2015-10-26 00:56:00 +00:00
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;;; ob-octave.el --- Babel Functions for Octave and Matlab -*- lexical-binding: t; -*-
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2010-03-18 18:45:39 +00:00
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2021-01-01 19:55:31 +00:00
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;; Copyright (C) 2010-2021 Free Software Foundation, Inc.
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2010-03-18 18:45:39 +00:00
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;; Author: Dan Davison
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;; Keywords: literate programming, reproducible research
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2018-01-16 16:22:00 +00:00
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;; Homepage: https://orgmode.org
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2010-03-18 18:45:39 +00:00
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2010-06-25 16:32:35 +00:00
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;; This file is part of GNU Emacs.
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2010-03-18 18:45:39 +00:00
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2010-06-25 16:32:35 +00:00
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;; GNU Emacs is free software: you can redistribute it and/or modify
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2010-03-18 18:45:39 +00:00
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;; it under the terms of the GNU General Public License as published by
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2010-06-25 16:32:35 +00:00
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; GNU Emacs is distributed in the hope that it will be useful,
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2010-03-18 18:45:39 +00:00
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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2010-06-25 16:32:35 +00:00
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2010-03-18 18:45:39 +00:00
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;; You should have received a copy of the GNU General Public License
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2017-09-13 22:52:52 +00:00
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;; along with GNU Emacs. If not, see <https://www.gnu.org/licenses/>.
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2010-03-18 18:45:39 +00:00
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;;; Commentary:
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;;; Requirements:
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;; octave
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;; octave-mode.el and octave-inf.el come with GNU emacs
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;;; Code:
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2010-06-11 23:02:42 +00:00
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(require 'ob)
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2018-05-10 00:04:12 +00:00
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(require 'org-macs)
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2010-03-18 18:45:39 +00:00
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2010-07-04 15:24:08 +00:00
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(declare-function matlab-shell "ext:matlab-mode")
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(declare-function matlab-shell-run-region "ext:matlab-mode")
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2010-07-03 02:21:31 +00:00
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(defvar org-babel-default-header-args:matlab '())
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2010-06-25 17:12:54 +00:00
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(defvar org-babel-default-header-args:octave '())
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2010-07-03 02:21:31 +00:00
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(defvar org-babel-matlab-shell-command "matlab -nosplash"
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2010-07-13 23:20:08 +00:00
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"Shell command to run matlab as an external process.")
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2010-03-18 18:45:39 +00:00
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(defvar org-babel-octave-shell-command "octave -q"
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2010-07-13 23:20:08 +00:00
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"Shell command to run octave as an external process.")
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2010-03-18 18:45:39 +00:00
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2010-07-03 02:21:31 +00:00
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(defvar org-babel-matlab-with-emacs-link nil
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2010-07-13 23:20:08 +00:00
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"If non-nil use matlab-shell-run-region for session evaluation.
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This will use EmacsLink if (matlab-with-emacs-link) evaluates
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to a non-nil value.")
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2010-07-03 02:21:31 +00:00
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(defvar org-babel-matlab-emacs-link-wrapper-method
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2012-08-11 17:10:44 +00:00
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"%s
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2010-07-03 02:21:31 +00:00
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if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
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else, save -ascii %s ans
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end
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delete('%s')
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")
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2010-07-04 20:48:41 +00:00
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(defvar org-babel-octave-wrapper-method
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"%s
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if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
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2010-08-04 03:54:24 +00:00
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else, dlmwrite('%s', ans, '\\t')
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2010-07-04 20:48:41 +00:00
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end")
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2015-09-17 23:08:20 +00:00
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(defvar org-babel-octave-eoe-indicator "'org_babel_eoe'")
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2010-07-04 20:48:41 +00:00
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(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
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2010-07-03 02:21:31 +00:00
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(defun org-babel-execute:matlab (body params)
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2010-07-13 23:20:08 +00:00
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"Execute a block of matlab code with Babel."
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2010-07-03 02:21:31 +00:00
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(org-babel-execute:octave body params 'matlab))
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2010-08-01 18:34:28 +00:00
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2010-03-18 18:45:39 +00:00
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(defun org-babel-execute:octave (body params &optional matlabp)
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2010-07-13 23:20:08 +00:00
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"Execute a block of octave code with Babel."
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2010-10-21 11:52:24 +00:00
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(let* ((session
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2010-07-03 02:21:31 +00:00
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(funcall (intern (format "org-babel-%s-initiate-session"
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(if matlabp "matlab" "octave")))
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2016-09-22 17:45:15 +00:00
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(cdr (assq :session params)) params))
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(result-type (cdr (assq :result-type params)))
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2010-10-21 11:18:43 +00:00
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(full-body
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(org-babel-expand-body:generic
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body params (org-babel-variable-assignments:octave params)))
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2014-05-16 03:26:30 +00:00
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(gfx-file (ignore-errors (org-babel-graphical-output-file params)))
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2010-07-04 20:48:41 +00:00
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(result (org-babel-octave-evaluate
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2011-12-16 19:12:39 +00:00
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session
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2014-05-16 03:26:30 +00:00
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(if gfx-file
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2011-12-16 19:12:39 +00:00
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(mapconcat 'identity
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(list
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"set (0, \"defaultfigurevisible\", \"off\");"
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full-body
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2014-05-16 03:26:30 +00:00
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(format "print -dpng %s" gfx-file))
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2011-12-16 19:12:39 +00:00
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"\n")
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full-body)
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result-type matlabp)))
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2014-05-16 03:26:30 +00:00
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(if gfx-file
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2011-12-16 19:12:39 +00:00
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nil
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(org-babel-reassemble-table
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result
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(org-babel-pick-name
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2016-09-22 17:45:15 +00:00
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(cdr (assq :colname-names params)) (cdr (assq :colnames params)))
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2011-12-16 19:12:39 +00:00
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(org-babel-pick-name
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2016-09-22 17:45:15 +00:00
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(cdr (assq :rowname-names params)) (cdr (assq :rownames params)))))))
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2010-03-18 18:45:39 +00:00
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2010-07-03 02:21:31 +00:00
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(defun org-babel-prep-session:matlab (session params)
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"Prepare SESSION according to PARAMS."
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(org-babel-prep-session:octave session params 'matlab))
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2010-08-01 18:34:28 +00:00
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2010-10-21 11:18:43 +00:00
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(defun org-babel-variable-assignments:octave (params)
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2012-07-30 08:08:15 +00:00
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"Return list of octave statements assigning the block's variables."
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2010-10-14 20:56:41 +00:00
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(mapcar
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(lambda (pair)
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2011-03-31 05:28:59 +00:00
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(format "%s=%s;"
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2010-10-14 20:56:41 +00:00
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(car pair)
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(org-babel-octave-var-to-octave (cdr pair))))
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2015-10-29 19:26:11 +00:00
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(org-babel--get-vars params)))
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2010-10-14 20:56:41 +00:00
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2010-10-21 11:18:43 +00:00
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(defalias 'org-babel-variable-assignments:matlab
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'org-babel-variable-assignments:octave)
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2010-03-18 18:45:39 +00:00
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(defun org-babel-octave-var-to-octave (var)
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2010-07-13 23:20:08 +00:00
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"Convert an emacs-lisp value into an octave variable.
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2010-03-18 18:45:39 +00:00
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Converts an emacs-lisp variable into a string of octave code
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specifying a variable of the same value."
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(if (listp var)
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From: Juan <Pechiar@computer.org>
Hi,
I'm starting to work with ob-octave and found several problems:
The first, for which I have a fix (see patch below) is that octave's
output was passed on as a string instead of being interpreted as a table:
[diff removed]
Now this works:
8<------------------------------------------------------------
#+source: test_output
#+begin_src octave :results value vector
[[1 2 3];[4 5 6]]
#+end_src
#+results: test_output
| 1.00000000e+00 | 2.00000000e+00 | 3.00000000e+00 |
| 4.00000000e+00 | 5.00000000e+00 | 6.00000000e+00 |
8<------------------------------------------------------------
(before the patch you'd get a single table element with something like
"1 2 3\n 4 5 6\n" inside).
The second problem is that if I use octave table output as input to
another block, it gets interpreted as a string instead of a vector:
8<------------------------------------------------------------
#+results: test_output
| 1.25000000e+00 |
#+source: check_input
#+begin_src octave :var input=test_output() :results output
ischar( input )
size( input )
#+end_src
#+results: check_input
: input = 1.25000000e+00
: ans = 1
: ans =
: 1 14
8<------------------------------------------------------------
This has to do with the EXP notation. The 'e+00' suffix makes the
whole table into a string. The problem is with "%S" in the formatting
inside org-babel-octave-var-to-octave.
The following patch seems to fix it (and makes it possible to work with
complex numbers inside the tables)::
[diff removed]
A third problem is with org-babel-octave-var-to-octave.
For example:
: (org-babel-octave-var-to-octave '( ( 1 2 3 ) ( 4 5 6 ) ))
: -> "[[1, 2, 3], [4, 5, 6]]"
This is not a 2x3 matrix, but a 1x6 vector:
: octave-3.2.3:1> [[1,2,3],[4,5,6]]
: ans =
: 1 2 3 4 5 6
a semicolon ';' or '\n' is needed between rows instead of a comma.
To sum up:
- 2 patches for prepare-session and importing the results back as
org-tables (I don't know if these patches break anything).
- 1 problem with matrix notation in org-babel-octave-var-to-octave.
I'll try to provide a patch for this today.
2010-08-01 Juan Pechiar <Pechiar@computer.org>
* ob-octave.el (org-babel-octave-evaluate-external-process):
use `org-babel-octave-import-elisp-from-file' instead of
`org-babel-eval-read-file'.
(org-babel-octave-var-to-octave): separate matrix rows with
';', and use '%s' as format specifier instead of '%S'
2010-08-01 22:09:24 +00:00
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(concat "[" (mapconcat #'org-babel-octave-var-to-octave var
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(if (listp (car var)) "; " ",")) "]")
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2011-11-08 21:19:04 +00:00
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(cond
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((stringp var)
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2015-09-17 23:08:20 +00:00
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(format "'%s'" var))
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2011-11-08 21:19:04 +00:00
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(t
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(format "%s" var)))))
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2010-03-18 18:45:39 +00:00
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(defun org-babel-prep-session:octave (session params &optional matlabp)
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"Prepare SESSION according to the header arguments specified in PARAMS."
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(let* ((session (org-babel-octave-initiate-session session params matlabp))
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2010-10-21 11:18:43 +00:00
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(var-lines (org-babel-variable-assignments:octave params)))
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2010-03-18 18:45:39 +00:00
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(org-babel-comint-in-buffer session
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(mapc (lambda (var)
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Xemacs incompatibilities
Carsten Dominik <carsten.dominik@gmail.com> writes:
> On May 17, 2010, at 4:39 PM, Michael Sperber wrote:
>
>> In particular, fixing the require won't be enough: org-babel-python.el
>> uses `run-python' and interacts with the inferior Python, whereas
>> python-mode.el defines `py-shell'.
>>
>> Should I try to abstract over the differences?
>
> Yes, this would be much appreciated. (I think, Eric or Dan?)
OK, I've attached a patch that makes `org-babel-python' work on XEmacs.
Most of the issues are pure XEmacs issues. Notes:
- XEmacs doesn't have [[:digit:]] - I hope to rectify this in the
future, but it seems there's no downside in this particular case to
replacing by [0-9].
- XEmacs doesn't have `move-end-of-line', but does have `end-of-line'.
I don't understand the intent of having both of these, but the code
seems fine with `end-of-line'.
- It seems there are way too few `require's throughout org-babel. I
don't know if it's OK to add the ones I needed.
- `org-babel-python-evaluate' looked broken as-is: It doesn't use the
`body' argument properly, the result is (I think) processed in the
wrong order and not properly split into lines. I've fixed all these,
but a review is probably in order.
2010-05-24 19:22:50 +00:00
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(end-of-line 1) (insert var) (comint-send-input nil t)
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2020-02-18 21:57:37 +00:00
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(org-babel-comint-wait-for-output session))
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var-lines))
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2010-03-18 18:45:39 +00:00
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session))
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2010-07-03 02:21:31 +00:00
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(defun org-babel-matlab-initiate-session (&optional session params)
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2010-07-13 23:20:08 +00:00
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"Create a matlab inferior process buffer.
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If there is not a current inferior-process-buffer in SESSION then
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2012-08-11 17:10:44 +00:00
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create. Return the initialized session."
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2010-07-03 02:21:31 +00:00
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(org-babel-octave-initiate-session session params 'matlab))
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2010-08-01 18:34:28 +00:00
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2015-10-26 00:56:00 +00:00
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(defun org-babel-octave-initiate-session (&optional session _params matlabp)
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2010-07-13 23:20:08 +00:00
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"Create an octave inferior process buffer.
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If there is not a current inferior-process-buffer in SESSION then
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2012-08-11 17:10:44 +00:00
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create. Return the initialized session."
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2013-05-19 18:49:38 +00:00
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(if matlabp (require 'matlab) (or (require 'octave-inf nil 'noerror)
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(require 'octave)))
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2010-03-18 18:45:39 +00:00
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(unless (string= session "none")
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2010-07-04 20:48:41 +00:00
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(let ((session (or session
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(if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
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2010-03-18 18:45:39 +00:00
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(if (org-babel-comint-buffer-livep session) session
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(save-window-excursion
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2010-04-30 20:47:07 +00:00
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(if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
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(run-octave))
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2010-03-18 18:45:39 +00:00
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(rename-buffer (if (bufferp session) (buffer-name session)
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2010-07-04 20:48:41 +00:00
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(if (stringp session) session (buffer-name))))
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(current-buffer))))))
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2010-03-18 18:45:39 +00:00
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2010-07-03 02:21:31 +00:00
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(defun org-babel-octave-evaluate
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2010-08-01 16:17:47 +00:00
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(session body result-type &optional matlabp)
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2010-07-13 23:20:08 +00:00
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"Pass BODY to the octave process in SESSION.
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2015-09-21 04:24:12 +00:00
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If RESULT-TYPE equals `output' then return the outputs of the
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statements in BODY, if RESULT-TYPE equals `value' then return the
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2010-07-13 23:20:08 +00:00
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value of the last statement in BODY, as elisp."
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2010-03-18 18:45:39 +00:00
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(if session
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2010-07-04 20:48:41 +00:00
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(org-babel-octave-evaluate-session session body result-type matlabp)
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2010-03-18 18:45:39 +00:00
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(org-babel-octave-evaluate-external-process body result-type matlabp)))
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(defun org-babel-octave-evaluate-external-process (body result-type matlabp)
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2010-06-12 00:12:15 +00:00
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"Evaluate BODY in an external octave process."
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2010-07-04 20:48:41 +00:00
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(let ((cmd (if matlabp
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org-babel-matlab-shell-command
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org-babel-octave-shell-command)))
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2016-07-25 14:34:48 +00:00
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(pcase result-type
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(`output (org-babel-eval cmd body))
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(`value (let ((tmp-file (org-babel-temp-file "octave-")))
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2010-07-04 20:48:41 +00:00
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(org-babel-eval
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cmd
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2010-09-22 20:40:14 +00:00
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(format org-babel-octave-wrapper-method body
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(org-babel-process-file-name tmp-file 'noquote)
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(org-babel-process-file-name tmp-file 'noquote)))
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(org-babel-octave-import-elisp-from-file tmp-file))))))
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2010-07-03 02:21:31 +00:00
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(defun org-babel-octave-evaluate-session
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2016-07-25 14:34:48 +00:00
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(session body result-type &optional matlabp)
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2010-06-12 00:12:15 +00:00
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"Evaluate BODY in SESSION."
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2010-09-20 23:38:31 +00:00
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(let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
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2010-08-25 20:43:07 +00:00
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(wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
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2010-03-18 18:45:39 +00:00
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(full-body
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2016-07-25 14:34:48 +00:00
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(pcase result-type
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(`output
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2010-03-18 18:45:39 +00:00
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(mapconcat
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#'org-babel-chomp
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(list body org-babel-octave-eoe-indicator) "\n"))
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2016-07-25 14:34:48 +00:00
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(`value
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2010-05-04 01:43:23 +00:00
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(if (and matlabp org-babel-matlab-with-emacs-link)
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(concat
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(format org-babel-matlab-emacs-link-wrapper-method
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2010-09-22 20:40:14 +00:00
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body
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(org-babel-process-file-name tmp-file 'noquote)
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(org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
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2010-05-04 01:43:23 +00:00
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(mapconcat
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#'org-babel-chomp
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2010-07-03 02:21:31 +00:00
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(list (format org-babel-octave-wrapper-method
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2010-09-22 20:40:14 +00:00
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body
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(org-babel-process-file-name tmp-file 'noquote)
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(org-babel-process-file-name tmp-file 'noquote))
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2010-05-04 01:43:23 +00:00
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org-babel-octave-eoe-indicator) "\n")))))
|
2010-03-19 01:04:25 +00:00
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(raw (if (and matlabp org-babel-matlab-with-emacs-link)
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|
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(save-window-excursion
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(with-temp-buffer
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|
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(insert full-body)
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2010-05-04 01:43:23 +00:00
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(write-region "" 'ignored wait-file nil nil nil 'excl)
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2010-03-19 01:04:25 +00:00
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(matlab-shell-run-region (point-min) (point-max))
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2010-05-04 01:43:23 +00:00
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(message "Waiting for Matlab Emacs Link")
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(while (file-exists-p wait-file) (sit-for 0.01))
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2010-03-19 01:04:25 +00:00
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"")) ;; matlab-shell-run-region doesn't seem to
|
2012-08-11 17:10:44 +00:00
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;; make *matlab* buffer contents easily
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;; available, so :results output currently
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;; won't work
|
2010-06-12 22:57:38 +00:00
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|
(org-babel-comint-with-output
|
2010-06-15 00:00:49 +00:00
|
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|
(session
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|
|
(if matlabp
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org-babel-octave-eoe-indicator
|
|
|
|
org-babel-octave-eoe-output)
|
|
|
|
t full-body)
|
2020-02-18 21:57:37 +00:00
|
|
|
(insert full-body) (comint-send-input nil t))))
|
|
|
|
results)
|
2016-07-25 14:34:48 +00:00
|
|
|
(pcase result-type
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|
|
|
(`value
|
2010-09-22 20:40:14 +00:00
|
|
|
(org-babel-octave-import-elisp-from-file tmp-file))
|
2016-07-25 14:34:48 +00:00
|
|
|
(`output
|
|
|
|
(setq results
|
|
|
|
(if matlabp
|
2018-10-06 07:40:33 +00:00
|
|
|
(cdr (reverse (delq "" (mapcar #'org-strip-quotes
|
|
|
|
(mapcar #'org-trim raw)))))
|
2016-07-25 14:34:48 +00:00
|
|
|
(cdr (member org-babel-octave-eoe-output
|
2018-10-06 07:40:33 +00:00
|
|
|
(reverse (mapcar #'org-strip-quotes
|
|
|
|
(mapcar #'org-trim raw)))))))
|
2016-07-25 14:34:48 +00:00
|
|
|
(mapconcat #'identity (reverse results) "\n")))))
|
2010-03-18 18:45:39 +00:00
|
|
|
|
2010-04-07 19:51:04 +00:00
|
|
|
(defun org-babel-octave-import-elisp-from-file (file-name)
|
2010-07-13 23:20:08 +00:00
|
|
|
"Import data from FILE-NAME.
|
|
|
|
This removes initial blank and comment lines and then calls
|
|
|
|
`org-babel-import-elisp-from-file'."
|
2010-09-20 23:38:31 +00:00
|
|
|
(let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
|
2010-04-07 19:51:04 +00:00
|
|
|
(with-temp-file temp-file
|
|
|
|
(insert-file-contents file-name)
|
|
|
|
(re-search-forward "^[ \t]*[^# \t]" nil t)
|
2018-05-10 00:14:24 +00:00
|
|
|
(when (< (setq beg (point-min))
|
|
|
|
(setq end (point-at-bol)))
|
|
|
|
(delete-region beg end)))
|
2010-08-04 03:54:24 +00:00
|
|
|
(org-babel-import-elisp-from-file temp-file '(16))))
|
2010-04-07 19:51:04 +00:00
|
|
|
|
2010-06-11 23:02:42 +00:00
|
|
|
(provide 'ob-octave)
|
2010-06-25 16:32:35 +00:00
|
|
|
|
2010-06-11 23:02:42 +00:00
|
|
|
;;; ob-octave.el ends here
|