2010-06-11 23:02:42 +00:00
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;;; ob-python.el --- org-babel functions for python evaluation
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2009-06-12 15:46:00 +00:00
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2012-01-05 08:43:21 +00:00
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;; Copyright (C) 2009-2012 Free Software Foundation, Inc.
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2009-06-12 15:46:00 +00:00
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2012-04-01 22:53:28 +00:00
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;; Authors: Eric Schulte
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;; Dan Davison
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2009-06-12 15:46:00 +00:00
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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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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2009-06-12 15:46:00 +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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2009-06-12 15:46:00 +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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2009-06-12 15:46:00 +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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2009-06-12 15:46:00 +00:00
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;; You should have received a copy of the GNU General Public License
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2010-06-25 16:32:35 +00:00
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;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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2009-06-12 15:46:00 +00:00
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;;; Commentary:
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;; Org-Babel support for evaluating python source code.
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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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2010-07-03 02:21:31 +00:00
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(require 'ob-ref)
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2010-06-11 23:02:42 +00:00
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(require 'ob-comint)
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2010-07-04 21:46:13 +00:00
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(require 'ob-eval)
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2010-07-03 02:21:31 +00:00
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(eval-when-compile (require 'cl))
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(declare-function org-remove-indentation "org" )
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2010-07-09 17:58:12 +00:00
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(declare-function py-shell "ext:python-mode" (&optional argprompt))
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2010-12-14 01:45:26 +00:00
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(declare-function py-toggle-shells "ext:python-mode" (arg))
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2010-07-09 17:58:12 +00:00
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(declare-function run-python "ext:python" (&optional cmd noshow new))
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2009-06-12 15:46:00 +00:00
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2011-06-21 22:34:41 +00:00
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(defvar org-babel-tangle-lang-exts)
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2010-06-17 17:21:14 +00:00
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(add-to-list 'org-babel-tangle-lang-exts '("python" . "py"))
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2010-06-25 17:12:54 +00:00
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(defvar org-babel-default-header-args:python '())
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2010-07-04 16:48:12 +00:00
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(defvar org-babel-python-command "python"
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2010-07-13 23:20:08 +00:00
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"Name of command for executing python code.")
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2010-07-04 16:48:12 +00:00
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2010-07-09 17:58:12 +00:00
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(defvar org-babel-python-mode (if (featurep 'xemacs) 'python-mode 'python)
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2011-01-20 15:05:22 +00:00
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"Preferred python mode for use in running python interactively.
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This will typically be either 'python or 'python-mode.")
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2010-07-09 17:58:12 +00:00
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2010-10-13 04:59:24 +00:00
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(defvar org-src-preserve-indentation)
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2010-04-16 05:14:10 +00:00
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2009-07-08 04:13:07 +00:00
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(defun org-babel-execute:python (body params)
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2010-07-13 23:20:08 +00:00
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"Execute a block of Python code with Babel.
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This function is called by `org-babel-execute-src-block'."
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2010-10-21 11:52:24 +00:00
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(let* ((session (org-babel-python-initiate-session
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(cdr (assoc :session params))))
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(result-params (cdr (assoc :result-params params)))
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(result-type (cdr (assoc :result-type params)))
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2010-11-27 23:59:51 +00:00
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(return-val (when (and (eq result-type 'value) (not session))
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(cdr (assoc :return params))))
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2010-12-03 14:29:28 +00:00
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(preamble (cdr (assoc :preamble params)))
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2010-10-21 11:28:19 +00:00
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(full-body
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(org-babel-expand-body:generic
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2012-04-23 15:39:28 +00:00
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(concat body (if return-val (format "\nreturn %s" return-val) ""))
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2010-11-27 23:59:51 +00:00
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params (org-babel-variable-assignments:python params)))
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2010-07-03 02:21:31 +00:00
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(result (org-babel-python-evaluate
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2010-12-03 14:29:28 +00:00
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session full-body result-type result-params preamble)))
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2010-12-21 10:21:28 +00:00
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(org-babel-reassemble-table
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result
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(org-babel-pick-name (cdr (assoc :colname-names params))
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(cdr (assoc :colnames params)))
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(org-babel-pick-name (cdr (assoc :rowname-names params))
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(cdr (assoc :rownames params))))))
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2009-06-12 15:46:00 +00:00
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2009-06-14 18:34:06 +00:00
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(defun org-babel-prep-session:python (session params)
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2010-10-21 11:28:19 +00:00
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"Prepare SESSION according to the header arguments in PARAMS.
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VARS contains resolved variable references"
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2009-06-14 18:34:06 +00:00
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(let* ((session (org-babel-python-initiate-session session))
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2010-10-21 11:28:19 +00:00
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(var-lines
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(org-babel-variable-assignments:python params)))
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2009-06-14 18:34:06 +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)
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2010-01-11 17:14:30 +00:00
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(org-babel-comint-wait-for-output session)) var-lines))
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session))
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(defun org-babel-load-session:python (session body params)
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"Load BODY into SESSION."
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(save-window-excursion
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(let ((buffer (org-babel-prep-session:python session params)))
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(with-current-buffer buffer
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert (org-babel-chomp body)))
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buffer)))
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2009-06-14 18:34:06 +00:00
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;; helper functions
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2010-10-21 11:28:19 +00:00
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(defun org-babel-variable-assignments:python (params)
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2010-10-14 21:01:53 +00:00
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"Return list of python statements assigning the block's variables"
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2010-10-14 20:05:02 +00:00
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(mapcar
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(lambda (pair)
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(format "%s=%s"
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(car pair)
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(org-babel-python-var-to-python (cdr pair))))
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2010-10-16 03:35:45 +00:00
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(mapcar #'cdr (org-babel-get-header params :var))))
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2010-10-14 20:05:02 +00:00
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2009-06-12 15:46:00 +00:00
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(defun org-babel-python-var-to-python (var)
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2010-07-13 23:20:08 +00:00
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"Convert an elisp value to a python variable.
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Convert an elisp value, VAR, into a string of python source code
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specifying a variable of the same value."
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2009-06-12 15:46:00 +00:00
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(if (listp var)
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(concat "[" (mapconcat #'org-babel-python-var-to-python var ", ") "]")
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2010-07-14 18:31:38 +00:00
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(if (equal var 'hline)
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"None"
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(format
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(if (and (stringp var) (string-match "[\n\r]" var)) "\"\"%S\"\"" "%S")
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var))))
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2009-06-12 15:46:00 +00:00
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2009-07-05 23:55:54 +00:00
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(defun org-babel-python-table-or-string (results)
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2010-07-13 23:20:08 +00:00
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"Convert RESULTS into an appropriate elisp value.
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If the results look like a list or tuple, then convert them into an
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2009-06-12 15:46:00 +00:00
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Emacs-lisp table, otherwise return the results as a string."
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2010-11-23 01:20:56 +00:00
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(org-babel-script-escape results))
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2009-06-12 15:46:00 +00:00
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2010-07-01 22:09:34 +00:00
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(defvar org-babel-python-buffers '((:default . nil)))
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2009-06-12 21:48:40 +00:00
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(defun org-babel-python-session-buffer (session)
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2010-06-12 00:12:15 +00:00
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"Return the buffer associated with SESSION."
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2009-06-12 21:48:40 +00:00
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(cdr (assoc session org-babel-python-buffers)))
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2011-03-01 07:08:36 +00:00
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(defvar py-default-interpreter)
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2009-06-14 18:34:06 +00:00
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(defun org-babel-python-initiate-session-by-key (&optional session)
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2010-07-13 23:20:08 +00:00
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"Initiate a python session.
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If there is not a current inferior-process-buffer in SESSION
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2009-06-12 15:46:00 +00:00
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then create. Return the initialized session."
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2010-07-09 17:58:12 +00:00
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(require org-babel-python-mode)
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2009-06-12 21:48:40 +00:00
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(save-window-excursion
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(let* ((session (if session (intern session) :default))
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(python-buffer (org-babel-python-session-buffer session)))
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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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(cond
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2010-08-16 15:08:37 +00:00
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((and (eq 'python org-babel-python-mode)
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2010-07-09 17:58:12 +00:00
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(fboundp 'run-python)) ; python.el
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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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(run-python))
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2010-08-16 15:08:37 +00:00
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((and (eq 'python-mode org-babel-python-mode)
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2010-07-09 17:58:12 +00:00
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(fboundp 'py-shell)) ; python-mode.el
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2010-12-14 01:45:26 +00:00
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;; Make sure that py-which-bufname is initialized, as otherwise
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;; it will be overwritten the first time a Python buffer is
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;; created.
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2011-01-14 21:53:28 +00:00
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(py-toggle-shells py-default-interpreter)
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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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;; `py-shell' creates a buffer whose name is the value of
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;; `py-which-bufname' with '*'s at the beginning and end
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2011-01-14 21:53:28 +00:00
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(let* ((bufname (if (and python-buffer (buffer-live-p python-buffer))
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2010-07-04 16:48:12 +00:00
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(replace-regexp-in-string ;; zap surrounding *
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"^\\*\\([^*]+\\)\\*$" "\\1" python-buffer)
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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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(concat "Python-" (symbol-name session))))
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2010-07-04 16:48:12 +00:00
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(py-which-bufname bufname))
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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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(py-shell)
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(setq python-buffer (concat "*" bufname "*"))))
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(t
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(error "No function available for running an inferior python.")))
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2010-07-04 16:48:12 +00:00
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(setq org-babel-python-buffers
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(cons (cons session python-buffer)
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(assq-delete-all session org-babel-python-buffers)))
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2009-06-12 21:48:40 +00:00
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session)))
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2009-06-12 15:46:00 +00:00
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2010-03-13 17:59:41 +00:00
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(defun org-babel-python-initiate-session (&optional session params)
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2010-06-12 00:12:15 +00:00
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"Create a session named SESSION according to PARAMS."
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2009-06-15 18:14:32 +00:00
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(unless (string= session "none")
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2010-07-04 16:48:12 +00:00
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(org-babel-python-session-buffer
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(org-babel-python-initiate-session-by-key session))))
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2009-06-12 15:46:00 +00:00
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(defvar org-babel-python-eoe-indicator "'org_babel_python_eoe'"
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2010-07-13 23:20:08 +00:00
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"A string to indicate that evaluation has completed.")
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2009-06-15 18:14:32 +00:00
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(defvar org-babel-python-wrapper-method
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"
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def main():
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%s
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open('%s', 'w').write( str(main()) )")
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2009-10-18 19:14:39 +00:00
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(defvar org-babel-python-pp-wrapper-method
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"
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import pprint
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def main():
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%s
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open('%s', 'w').write( pprint.pformat(main()) )")
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2009-06-12 15:46:00 +00:00
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2010-07-03 02:21:31 +00:00
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(defun org-babel-python-evaluate
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2010-12-03 14:29:28 +00:00
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(session body &optional result-type result-params preamble)
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2010-09-08 01:58:58 +00:00
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"Evaluate BODY as python code."
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(if session
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(org-babel-python-evaluate-session
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session body result-type result-params)
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(org-babel-python-evaluate-external-process
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2010-12-03 14:29:28 +00:00
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body result-type result-params preamble)))
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2010-09-08 01:58:58 +00:00
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(defun org-babel-python-evaluate-external-process
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2010-12-03 14:29:28 +00:00
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(body &optional result-type result-params preamble)
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2010-09-08 01:58:58 +00:00
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"Evaluate BODY in external python process.
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If RESULT-TYPE equals 'output then return standard output as a
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string. If RESULT-TYPE equals 'value then return the value of the
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last statement in BODY, as elisp."
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2011-04-15 02:24:10 +00:00
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((lambda (raw)
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(if (or (member "code" result-params)
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(member "pp" result-params)
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(and (member "output" result-params)
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(not (member "table" result-params))))
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raw
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(org-babel-python-table-or-string (org-babel-trim raw))))
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(case result-type
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(output (org-babel-eval org-babel-python-command
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(concat (if preamble (concat preamble "\n") "")
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body)))
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(value (let ((tmp-file (org-babel-temp-file "python-")))
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(org-babel-eval
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org-babel-python-command
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(concat
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(if preamble (concat preamble "\n") "")
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(format
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(if (member "pp" result-params)
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org-babel-python-pp-wrapper-method
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org-babel-python-wrapper-method)
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(mapconcat
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(lambda (line) (format "\t%s" line))
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(split-string
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(org-remove-indentation
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(org-babel-trim body))
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"[\r\n]") "\n")
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(org-babel-process-file-name tmp-file 'noquote))))
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2010-09-08 01:58:58 +00:00
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(org-babel-eval-read-file tmp-file))))))
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(defun org-babel-python-evaluate-session
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(session body &optional result-type result-params)
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"Pass BODY to the Python process in SESSION.
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If RESULT-TYPE equals 'output then return standard output as a
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string. If RESULT-TYPE equals 'value then return the value of the
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last statement in BODY, as elisp."
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2012-07-19 04:11:36 +00:00
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(org-flet ((send-wait () (comint-send-input nil t) (sleep-for 0 5))
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2011-07-03 15:10:43 +00:00
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(dump-last-value
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2010-09-08 01:58:58 +00:00
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(tmp-file pp)
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(mapc
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2011-07-03 15:10:43 +00:00
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(lambda (statement) (insert statement) (send-wait))
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2010-09-08 01:58:58 +00:00
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(if pp
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(list
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2010-12-01 16:54:09 +00:00
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"import pprint"
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2010-09-22 20:40:14 +00:00
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(format "open('%s', 'w').write(pprint.pformat(_))"
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(org-babel-process-file-name tmp-file 'noquote)))
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(list (format "open('%s', 'w').write(str(_))"
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(org-babel-process-file-name tmp-file 'noquote))))))
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2010-09-08 01:58:58 +00:00
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(input-body (body)
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2011-07-03 15:10:43 +00:00
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(mapc (lambda (line) (insert line) (send-wait))
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(split-string body "[\r\n]"))
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(send-wait)))
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2011-04-15 02:24:10 +00:00
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((lambda (results)
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2011-07-03 18:12:11 +00:00
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(unless (string= (substring org-babel-python-eoe-indicator 1 -1) results)
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(if (or (member "code" result-params)
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(member "pp" result-params)
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(and (member "output" result-params)
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(not (member "table" result-params))))
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results
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(org-babel-python-table-or-string results))))
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2011-04-15 02:24:10 +00:00
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(case result-type
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(output
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(mapconcat
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#'org-babel-trim
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(butlast
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(org-babel-comint-with-output
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(session org-babel-python-eoe-indicator t body)
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2011-07-03 15:10:43 +00:00
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(input-body body)
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2011-07-03 18:08:13 +00:00
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(send-wait) (send-wait)
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2011-07-03 15:10:43 +00:00
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(insert org-babel-python-eoe-indicator)
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2011-07-03 18:08:13 +00:00
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(send-wait))
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2011-06-20 19:18:09 +00:00
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2) "\n"))
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2011-04-15 02:24:10 +00:00
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(value
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2010-09-22 20:52:48 +00:00
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(let ((tmp-file (org-babel-temp-file "python-")))
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2010-09-08 01:58:58 +00:00
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(org-babel-comint-with-output
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2011-02-06 15:03:02 +00:00
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(session org-babel-python-eoe-indicator nil body)
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2010-09-08 01:58:58 +00:00
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(let ((comint-process-echoes nil))
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(input-body body)
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(dump-last-value tmp-file (member "pp" result-params))
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2011-07-03 15:10:43 +00:00
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(send-wait) (send-wait)
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2010-09-08 01:58:58 +00:00
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(insert org-babel-python-eoe-indicator)
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2011-07-03 15:10:43 +00:00
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(send-wait)))
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2010-09-08 01:58:58 +00:00
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(org-babel-eval-read-file tmp-file)))))))
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2009-06-12 15:46:00 +00:00
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2009-06-12 23:23:28 +00:00
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(defun org-babel-python-read-string (string)
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2010-02-19 16:34:16 +00:00
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"Strip 's from around python string"
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(if (string-match "^'\\([^\000]+\\)'$" string)
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2009-06-12 23:23:28 +00:00
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(match-string 1 string)
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string))
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2010-06-11 23:02:42 +00:00
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(provide 'ob-python)
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2010-06-25 16:32:35 +00:00
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2011-08-15 18:04:38 +00:00
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2010-06-25 16:32:35 +00:00
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2010-06-11 23:02:42 +00:00
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;;; ob-python.el ends here
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