreters' and update
`org-babel-src-block-regexp' appropriately."
(unless (member interpreter org-babel-interpreters)
(setq org-babel-interpreters (cons interpreter org-babel-interpreters))
;; (add-to-list 'org-babel-session-defaults (cons interpreter (format "org-babel-%s" interpreter)))
2009-05-24 16:38:01 -04:00
(org-babel-set-interpreters 'org-babel-interpreters org-babel-interpreters)))
2009-02-23 19:07:07 -05:00
2009-05-24 16:38:01 -04:00
(defcustom org-babel-interpreters '()
"Interpreters allows for evaluation tags.
This is a list of program names (as strings) that can evaluate code and
insert the output into an Org-mode buffer. Valid choices are
R Evaluate R code
emacs-lisp Evaluate Emacs Lisp code and display the result
sh Pass command to the shell and display the result
perl The perl interpreter
python The python interpreter
2009-02-23 19:07:07 -05:00
ruby The ruby interpreter
babel A degenerate source block (no body) to implement library-of-babel calls
2009-02-23 19:07:07 -05:00
2009-05-24 16:38:01 -04:00
The source block regexp `org-babel-src-block-regexp' is updated
2009-02-23 19:07:07 -05:00
when a new interpreter is added to this list through the
customize interface. To add interpreters to this variable from
2009-05-24 16:38:01 -04:00
lisp code use the `org-babel-add-interpreter' function."
:group 'org-babel
:set 'org-babel-set-interpreters
:type '(set :greedy t
(const "R")
(const "emacs-lisp")
(const "sh")
(const "perl")
(const "python")
(const "ruby")
(const "babel")))
;;; functions
(defun org-babel-pop-to-session (&optional arg info)
"Pop to the session of the current source-code block. If
called with a prefix argument then evaluate the header arguments
for the source block before entering the session. Copy the body
of the source block to the kill ring."
(interactive)
(let* ((info (or info (org-babel-get-src-block-info)))
(lang (first info))
(body (second info))
(params (third info))
(session (cdr (assoc :session params))))
(unless (member lang org-babel-interpreters)
(error "Language is not in `org-babel-interpreters': %s" lang))
;; copy body to the kill ring
(with-temp-buffer (insert (org-babel-trim body)) (copy-region-as-kill (point-min) (point-max)))
;; if called with a prefix argument, then process header arguments
(if arg (funcall (intern (concat "org-babel-prep-session:" lang)) session params))
;; just to the session using pop-to-buffer
2009-06-14 14:34:06 -04:00
(pop-to-buffer (funcall (intern (format "org-babel-%s-initiate-session" lang)) session))
(move-end-of-line 1)))
2009-05-24 16:38:01 -04:00
(defun org-babel-execute-src-block (&optional arg info params)
"Execute the current source code block, and dump the results
into the buffer immediately following the block. Results are
commented by `org-toggle-fixed-width-section'. With optional
prefix don't dump results into buffer but rather return the
results in raw elisp (this is useful for automated execution of a
source block).
Optionally supply a value for INFO in the form returned by
2009-05-24 16:38:01 -04:00
`org-babel-get-src-block-info'.
Optionally supply a value for PARAMS which will be merged with
the header arguments specified at the source code block."
(interactive)
2009-05-24 16:38:01 -04:00
(let* ((info (or info (org-babel-get-src-block-info)))
(lang (first info))
(body (second info))
(params (org-combine-plists params (third info)))
2009-05-24 16:38:01 -04:00
(cmd (intern (concat "org-babel-execute:" lang)))
result)
;; (message (format "params=%S" params)) ;; debugging statement
2009-05-24 16:38:01 -04:00
(unless (member lang org-babel-interpreters)
(error "Language is not in `org-babel-interpreters': %s" lang))
(setq result (funcall cmd body params))
;; possibly force result into a vector
(if (and (not (listp result)) (cdr (assoc :results params))
(member "vector" (split-string (cdr (assoc :results params)))))
(setq result (list result)))
(if arg
2009-06-12 16:07:56 -04:00
(message (replace-regexp-in-string "%" "%%" (format "%S" result)))
2009-05-24 16:38:01 -04:00
(org-babel-insert-result result (cdr (assoc :results params))))
result))
2009-05-24 16:38:01 -04:00
(defun org-babel-eval-buffer (&optional arg)
2009-02-23 18:14:48 -05:00
"Replace EVAL snippets in the entire buffer."
(interactive "P")
(save-excursion
(goto-char (point-min))
2009-05-24 16:38:01 -04:00
(while (re-search-forward org-babel-regexp nil t)
(org-babel-eval-src-block arg))))
2009-02-23 18:14:48 -05:00
2009-05-24 16:38:01 -04:00
(defun org-babel-eval-subtree (&optional arg)
"Replace EVAL snippets in the entire subtree."
(interactive "P")
(save-excursion
(org-narrow-to-subtree)
2009-05-24 16:38:01 -04:00
(org-babel-eval-buffer)
(widen)))
2009-05-24 16:38:01 -04:00
(defun org-babel-get-src-block-name ()
"Return the name of the current source block if one exists"
(let ((case-fold-search t))
(save-excursion
2009-05-24 16:38:01 -04:00
(goto-char (org-babel-where-is-src-block-head))
(if (save-excursion (forward-line -1)
(looking-at "#\\+srcname:[ \f\t\n\r\v]*\\([^ \f\t\n\r\v]+\\)"))
2009-05-24 16:38:01 -04:00
(org-babel-clean-text-properties (match-string 1))))))
2009-05-24 16:38:01 -04:00
(defun org-babel-get-src-block-info ()
"Return the information of the current source block as a list
of the following form. (language body header-arguments-alist)"
(let ((case-fold-search t) head)
2009-05-24 16:38:01 -04:00
(if (setq head (org-babel-where-is-src-block-head))
(save-excursion (goto-char head) (org-babel-parse-src-block-match))
(if (save-excursion ;; inline source block
(re-search-backward "[ \f\t\n\r\v]" nil t)
(forward-char 1)
2009-05-24 16:38:01 -04:00
(looking-at org-babel-inline-src-block-regexp))
(org-babel-parse-inline-src-block-match)
nil)))) ;; indicate that no source block was found
(defmacro org-babel-map-source-blocks (file &rest body)
"Evaluate BODY forms on each source-block in FILE."
(declare (indent 1))
`(save-window-excursion
(find-file ,file) (goto-char (point-min))
(while (re-search-forward org-babel-src-block-regexp nil t)
(goto-char (match-beginning 0))
(save-match-data ,@body)
(goto-char (match-end 0)))))
2009-05-24 16:38:01 -04:00
(defun org-babel-parse-src-block-match ()
(list (org-babel-clean-text-properties (match-string 1))
2009-06-02 19:26:57 -04:00
(org-babel-strip-protective-comas (org-babel-clean-text-properties (match-string 4)))
2009-05-24 16:38:01 -04:00
(org-combine-plists org-babel-default-header-args
(org-babel-parse-header-arguments (org-babel-clean-text-properties (or (match-string 3) ""))))))
2009-05-24 16:38:01 -04:00
(defun org-babel-parse-inline-src-block-match ()
(list (org-babel-clean-text-properties (match-string 1))
2009-06-02 19:26:57 -04:00
(org-babel-strip-protective-comas (org-babel-clean-text-properties (match-string 4)))
2009-05-24 16:38:01 -04:00
(org-combine-plists org-babel-default-inline-header-args
(org-babel-parse-header-arguments (org-babel-clean-text-properties (or (match-string 3) ""))))))
2009-05-24 16:38:01 -04:00
(defun org-babel-parse-header-arguments (arg-string)
"Parse a string of header arguments returning an alist."
(delq nil
(mapcar
(lambda (arg) (if (string-match "\\([^ \f\t\n\r\v]+\\)[ \f\t\n\r\v]*\\([^ \f\t\n\r\v]+.*\\)" arg)
(cons (intern (concat ":" (match-string 1 arg))) (org-babel-chomp (match-string 2 arg)))))
(split-string (concat " " arg-string) "[ \f\t\n\r\v]+:" t))))
2009-05-24 16:38:01 -04:00
(defun org-babel-where-is-src-block-head ()
"Return the point at the beginning of the current source
block. Specifically at the beginning of the #+BEGIN_SRC line.
If the point is not on a source block then return nil."
(let ((initial (point)) top bottom)
(or
(save-excursion ;; on a #+srcname: line
(beginning-of-line 1)
(and (looking-at "#\\+srcname") (forward-line 1)
2009-05-24 16:38:01 -04:00
(looking-at org-babel-src-block-regexp)
(point)))
(save-excursion ;; on a #+begin_src line
(beginning-of-line 1)
2009-05-24 16:38:01 -04:00
(and (looking-at org-babel-src-block-regexp)
(point)))
(save-excursion ;; inside a src block
(and
(re-search-backward "#\\+begin_src" nil t) (setq top (point))
(re-search-forward "#\\+end_src" nil t) (setq bottom (point))
(< top initial) (< initial bottom)
2009-05-24 16:38:01 -04:00
(goto-char top) (looking-at org-babel-src-block-regexp)
(point))))))
(defun org-babel-find-named-block (name)
"Find a named source-code block.
Return the location of the source block identified by
#+srcname NAME, or nil if no such block exists. Set match data
according to org-babel-named-src-block-regexp."
(save-excursion
(let ((case-fold-search t)
(regexp (org-babel-named-src-block-regexp-for-name name)) msg)
(unless (or (re-search-forward regexp nil t)
(re-search-backward regexp nil t))
(progn (setq msg (format "source-code block '%s' not found in this buffer" name))
(message msg) (error msg))))
(point)))
2009-05-24 16:38:01 -04:00
(defun org-babel-find-named-result (name)
"Return the location of the result named NAME in the current
buffer or nil if no such result exists."
(save-excursion
(goto-char (point-min))
(when (re-search-forward (concat "#\\+resname:[ \t]*" (regexp-quote name)) nil t)
(move-beginning-of-line 1) (point))))
2009-05-24 16:38:01 -04:00
(defun org-babel-where-is-src-block-result ()
"Return the point at the beginning of the result of the current
source block. Specifically at the beginning of the #+RESNAME:
line. If no result exists for this block then create a
#+RESNAME: line following the source block."
(save-excursion
2009-05-24 16:38:01 -04:00
(goto-char (org-babel-where-is-src-block-head))
(let ((name (org-babel-get-src-block-name)) end head)
(or (and name (message name) (org-babel-find-named-result name))
(and (re-search-forward "#\\+end_src" nil t)
(progn (move-end-of-line 1)
(if (eobp) (insert "\n") (forward-char 1))
(setq end (point))
(or (progn ;; either an unnamed #+resname: line already exists
(re-search-forward "[^ \f\t\n\r\v]" nil t)
(move-beginning-of-line 1) (looking-at "#\\+resname:"))
(progn ;; or we need to back up and make one ourselves
(goto-char end) (open-line 2) (forward-char 1)
(insert (concat "#+resname:" (if name (concat " " name))))
(move-beginning-of-line 1) t)))
(point))))))
2009-05-24 16:38:01 -04:00
(defun org-babel-insert-result (result &optional insert)
"Insert RESULT into the current buffer after the end of the
current source block. With optional argument INSERT controls
insertion of results in the org-mode file. INSERT can take the
following values...
t ------ the default options, simply insert the results after the
source block
replace - insert results after the source block replacing any
previously inserted results
silent -- no results are inserted"
2009-05-22 18:12:51 -04:00
(if insert (setq insert (split-string insert)))
2009-05-22 18:38:51 -04:00
(if (stringp result)
(progn
2009-05-24 16:38:01 -04:00
(setq result (org-babel-clean-text-properties result))
(if (member "file" insert) (setq result (org-babel-result-to-file result))))
(unless (listp result) (setq result (format "%S" result))))
2009-05-24 16:38:01 -04:00
(if (and insert (member "replace" insert)) (org-babel-remove-result))
(if (= (length result) 0)
(message "no result returned by source block")
2009-05-22 18:12:51 -04:00
(if (and insert (member "silent" insert))
2009-06-12 16:07:56 -04:00
(progn (message (replace-regexp-in-string "%" "%%" (format "%S" result))) result)
(when (and (stringp result) ;; ensure results end in a newline
(not (or (string-equal (substring result -1) "\n")
(string-equal (substring result -1) "\r"))))
(setq result (concat result "\n")))
(save-excursion
2009-05-24 16:38:01 -04:00
(goto-char (org-babel-where-is-src-block-result)) (forward-line 1)
(if (stringp result) ;; assume the result is a table if it's not a string
2009-05-22 18:38:51 -04:00
(if (member "file" insert)
(insert result)
2009-05-24 16:38:01 -04:00
(org-babel-examplize-region (point) (progn (insert result) (point))))
(progn
2009-05-22 18:38:51 -04:00
(insert
(concat (orgtbl-to-orgtbl
(if (consp (car result)) result (list result))
'(:fmt (lambda (cell) (format "%S" cell)))) "\n"))
(forward-line -1)
(org-cycle))))
(message "finished"))))
2009-05-24 16:38:01 -04:00
(defun org-babel-result-to-org-string (result)
"Return RESULT as a string in org-mode format. This function
2009-05-24 16:38:01 -04:00
relies on `org-babel-insert-result'."
(with-temp-buffer (org-babel-insert-result result) (buffer-string)))
2009-05-24 16:38:01 -04:00
(defun org-babel-remove-result ()
"Remove the result of the current source block."
(interactive)
(save-excursion
2009-05-24 16:38:01 -04:00
(goto-char (org-babel-where-is-src-block-result)) (forward-line 1)
(delete-region (point) (org-babel-result-end))))
(defun org-babel-result-end ()
"Return the point at the end of the current set of results"
(save-excursion
(if (org-at-table-p)
(org-table-end)
(while (if (looking-at "\\(: \\|\\[\\[\\)")
(progn (while (looking-at "\\(: \\|\\[\\[\\)")
(forward-line 1)) t))
(forward-line 1))
(forward-line -1)
(point))))
2009-05-24 16:38:01 -04:00
(defun org-babel-result-to-file (result)
2009-05-22 18:38:51 -04:00
"Return an `org-mode' link with the path being the value or
RESULT, and the display being the `file-name-nondirectory' if
non-nil."
(let ((name (file-name-nondirectory result)))
(concat "[[" result (if name (concat "][" name "]]") "]]"))))
2009-05-24 16:38:01 -04:00
(defun org-babel-examplize-region (beg end)
"Comment out region using the ': ' org example quote."
(interactive "*r")
(let ((size (abs (- (line-number-at-pos end)
(line-number-at-pos beg)))))
(if (= size 0)
(let ((result (buffer-substring beg end)))
(delete-region beg end)
(insert (concat ": " result)))
(save-excursion
(goto-char beg)
(dotimes (n size)
(move-beginning-of-line 1) (insert ": ") (forward-line 1))))))
2009-05-24 16:38:01 -04:00
(defun org-babel-clean-text-properties (text)
"Strip all properties from text return."
(set-text-properties 0 (length text) nil text) text)
2009-06-02 19:26:57 -04:00
(defun org-babel-strip-protective-comas (body)
"Strip protective comas from bodies of source blocks."
(replace-regexp-in-string "^,#" "#" body))
2009-05-24 16:38:01 -04:00
(defun org-babel-read (cell)
"Convert the string value of CELL to a number if appropriate.
Otherwise if cell looks like a list (meaning it starts with a
'(') then read it as lisp, otherwise return it unmodified as a
string.
This is taken almost directly from `org-read-prop'."
(if (and (stringp cell) (not (equal cell "")))
(or (org-babel-number-p cell)
(if (or (equal "(" (substring cell 0 1))
(equal "'" (substring cell 0 2)))
(read cell)
(progn (set-text-properties 0 (length cell) nil cell) cell)))
cell))
2009-05-24 16:38:01 -04:00
(defun org-babel-number-p (string)
"Return t if STRING represents a number"
(if (string-match "^[[:digit:]]*\\.?[[:digit:]]*$" string)
(string-to-number string)))
(defun org-babel-import-elisp-from-file (file-name)
"Read the results located at FILE-NAME into an elisp table. If
the table is trivial, then return it as a scalar."
(let (result)
(with-temp-buffer
(condition-case nil
(progn
(org-table-import file-name nil)
(delete-file file-name)
(setq result (mapcar (lambda (row)
(mapcar #'org-babel-string-read row))
(org-table-to-lisp))))
(error nil))
(if (null (cdr result)) ;; if result is trivial vector, then scalarize it
(if (consp (car result))
(if (null (cdr (car result)))
(caar result)
result)
(car result))
result))))
(defun org-babel-string-read (cell)
"Strip nested \"s from around strings in exported R values."
(org-babel-read (or (and (stringp cell)
(string-match "\\\"\\(.+\\)\\\"" cell)
(match-string 1 cell))
cell)))
(defun org-babel-reverse-string (string)
(apply 'string (reverse (string-to-list string))))
2009-05-24 16:38:01 -04:00
(defun org-babel-chomp (string &optional regexp)
"Remove any trailing space or carriage returns characters from
STRING. Default regexp used is \"[ \f\t\n\r\v]\" but can be
overwritten by specifying a regexp as a second argument."
2009-06-10 19:17:04 -04:00
(while (and (> (length string) 0) (string-match "[ \f\t\n\r\v]" (substring string -1)))
(setq string (substring string 0 -1)))
string)
(defun org-babel-trim (string &optional regexp)
"Like `org-babel-chomp' only it runs on both the front and back of the string"
(org-babel-chomp (org-babel-reverse-string
(org-babel-chomp (org-babel-reverse-string string) regexp)) regexp))
2009-05-24 16:38:01 -04:00
(provide 'org-babel)
;;; org-babel.el ends here