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org-mode/lisp/ob-python.el

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;;; ob-python.el --- org-babel functions for python evaluation
;; Copyright (C) 2009-2012 Free Software Foundation, Inc.
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;; Authors: Eric Schulte
;; Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; This file is part of GNU Emacs.
;; GNU Emacs is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;; GNU Emacs is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
;;; Commentary:
;; Org-Babel support for evaluating python source code.
;;; Code:
(require 'ob)
(require 'ob-ref)
(require 'ob-comint)
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(require 'ob-eval)
(eval-when-compile (require 'cl))
(declare-function org-remove-indentation "org" )
(declare-function py-shell "ext:python-mode" (&optional argprompt))
(declare-function py-toggle-shells "ext:python-mode" (arg))
(declare-function run-python "ext:python" (&optional cmd noshow new))
(defvar org-babel-tangle-lang-exts)
(add-to-list 'org-babel-tangle-lang-exts '("python" . "py"))
(defvar org-babel-default-header-args:python '())
(defvar org-babel-python-command "python"
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"Name of command for executing python code.")
(defvar org-babel-python-mode (if (featurep 'xemacs) 'python-mode 'python)
"Preferred python mode for use in running python interactively.
This will typically be either 'python or 'python-mode.")
(defvar org-src-preserve-indentation)
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(defun org-babel-execute:python (body params)
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"Execute a block of Python code with Babel.
This function is called by `org-babel-execute-src-block'."
babel:removing calls to ob-process-params, and updating use of results * lisp/ob-C.el (org-babel-C-execute): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-R.el (org-babel-execute:R): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-R-variable-assignments): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-asymptote.el (org-babel-execute:asymptote): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-clojure.el (org-babel-execute:clojure): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-dot.el (org-babel-execute:dot): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-emacs-lisp.el (org-babel-expand-body:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-execute:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-haskell.el (org-babel-execute:haskell): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-js.el (org-babel-execute:js): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-lisp.el (org-babel-execute:lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ocaml.el (org-babel-execute:ocaml): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-octave.el (org-babel-execute:octave): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-perl.el (org-babel-execute:perl): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-python.el (org-babel-execute:python): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ruby.el (org-babel-execute:ruby): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-scheme.el (org-babel-execute:scheme): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-screen.el (org-babel-execute:screen): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-prep-session:screen): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sh.el (org-babel-execute:sh): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sql.el (org-babel-execute:sql): removing call to org-babel-process-params which should no longer be called from within a language file * ob-haskell.el (org-babel-execute:haskell): Remove reference to processed params * ob-clojure.el (org-babel-execute:clojure): Remove reference to processed params * ob-R.el (org-babel-execute:R): Remove reference to processed params
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(let* ((session (org-babel-python-initiate-session
(cdr (assoc :session params))))
(result-params (cdr (assoc :result-params params)))
(result-type (cdr (assoc :result-type params)))
(return-val (when (and (eq result-type 'value) (not session))
(cdr (assoc :return params))))
(preamble (cdr (assoc :preamble params)))
(full-body
(org-babel-expand-body:generic
(concat body (if return-val (format "\nreturn %s" return-val) ""))
params (org-babel-variable-assignments:python params)))
(result (org-babel-python-evaluate
session full-body result-type result-params preamble)))
ob: language-specific changes in response to :file arg changes These languages are capable of writing results to file; for several of them this is their only mode of operation. These changes cause the languages to return to ob.el either the computed result, or nil, when they have written results to file themselves. This is in place of the previous method of returning the output file name as a string to ob.el. * lisp/ob-asymptote.el (org-babel-execute:asymptote): Return nil to signal that the intended content has been written to file. * lisp/ob-ditaa.el (org-babel-execute:ditaa): Return nil to signal that the intended content has been written to file. * lisp/ob-dot.el (org-babel-execute:dot): Return nil to signal that the intended content has been written to file. * lisp/ob-gnuplot.el (org-babel-execute:gnuplot): Return nil to signal that the intended content has been written to file. * lisp/ob-latex.el (org-babel-execute:latex): Return nil to signal that the intended content has been written to file. * lisp/ob-mscgen.el (org-babel-execute:mscgen): Return nil to signal that the intended content has been written to file. * lisp/ob-octave.el (org-babel-execute:octave): Return result; not name of output file. * lisp/ob-plantuml.el (org-babel-execute:plantuml): Return nil to signal that the intended content has been written to file. * lisp/ob-python.el (org-babel-execute:python): Return result; not name of output file. * lisp/ob-ruby.el (org-babel-execute:ruby): Return result; not name of output file. * lisp/ob-sass.el (org-babel-execute:sass): Return nil if result has been written to file
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(org-babel-reassemble-table
result
(org-babel-pick-name (cdr (assoc :colname-names params))
(cdr (assoc :colnames params)))
(org-babel-pick-name (cdr (assoc :rowname-names params))
(cdr (assoc :rownames params))))))
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(defun org-babel-prep-session:python (session params)
"Prepare SESSION according to the header arguments in PARAMS.
VARS contains resolved variable references"
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(let* ((session (org-babel-python-initiate-session session))
(var-lines
(org-babel-variable-assignments:python params)))
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(org-babel-comint-in-buffer session
(mapc (lambda (var)
(end-of-line 1) (insert var) (comint-send-input)
(org-babel-comint-wait-for-output session)) var-lines))
session))
(defun org-babel-load-session:python (session body params)
"Load BODY into SESSION."
(save-window-excursion
(let ((buffer (org-babel-prep-session:python session params)))
(with-current-buffer buffer
(goto-char (process-mark (get-buffer-process (current-buffer))))
(insert (org-babel-chomp body)))
buffer)))
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;; helper functions
(defun org-babel-variable-assignments:python (params)
"Return list of python statements assigning the block's variables"
(mapcar
(lambda (pair)
(format "%s=%s"
(car pair)
(org-babel-python-var-to-python (cdr pair))))
removing obsoleted optional third argument from org-babel-expand-body:LANG * lisp/ob-C.el (org-babel-expand-body:c++): removing obsoleted optional third argument (org-babel-expand-body:c++): removing obsoleted optional third argument (org-babel-C-expand): removing obsoleted optional third argument * lisp/ob-R.el: (org-babel-expand-body:R): removing obsoleted optional third argument (org-babel-execute:R): removing obsoleted optional third argument (org-babel-R-variable-assignments): removing obsoleted optional third argument * lisp/ob-asymptote.el: (org-babel-expand-body:asymptote): removing obsoleted optional third argument (org-babel-execute:asymptote): removing obsoleted optional third argument * lisp/ob-clojure.el: (org-babel-expand-body:clojure): removing obsoleted optional third argument (org-babel-execute:clojure): removing obsoleted optional third argument * lisp/ob-css.el: (org-babel-expand-body:css): removing obsoleted optional third argument * lisp/ob-ditaa.el: (org-babel-expand-body:ditaa): removing obsoleted optional third argument * lisp/ob-dot.el: (org-babel-expand-body:dot): removing obsoleted optional third argument (org-babel-execute:dot): removing obsoleted optional third argument * lisp/ob-emacs-lisp.el: (org-babel-expand-body:emacs-lisp): removing obsoleted optional third argument (org-babel-execute:emacs-lisp): removing obsoleted optional third argument * lisp/ob-gnuplot.el: (org-babel-expand-body:gnuplot): removing obsoleted optional third argument * lisp/ob-haskell.el: (org-babel-expand-body:haskell): removing obsoleted optional third argument (org-babel-execute:haskell): removing obsoleted optional third argument (org-babel-load-session:haskell): removing obsoleted optional third (org-babel-prep-session:haskell): removing obsoleted optional third * lisp/ob-js.el: (org-babel-expand-body:js): removing obsoleted optional third argument (org-babel-execute:js): removing obsoleted optional third argument * lisp/ob-latex.el: (org-babel-expand-body:latex): removing obsoleted optional third argument * lisp/ob-lisp.el: (org-babel-expand-body:lisp): removing obsoleted optional third argument (org-babel-execute:lisp): removing obsoleted optional third argument * lisp/ob-mscgen.el: (org-babel-expand-body:mscgen): removing obsoleted optional third argument * lisp/ob-ocaml.el: (org-babel-expand-body:ocaml): removing obsoleted optional third argument (org-babel-execute:ocaml): removing obsoleted optional third argument * lisp/ob-octave.el: (org-babel-expand-body:matlab): removing obsoleted optional third argument (org-babel-expand-body:octave): removing obsoleted optional third argument (org-babel-execute:octave): removing obsoleted optional third argument (org-babel-octave-variable-assignments): removing obsoleted optional third * lisp/ob-org.el: (org-babel-expand-body:org): removing obsoleted optional third argument * lisp/ob-perl.el: (org-babel-expand-body:perl): removing obsoleted optional third argument (org-babel-execute:perl): removing obsoleted optional third argument * lisp/ob-plantuml.el: (org-babel-expand-body:plantuml): removing obsoleted optional third argument * lisp/ob-python.el: (org-babel-expand-body:python): removing obsoleted optional third argument (org-babel-execute:python): removing obsoleted optional third argument (org-babel-python-variable-assignments): removing obsoleted optional third * lisp/ob-ruby.el: (org-babel-expand-body:ruby): removing obsoleted optional third argument (org-babel-execute:ruby): removing obsoleted optional third argument * lisp/ob-sass.el: (org-babel-expand-body:sass): removing obsoleted optional third argument * lisp/ob-scheme.el: (org-babel-expand-body:scheme): removing obsoleted optional third argument (org-babel-execute:scheme): removing obsoleted optional third argument * lisp/ob-screen.el: (org-babel-expand-body:screen): removing obsoleted optional third argument * lisp/ob-sh.el: (org-babel-expand-body:sh): removing obsoleted optional third argument (org-babel-execute:sh): removing obsoleted optional third argument (org-babel-sh-variable-assignments): removing obsoleted optional third * lisp/ob-sql.el: (org-babel-expand-body:sql): removing obsoleted optional third argument * lisp/ob-sqlite.el: (org-babel-expand-body:sqlite): removing obsoleted optional third argument (org-babel-execute:sqlite): removing obsoleted optional third argument * lisp/ob.el: (org-babel-expand-body:generic): removing obsoleted optional third argument
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(mapcar #'cdr (org-babel-get-header params :var))))
(defun org-babel-python-var-to-python (var)
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"Convert an elisp value to a python variable.
Convert an elisp value, VAR, into a string of python source code
specifying a variable of the same value."
(if (listp var)
(concat "[" (mapconcat #'org-babel-python-var-to-python var ", ") "]")
(if (equal var 'hline)
"None"
(format
(if (and (stringp var) (string-match "[\n\r]" var)) "\"\"%S\"\"" "%S")
var))))
(defun org-babel-python-table-or-string (results)
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"Convert RESULTS into an appropriate elisp value.
If the results look like a list or tuple, then convert them into an
Emacs-lisp table, otherwise return the results as a string."
(org-babel-script-escape results))
(defvar org-babel-python-buffers '((:default . nil)))
(defun org-babel-python-session-buffer (session)
"Return the buffer associated with SESSION."
(cdr (assoc session org-babel-python-buffers)))
(defvar py-default-interpreter)
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(defun org-babel-python-initiate-session-by-key (&optional session)
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"Initiate a python session.
If there is not a current inferior-process-buffer in SESSION
then create. Return the initialized session."
(require org-babel-python-mode)
(save-window-excursion
(let* ((session (if session (intern session) :default))
(python-buffer (org-babel-python-session-buffer session)))
(cond
((and (eq 'python org-babel-python-mode)
(fboundp 'run-python)) ; python.el
(run-python))
((and (eq 'python-mode org-babel-python-mode)
(fboundp 'py-shell)) ; python-mode.el
;; Make sure that py-which-bufname is initialized, as otherwise
;; it will be overwritten the first time a Python buffer is
;; created.
(py-toggle-shells py-default-interpreter)
;; `py-shell' creates a buffer whose name is the value of
;; `py-which-bufname' with '*'s at the beginning and end
(let* ((bufname (if (and python-buffer (buffer-live-p python-buffer))
(replace-regexp-in-string ;; zap surrounding *
"^\\*\\([^*]+\\)\\*$" "\\1" python-buffer)
(concat "Python-" (symbol-name session))))
(py-which-bufname bufname))
(py-shell)
(setq python-buffer (concat "*" bufname "*"))))
(t
(error "No function available for running an inferior python.")))
(setq org-babel-python-buffers
(cons (cons session python-buffer)
(assq-delete-all session org-babel-python-buffers)))
session)))
(defun org-babel-python-initiate-session (&optional session params)
"Create a session named SESSION according to PARAMS."
(unless (string= session "none")
(org-babel-python-session-buffer
(org-babel-python-initiate-session-by-key session))))
(defvar org-babel-python-eoe-indicator "'org_babel_python_eoe'"
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"A string to indicate that evaluation has completed.")
(defvar org-babel-python-wrapper-method
"
def main():
%s
open('%s', 'w').write( str(main()) )")
(defvar org-babel-python-pp-wrapper-method
"
import pprint
def main():
%s
open('%s', 'w').write( pprint.pformat(main()) )")
(defun org-babel-python-evaluate
(session body &optional result-type result-params preamble)
"Evaluate BODY as python code."
(if session
(org-babel-python-evaluate-session
session body result-type result-params)
(org-babel-python-evaluate-external-process
body result-type result-params preamble)))
(defun org-babel-python-evaluate-external-process
(body &optional result-type result-params preamble)
"Evaluate BODY in external python process.
If RESULT-TYPE equals 'output then return standard output as a
string. If RESULT-TYPE equals 'value then return the value of the
last statement in BODY, as elisp."
((lambda (raw)
(if (or (member "code" result-params)
(member "pp" result-params)
(and (member "output" result-params)
(not (member "table" result-params))))
raw
(org-babel-python-table-or-string (org-babel-trim raw))))
(case result-type
(output (org-babel-eval org-babel-python-command
(concat (if preamble (concat preamble "\n") "")
body)))
(value (let ((tmp-file (org-babel-temp-file "python-")))
(org-babel-eval
org-babel-python-command
(concat
(if preamble (concat preamble "\n") "")
(format
(if (member "pp" result-params)
org-babel-python-pp-wrapper-method
org-babel-python-wrapper-method)
(mapconcat
(lambda (line) (format "\t%s" line))
(split-string
(org-remove-indentation
(org-babel-trim body))
"[\r\n]") "\n")
(org-babel-process-file-name tmp-file 'noquote))))
(org-babel-eval-read-file tmp-file))))))
(defun org-babel-python-evaluate-session
(session body &optional result-type result-params)
"Pass BODY to the Python process in SESSION.
If RESULT-TYPE equals 'output then return standard output as a
string. If RESULT-TYPE equals 'value then return the value of the
last statement in BODY, as elisp."
replace flet/labels with org-flet/org-labels This patch ensure Org-mode will build on all supported versions of Emacs, after the renaming of the cl macros behind the cl- prefix in the recent Emacs trunk. * lisp/org-compat.el (org-flet): Compatibility function now that flet has been removed from cl-macs. (org-labels): Compatibility function now that labels has been removed from cl-macs. * lisp/ob-R.el (org-compat): Require org-compat. * lisp/ob-comint.el: Require org-compat. * lisp/ob-exp.el (org-babel-exp-do-export): Switch to compatibility function. * lisp/ob-gnuplot.el (org-babel-expand-body:gnuplot): Switch to compatibility function. * lisp/ob-lob.el (org-babel-lob-get-info): Switch to compatibility function. (org-babel-lob-execute): Switch to compatibility function. * lisp/ob-python.el (org-babel-python-evaluate-session): Switch to compatibility function. * lisp/ob-ref.el (org-babel-ref-index-list): Switch to compatibility function. * lisp/ob-sh.el (org-babel-sh-var-to-string): Switch to compatibility function. * lisp/ob-tangle.el (org-babel-load-file): Switch to compatibility function. (org-babel-tangle): Switch to compatibility function. (org-babel-spec-to-string): Switch to compatibility function. * lisp/ob.el (org-babel-view-src-block-info): Switch to compatibility function. (org-babel-execute-src-block): Switch to compatibility function. (org-babel-edit-distance): Switch to compatibility function. (org-babel-switch-to-session-with-code): Switch to compatibility function. (org-babel-sha1-hash): Switch to compatibility function. (org-babel-balanced-split): Switch to compatibility function. (org-babel-join-splits-near-ch): Switch to compatibility function. (org-babel-get-rownames): Switch to compatibility function. (org-babel-format-result): Switch to compatibility function. (org-babel-insert-result): Switch to compatibility function. (org-babel-examplize-region): Switch to compatibility function. (org-babel-merge-params): Switch to compatibility function. (org-babel-noweb-p): Switch to compatibility function. (org-babel-expand-noweb-references): Switch to compatibility function. * lisp/org-bibtex.el (org-bibtex-headline): Switch to compatibility function. (org-bibtex-fleshout): Switch to compatibility function. (org-bibtex-read): Switch to compatibility function. (org-bibtex-write): Switch to compatibility function. * lisp/org-exp-blocks.el (org-export-blocks-preprocess): Switch to compatibility function. * lisp/org-exp.el (org-export-format-source-code-or-example): Switch to compatibility function. * lisp/org-macs.el (org-called-interactively-p): Indentation fix. * lisp/org-mouse.el (org-mouse-timestamp-today): Switch to compatibility function. (org-mouse-set-priority): Switch to compatibility function. (org-mouse-popup-global-menu): Switch to compatibility function. (org-mouse-context-menu): Switch to compatibility function. * lisp/org-plot.el (org-plot/gnuplot-to-grid-data): Switch to compatibility function. (org-plot/gnuplot-script): Switch to compatibility function. * lisp/org.el (org-entry-get): Switch to compatibility function. (org-fill-paragraph): Switch to compatibility function. (org-auto-fill-function): Switch to compatibility function.
2012-07-19 04:11:36 +00:00
(org-flet ((send-wait () (comint-send-input nil t) (sleep-for 0 5))
(dump-last-value
(tmp-file pp)
(mapc
(lambda (statement) (insert statement) (send-wait))
(if pp
(list
"import pprint"
babel: New function to process file names for use in external processes * ob.el (org-babel-process-file-name): New function (org-babel-maybe-remote-file): Delete function * ob-sql.el (org-babel-execute:sql): Use org-babel-process-file-name * ob-scheme.el (org-babel-execute:scheme): Use org-babel-process-file-name * ob-sass.el (org-babel-execute:sass): Use org-babel-process-file-name * ob-ruby.el (org-babel-ruby-evaluate): Use org-babel-process-file-name * ob-python.el (org-babel-python-evaluate-external-process): Use org-babel-process-file-name (org-babel-python-evaluate-session): Use org-babel-process-file-name * ob-plantuml.el (org-babel-execute:plantuml): Use org-babel-process-file-name * ob-perl.el (org-babel-perl-evaluate): Use org-babel-process-file-name * ob-octave.el (org-babel-octave-evaluate-external-process): Use org-babel-process-file-name (org-babel-octave-evaluate-session): Use org-babel-process-file-name, don't use org-babel-maybe-remote-file * ob-lisp.el (org-babel-execute:lisp): Use org-babel-process-file-name * ob-ledger.el (org-babel-execute:ledger): Use org-babel-process-file-name * ob-js.el (org-babel-execute:js): Use org-babel-process-file-name * ob-haskell.el (org-babel-haskell-export-to-lhs): Use org-babel-process-file-name * ob-gnuplot.el (org-babel-execute:gnuplot): Use org-babel-process-file-name * ob-eval.el (org-babel-eval-read-file): Don't use org-babel-maybe-remote-file * ob-dot.el (org-babel-execute:dot): Use org-babel-process-file-name * ob-ditaa.el (org-babel-execute:ditaa): Use org-babel-process-file-name * ob-clojure.el (org-babel-clojure-evaluate-external-process): Use org-babel-process-file-name * ob-asymptote.el (org-babel-execute:asymptote): Use org-babel-process-file-name * ob-R.el (org-babel-R-assign-elisp): Don't use org-babel-maybe-remote-file, use org-babel-process-file-name (org-babel-R-evaluate-external-process): Use org-babel-process-file-name (org-babel-R-evaluate-session): Use org-babel-process-file-name * ob-C.el (org-babel-C-execute): Use org-babel-process-file-name In addition to passing the file path through `expand-file-name', tramp-style remote file names are converted to conventional (local) file paths. The reason is that, if a tramp file name was in use in emacs, then the shell command will be executing on the remote machine in question. Further, by default the file name is passed through `shell-quote-argument'.
2010-09-22 20:40:14 +00:00
(format "open('%s', 'w').write(pprint.pformat(_))"
(org-babel-process-file-name tmp-file 'noquote)))
(list (format "open('%s', 'w').write(str(_))"
(org-babel-process-file-name tmp-file 'noquote))))))
(input-body (body)
(mapc (lambda (line) (insert line) (send-wait))
(split-string body "[\r\n]"))
(send-wait)))
((lambda (results)
(unless (string= (substring org-babel-python-eoe-indicator 1 -1) results)
(if (or (member "code" result-params)
(member "pp" result-params)
(and (member "output" result-params)
(not (member "table" result-params))))
results
(org-babel-python-table-or-string results))))
(case result-type
(output
(mapconcat
#'org-babel-trim
(butlast
(org-babel-comint-with-output
(session org-babel-python-eoe-indicator t body)
(input-body body)
(send-wait) (send-wait)
(insert org-babel-python-eoe-indicator)
(send-wait))
2) "\n"))
(value
(let ((tmp-file (org-babel-temp-file "python-")))
(org-babel-comint-with-output
(session org-babel-python-eoe-indicator nil body)
(let ((comint-process-echoes nil))
(input-body body)
(dump-last-value tmp-file (member "pp" result-params))
(send-wait) (send-wait)
(insert org-babel-python-eoe-indicator)
(send-wait)))
(org-babel-eval-read-file tmp-file)))))))
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(defun org-babel-python-read-string (string)
"Strip 's from around python string"
(if (string-match "^'\\([^\000]+\\)'$" string)
2009-06-12 23:23:28 +00:00
(match-string 1 string)
string))
(provide 'ob-python)
;;; ob-python.el ends here