600 lines
25 KiB
EmacsLisp
600 lines
25 KiB
EmacsLisp
;;; org-babel.el --- facilitating communication between programming languages and people
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;; Copyright (C) 2009 Eric Schulte, Dan Davison
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;; Author: Eric Schulte, Dan Davison
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;;; License:
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation; either version 3, or (at your option)
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;; any later version.
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;;
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;; This program is distributed in the hope that it will be useful,
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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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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;; See org-babel.org in the parent directory for more information
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;;; Code:
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(require 'org)
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(defun org-babel-execute-src-block-maybe ()
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"Detect if this is context for a org-babel src-block and if so
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then run `org-babel-execute-src-block'."
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(interactive)
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(let ((info (org-babel-get-src-block-info)))
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(if info (progn (org-babel-execute-src-block current-prefix-arg info) t) nil)))
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(add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-execute-src-block-maybe)
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(defun org-babel-pop-to-session-maybe ()
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"Detect if this is context for a org-babel src-block and if so
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then run `org-babel-pop-to-session'."
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(interactive)
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(let ((info (org-babel-get-src-block-info)))
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(if info (progn (org-babel-pop-to-session current-prefix-arg info) t) nil)))
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(add-hook 'org-metadown-hook 'org-babel-pop-to-session-maybe)
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(defvar org-babel-default-header-args '((:session . "none") (:results . "replace"))
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"Default arguments to use when evaluating a source block.")
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(defvar org-babel-default-inline-header-args '((:results . "silent") (:exports . "results"))
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"Default arguments to use when evaluating an inline source block.")
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(defvar org-babel-src-block-regexp nil
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"Regexp used to test when inside of a org-babel src-block")
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(defvar org-babel-inline-src-block-regexp nil
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"Regexp used to test when on an inline org-babel src-block")
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(defun org-babel-named-src-block-regexp-for-name (name)
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"Regexp used to match named src block."
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(concat "#\\+srcname:[ \t]*" (regexp-quote name) "[ \t\n]*"
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org-babel-src-block-regexp))
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(defun org-babel-set-interpreters (var value)
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(set-default var value)
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(setq org-babel-src-block-regexp
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(concat "#\\+begin_src \\("
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(mapconcat 'regexp-quote value "\\|")
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"\\)[ \t]*"
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"\\([ \t]+\\([^\n]+\\)\\)?\n" ;; match header arguments
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"\\([^\000]+?\\)#\\+end_src"))
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(setq org-babel-inline-src-block-regexp
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(concat "src_\\("
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(mapconcat 'regexp-quote value "\\|")
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"\\)"
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"\\(\\|\\[\\(.*\\)\\]\\)"
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"{\\([^\n]+\\)}")))
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(defun org-babel-add-interpreter (interpreter)
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"Add INTERPRETER to `org-babel-interpreters' and update
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`org-babel-src-block-regexp' appropriately."
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(unless (member interpreter org-babel-interpreters)
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(setq org-babel-interpreters (cons interpreter org-babel-interpreters))
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;; (add-to-list 'org-babel-session-defaults (cons interpreter (format "org-babel-%s" interpreter)))
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(org-babel-set-interpreters 'org-babel-interpreters org-babel-interpreters)))
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(defcustom org-babel-interpreters '()
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"Interpreters allows for evaluation tags.
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This is a list of program names (as strings) that can evaluate code and
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insert the output into an Org-mode buffer. Valid choices are
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R Evaluate R code
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emacs-lisp Evaluate Emacs Lisp code and display the result
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sh Pass command to the shell and display the result
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perl The perl interpreter
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python The python interpreter
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ruby The ruby interpreter
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The source block regexp `org-babel-src-block-regexp' is updated
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when a new interpreter is added to this list through the
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customize interface. To add interpreters to this variable from
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lisp code use the `org-babel-add-interpreter' function."
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:group 'org-babel
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:set 'org-babel-set-interpreters
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:type '(set :greedy t
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(const "R")
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(const "emacs-lisp")
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(const "sh")
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(const "perl")
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(const "python")
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(const "ruby")))
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;;; functions
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(defun org-babel-pop-to-session (&optional arg info)
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"Pop to the session of the current source-code block. If
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called with a prefix argument then evaluate the header arguments
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for the source block before entering the session. Copy the body
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of the source block to the kill ring."
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(interactive)
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(let* ((info (or info (org-babel-get-src-block-info)))
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(lang (first info))
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(body (second info))
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(params (third info))
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(session (cdr (assoc :session params))))
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(unless (member lang org-babel-interpreters)
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(error "Language is not in `org-babel-interpreters': %s" lang))
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;; copy body to the kill ring
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(with-temp-buffer (insert (org-babel-trim body)) (copy-region-as-kill (point-min) (point-max)))
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;; if called with a prefix argument, then process header arguments
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(if arg (funcall (intern (concat "org-babel-prep-session:" lang)) session params))
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;; just to the session using pop-to-buffer
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(pop-to-buffer (funcall (intern (format "org-babel-%s-initiate-session" lang)) session))
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(move-end-of-line 1)))
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(defun org-babel-execute-src-block (&optional arg info params)
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"Execute the current source code block, and dump the results
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into the buffer immediately following the block. Results are
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commented by `org-toggle-fixed-width-section'. With optional
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prefix don't dump results into buffer but rather return the
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results in raw elisp (this is useful for automated execution of a
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source block).
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Optionally supply a value for INFO in the form returned by
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`org-babel-get-src-block-info'.
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Optionally supply a value for PARAMS which will be merged with
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the header arguments specified at the source code block."
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(interactive)
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(let* ((info (or info (org-babel-get-src-block-info)))
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(lang (first info))
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(body (second info))
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(params (org-babel-merge-params
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(third info) (org-babel-get-src-block-function-args) params))
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(result-params (split-string (or (cdr (assoc :results params)) "")))
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(result-type (cond ((member "output" result-params) 'output)
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((member "value" result-params) 'value)
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(t 'value)))
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(cmd (intern (concat "org-babel-execute:" lang)))
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result)
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;; (message (format "params=%S" params)) ;; debugging
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(unless (member lang org-babel-interpreters)
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(error "Language is not in `org-babel-interpreters': %s" lang))
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(when arg (setq result-params (cons "silent" result-params)))
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(setq result (org-babel-process-result (funcall cmd body params) result-type))
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(org-babel-insert-result result result-params)
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(case result-type (output nil) (value result))))
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(defun org-babel-process-result (result result-type)
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"This doesn't do anything currently.
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You can see below the various fragments of results-processing
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code that were present in the language-specific files. Out of
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those fragments, I've moved the
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org-babel-python-table-or-results and
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org-babel-import-elisp-from-file functionality into the
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org-babel-*-evaluate functions. I think those should only be
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used in the :results value case, as in the 'output case we are
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not concerned with creating elisp versions of results.
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The rest of the functionality below, concerned with vectorising
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or scalarising results is commented out, has not yet been
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replaced, and may need to be reinstated in this function. "
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result)
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;; ;; ruby
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;; (if (member "scalar" result-params)
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;; results
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;; (case result-type ;; process results based on the result-type
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;; ('output (let ((tmp-file (make-temp-file "org-babel-ruby")))
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;; (with-temp-file tmp-file (insert results))
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;; (org-babel-import-elisp-from-file tmp-file)))
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;; ('value (org-babel-ruby-table-or-results results))))))
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;; python
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;; (if (member "scalar" result-params)
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;; results
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;; (setq result (case result-type ;; process results based on the result-type
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;; ('output (let ((tmp-file (make-temp-file "org-babel-python")))
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;; (with-temp-file tmp-file (insert results))
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;; (org-babel-import-elisp-from-file tmp-file)))
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;; ('value (org-babel-python-table-or-results results))))
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;; (if (and (member "vector" results) (not (listp results)))
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;; (list (list results))
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;; results))))
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;; ;; sh
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;; (if (member "scalar" result-params)
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;; results
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;; (setq results (let ((tmp-file (make-temp-file "org-babel-shell")))
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;; (with-temp-file tmp-file (insert results))
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;; (org-babel-import-elisp-from-file tmp-file)))
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;; (if (and (member "vector" results) (not (listp results)))
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;; (list (list results))
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;; results))))
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;; ;; R
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;; (setq results (if (member "scalar" result-params)
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;; results
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;; (let ((tmp-file (make-temp-file "org-babel-R")))
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;; (with-temp-file tmp-file (insert results))
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;; (org-babel-import-elisp-from-file tmp-file))))
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;; (if (and (member "vector" result-params) (not (listp results)))
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;; (list (list results))
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;; results))))
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;; ;; rest of org-babel-execute-src-block
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;; ;; possibly force result into a vector
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;; (if (and (not (listp result)) (cdr (assoc :results params))
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;; (member "vector" (split-string (cdr (assoc :results params)))))
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;; (setq result (list result)))
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;; result))
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(defun org-babel-eval-buffer (&optional arg)
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"Replace EVAL snippets in the entire buffer."
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(interactive "P")
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(save-excursion
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(goto-char (point-min))
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(while (re-search-forward org-babel-regexp nil t)
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(org-babel-eval-src-block arg))))
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(defun org-babel-eval-subtree (&optional arg)
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"Replace EVAL snippets in the entire subtree."
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(interactive "P")
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(save-excursion
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(org-narrow-to-subtree)
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(org-babel-eval-buffer)
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(widen)))
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(defun org-babel-get-src-block-name ()
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"Return the name of the current source block if one exists.
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This function is analogous to org-babel-lob-get-info. For both
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functions, after they are called, (match-string 1) matches the
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function name, and (match-string 2) matches the function
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arguments inside the parentheses. I think perhaps these functions
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should be renamed to bring out this similarity, perhaps involving
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the word 'call'."
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(let ((case-fold-search t)
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(head (org-babel-where-is-src-block-head)))
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(if head
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(save-excursion
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(goto-char head)
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(if (save-excursion
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(forward-line -1)
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(looking-at "#\\+srcname:[ \f\t\n\r\v]*\\([^ \f\t\n\r\v]+\\)\(\\(.*\\)\)"))
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(org-babel-clean-text-properties (match-string 1)))))))
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(defun org-babel-get-src-block-info ()
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"Return the information of the current source block as a list
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of the following form. (language body header-arguments-alist)"
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(let ((case-fold-search t) head)
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(if (setq head (org-babel-where-is-src-block-head))
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(save-excursion (goto-char head) (org-babel-parse-src-block-match))
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(if (save-excursion ;; inline source block
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(re-search-backward "[ \f\t\n\r\v]" nil t)
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(forward-char 1)
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(looking-at org-babel-inline-src-block-regexp))
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(org-babel-parse-inline-src-block-match)
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nil)))) ;; indicate that no source block was found
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(defun org-babel-get-src-block-function-args ()
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(when (org-babel-get-src-block-name)
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(mapcar (lambda (ref) (cons :var ref))
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(split-string (org-babel-clean-text-properties (match-string 2))
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",[ \f\t\n\r\v]*"))))
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(defmacro org-babel-map-source-blocks (file &rest body)
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"Evaluate BODY forms on each source-block in FILE."
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(declare (indent 1))
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`(save-window-excursion
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(find-file ,file) (goto-char (point-min))
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(while (re-search-forward org-babel-src-block-regexp nil t)
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(goto-char (match-beginning 0))
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(save-match-data ,@body)
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(goto-char (match-end 0)))))
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(defun org-babel-parse-src-block-match ()
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(list (org-babel-clean-text-properties (match-string 1))
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(org-babel-strip-protective-commas (org-babel-clean-text-properties (match-string 4)))
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(org-babel-merge-params org-babel-default-header-args
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(org-babel-parse-header-arguments
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(org-babel-clean-text-properties (or (match-string 3) ""))))))
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(defun org-babel-parse-inline-src-block-match ()
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(list (org-babel-clean-text-properties (match-string 1))
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(org-babel-strip-protective-commas (org-babel-clean-text-properties (match-string 4)))
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(org-combine-plists org-babel-default-inline-header-args
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(org-babel-parse-header-arguments
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(org-babel-clean-text-properties (or (match-string 3) ""))))))
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(defun org-babel-parse-header-arguments (arg-string)
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"Parse a string of header arguments returning an alist."
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(if (> (length arg-string) 0)
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(delq nil
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(mapcar
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(lambda (arg)
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(if (string-match "\\([^ \f\t\n\r\v]+\\)[ \f\t\n\r\v]+\\([^ \f\t\n\r\v]+.*\\)" arg)
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(cons (intern (concat ":" (match-string 1 arg)))
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(org-babel-chomp (match-string 2 arg)))
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(cons (intern (concat ":" arg)) nil)))
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(split-string (concat " " arg-string) "[ \f\t\n\r\v]+:" t)))))
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(defun org-babel-where-is-src-block-head ()
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"Return the point at the beginning of the current source
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block. Specifically at the beginning of the #+BEGIN_SRC line.
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If the point is not on a source block then return nil."
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(let ((initial (point)) top bottom)
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(or
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(save-excursion ;; on a #+srcname: line
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(beginning-of-line 1)
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(and (looking-at "#\\+srcname") (forward-line 1)
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(looking-at org-babel-src-block-regexp)
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(point)))
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(save-excursion ;; on a #+begin_src line
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(beginning-of-line 1)
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(and (looking-at org-babel-src-block-regexp)
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(point)))
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(save-excursion ;; inside a src block
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(and
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(re-search-backward "#\\+begin_src" nil t) (setq top (point))
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(re-search-forward "#\\+end_src" nil t) (setq bottom (point))
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(< top initial) (< initial bottom)
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(goto-char top) (looking-at org-babel-src-block-regexp)
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(point))))))
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(defun org-babel-goto-named-source-block (&optional name)
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"Go to a named source-code block."
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(interactive "ssource-block name: ")
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(let ((point (org-babel-find-named-block name)))
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(if point
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;; taken from `org-open-at-point'
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(progn (goto-char point) (org-show-context))
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(message "source-code block '%s' not found in this buffer" name))))
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(defun org-babel-find-named-block (name)
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"Find a named source-code block.
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Return the location of the source block identified by
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#+srcname NAME, or nil if no such block exists. Set match data
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according to org-babel-named-src-block-regexp."
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(save-excursion
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(let ((case-fold-search t)
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(regexp (org-babel-named-src-block-regexp-for-name name)) msg)
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(goto-char (point-min))
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(when (or (re-search-forward regexp nil t)
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(re-search-backward regexp nil t))
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(match-beginning 0)))))
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(defun org-babel-find-named-result (name)
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"Return the location of the result named NAME in the current
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buffer or nil if no such result exists."
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(save-excursion
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(goto-char (point-min))
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(when (re-search-forward (concat "#\\+resname:[ \t]*" (regexp-quote name)) nil t)
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(move-beginning-of-line 1) (point))))
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(defun org-babel-where-is-src-block-result ()
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"Return the point at the beginning of the result of the current
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source block. Specifically at the beginning of the #+RESNAME:
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line. If no result exists for this block then create a
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#+RESNAME: line following the source block."
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(save-excursion
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(let* ((on-lob-line (progn (beginning-of-line 1)
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(looking-at org-babel-lob-one-liner-regexp)))
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(name (if on-lob-line (org-babel-lob-get-info) (org-babel-get-src-block-name)))
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end head)
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(unless on-lob-line (goto-char (org-babel-where-is-src-block-head)))
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(or (and name (message name) (org-babel-find-named-result name))
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(and (or on-lob-line (re-search-forward "#\\+end_src" nil t))
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(progn (move-end-of-line 1)
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(if (eobp) (insert "\n") (forward-char 1))
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(setq end (point))
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(or (progn ;; either an unnamed #+resname: line already exists
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(re-search-forward "[^ \f\t\n\r\v]" nil t)
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(move-beginning-of-line 1) (looking-at "#\\+resname:"))
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(progn ;; or we need to back up and make one ourselves
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(goto-char end) (open-line 2) (forward-char 1)
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(insert (concat "#+resname:" (if name (concat " " name))))
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(move-beginning-of-line 1) t)))
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(point))))))
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(defun org-babel-insert-result (result &optional insert)
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"Insert RESULT into the current buffer after the end of the
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current source block. With optional argument INSERT controls
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insertion of results in the org-mode file. INSERT can take the
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following values...
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t ------ the default options, simply insert the results after the
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source block
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replace - insert results after the source block replacing any
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previously inserted results
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silent -- no results are inserted"
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(if (stringp result)
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(progn
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(setq result (org-babel-clean-text-properties result))
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(if (member "file" insert) (setq result (org-babel-result-to-file result))))
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(unless (listp result) (setq result (format "%S" result))))
|
|
(if (and insert (member "replace" insert)) (org-babel-remove-result))
|
|
(if (= (length result) 0)
|
|
(if (member "value" result-params)
|
|
(message "No result returned by source block")
|
|
(message "Source block produced no output"))
|
|
(if (and insert (member "silent" insert))
|
|
(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
|
|
(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
|
|
(if (member "file" insert)
|
|
(insert result)
|
|
(org-babel-examplize-region (point) (progn (insert result) (point))))
|
|
(progn
|
|
(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"))))
|
|
|
|
(defun org-babel-result-to-org-string (result)
|
|
"Return RESULT as a string in org-mode format. This function
|
|
relies on `org-babel-insert-result'."
|
|
(with-temp-buffer (org-babel-insert-result result) (buffer-string)))
|
|
|
|
(defun org-babel-remove-result ()
|
|
"Remove the result of the current source block."
|
|
(interactive)
|
|
(save-excursion
|
|
(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))))
|
|
|
|
(defun org-babel-result-to-file (result)
|
|
"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 "]]") "]]"))))
|
|
|
|
(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))))))
|
|
|
|
(defun org-babel-merge-params (&rest plists)
|
|
"Combine all parameter association lists in PLISTS. Later
|
|
elements of PLISTS override the values of previous element. This
|
|
takes into account some special considerations for certain
|
|
parameters when merging lists."
|
|
(let (params results vars var ref)
|
|
(mapc (lambda (plist)
|
|
(mapc (lambda (pair)
|
|
(case (car pair)
|
|
(:var
|
|
;; we want only one specification per variable
|
|
(when (string-match "^\\([^= \f\t\n\r\v]+\\)=\\([^\f\n\r\v]+\\)$" (cdr pair))
|
|
;; TODO: When is this not true? Can there be whitespace around the '='?
|
|
(setq var (intern (match-string 1 (cdr pair)))
|
|
ref (match-string 2 (cdr pair))
|
|
vars (cons (cons var ref) (assq-delete-all var vars)))))
|
|
(:results
|
|
;; maintain list of unique :results specifications
|
|
(setq results (org-uniquify (append (split-string (cdr pair)) results))))
|
|
(t
|
|
;; replace: this covers e.g. :session
|
|
(setq params (cons pair (assq-delete-all (car pair) params))))))
|
|
plist))
|
|
plists)
|
|
(setq vars (mapcar (lambda (pair) (format "%s=%s" (car pair) (cdr pair))) vars))
|
|
(while vars (setq params (cons (cons :var (pop vars)) params)))
|
|
(cons (cons :results (mapconcat 'identity results " ")) params)))
|
|
|
|
(defun org-babel-clean-text-properties (text)
|
|
"Strip all properties from text return."
|
|
(set-text-properties 0 (length text) nil text) text)
|
|
|
|
(defun org-babel-strip-protective-commas (body)
|
|
"Strip protective commas from bodies of source blocks."
|
|
(replace-regexp-in-string "^,#" "#" body))
|
|
|
|
(defun org-babel-read (cell)
|
|
"Convert the string value of CELL to a number if appropriate.
|
|
Otherwise if cell looks like lisp (meaning it starts with a
|
|
\"(\" or a \"'\") then read it as lisp, otherwise return it
|
|
unmodified as a string.
|
|
|
|
This is taken almost directly from `org-read-prop'."
|
|
(if (and (stringp cell) (not (equal cell "")))
|
|
(or (org-babel-number-p cell)
|
|
(if (or (equal "(" (substring cell 0 1))
|
|
(equal "'" (substring cell 0 1)))
|
|
(read cell)
|
|
(progn (set-text-properties 0 (length cell) nil cell) cell)))
|
|
cell))
|
|
|
|
(defun org-babel-number-p (string)
|
|
"Return t if STRING represents a number"
|
|
(if (string-match "^[[:digit:]]*\\.?[[:digit:]]*$" 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))))
|
|
|
|
(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."
|
|
(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))
|
|
|
|
(provide 'org-babel)
|
|
;;; org-babel.el ends here
|