2010-06-11 23:02:42 +00:00
|
|
|
;;; ob-python.el --- org-babel functions for python evaluation
|
2009-06-12 15:46:00 +00:00
|
|
|
|
|
|
|
;; Copyright (C) 2009 Eric Schulte
|
|
|
|
|
|
|
|
;; Author: Eric Schulte
|
|
|
|
;; Keywords: literate programming, reproducible research
|
|
|
|
;; Homepage: http://orgmode.org
|
|
|
|
;; Version: 0.01
|
|
|
|
|
|
|
|
;;; License:
|
|
|
|
|
|
|
|
;; This program is free software; you can redistribute it and/or modify
|
|
|
|
;; it under the terms of the GNU General Public License as published by
|
|
|
|
;; the Free Software Foundation; either version 3, or (at your option)
|
|
|
|
;; any later version.
|
|
|
|
;;
|
|
|
|
;; This program is distributed in the hope that it will be useful,
|
|
|
|
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
|
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
|
;; GNU General Public License for more details.
|
|
|
|
;;
|
|
|
|
;; You should have received a copy of the GNU General Public License
|
|
|
|
;; along with GNU Emacs; see the file COPYING. If not, write to the
|
|
|
|
;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
|
|
|
|
;; Boston, MA 02110-1301, USA.
|
|
|
|
|
|
|
|
;;; Commentary:
|
|
|
|
|
|
|
|
;; Org-Babel support for evaluating python source code.
|
|
|
|
|
|
|
|
;;; Code:
|
2010-06-11 23:02:42 +00:00
|
|
|
(require 'ob)
|
|
|
|
(require 'ob-tangle)
|
|
|
|
(require 'ob-comint)
|
2010-05-14 12:40:44 +00:00
|
|
|
(require (if (featurep 'xemacs) 'python-mode 'python))
|
2009-06-12 15:46:00 +00:00
|
|
|
|
2010-04-16 05:14:10 +00:00
|
|
|
(defun org-babel-expand-body:python (body params &optional processed-params)
|
2010-06-12 00:12:15 +00:00
|
|
|
"Expand BODY according to PARAMS, return the expanded body."
|
2010-04-20 06:18:03 +00:00
|
|
|
(concat
|
|
|
|
(mapconcat ;; define any variables
|
|
|
|
(lambda (pair)
|
|
|
|
(format "%s=%s"
|
|
|
|
(car pair)
|
|
|
|
(org-babel-python-var-to-python (cdr pair))))
|
|
|
|
(second (or processed-params (org-babel-process-params params))) "\n")
|
|
|
|
"\n" (org-babel-trim body) "\n"))
|
2010-04-16 05:14:10 +00:00
|
|
|
|
2009-07-08 04:13:07 +00:00
|
|
|
(defun org-babel-execute:python (body params)
|
2009-06-12 15:46:00 +00:00
|
|
|
"Execute a block of Python code with org-babel. This function is
|
2009-11-10 20:42:05 +00:00
|
|
|
called by `org-babel-execute-src-block'."
|
2009-06-12 15:46:00 +00:00
|
|
|
(message "executing Python source code block")
|
2009-11-10 22:22:25 +00:00
|
|
|
(let* ((processed-params (org-babel-process-params params))
|
|
|
|
(session (org-babel-python-initiate-session (first processed-params)))
|
|
|
|
(result-params (third processed-params))
|
|
|
|
(result-type (fourth processed-params))
|
2010-04-16 05:14:10 +00:00
|
|
|
(full-body (org-babel-expand-body:python
|
|
|
|
body params processed-params)) ;; then the source block body
|
2009-11-10 22:22:25 +00:00
|
|
|
(result (org-babel-python-evaluate session full-body result-type)))
|
2010-04-19 01:06:34 +00:00
|
|
|
(or (cdr (assoc :file params))
|
|
|
|
(org-babel-reassemble-table
|
2010-04-20 05:33:47 +00:00
|
|
|
result
|
|
|
|
(org-babel-pick-name (nth 4 processed-params) (cdr (assoc :colnames params)))
|
|
|
|
(org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params)))))))
|
2009-06-12 15:46:00 +00:00
|
|
|
|
2009-06-14 18:34:06 +00:00
|
|
|
(defun org-babel-prep-session:python (session params)
|
|
|
|
"Prepare SESSION according to the header arguments specified in PARAMS."
|
|
|
|
(let* ((session (org-babel-python-initiate-session session))
|
|
|
|
(vars (org-babel-ref-variables params))
|
|
|
|
(var-lines (mapcar ;; define any variables
|
|
|
|
(lambda (pair)
|
|
|
|
(format "%s=%s"
|
|
|
|
(car pair)
|
|
|
|
(org-babel-python-var-to-python (cdr pair))))
|
|
|
|
vars)))
|
|
|
|
(org-babel-comint-in-buffer session
|
|
|
|
(mapc (lambda (var)
|
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
|
|
|
(end-of-line 1) (insert var) (comint-send-input)
|
2010-01-11 17:14:30 +00:00
|
|
|
(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)))
|
2009-06-14 18:34:06 +00:00
|
|
|
|
|
|
|
;; helper functions
|
|
|
|
|
2009-06-12 15:46:00 +00:00
|
|
|
(defun org-babel-python-var-to-python (var)
|
2009-06-12 16:24:03 +00:00
|
|
|
"Convert an elisp var into a string of python source code
|
|
|
|
specifying a var of the same value."
|
2009-06-12 15:46:00 +00:00
|
|
|
(if (listp var)
|
|
|
|
(concat "[" (mapconcat #'org-babel-python-var-to-python var ", ") "]")
|
|
|
|
(format "%S" var)))
|
|
|
|
|
2009-07-05 23:55:54 +00:00
|
|
|
(defun org-babel-python-table-or-string (results)
|
2010-02-19 16:46:36 +00:00
|
|
|
"If the results look like a list or tuple, then convert them into an
|
2009-06-12 15:46:00 +00:00
|
|
|
Emacs-lisp table, otherwise return the results as a string."
|
|
|
|
(org-babel-read
|
2010-02-19 16:46:36 +00:00
|
|
|
(if (or (string-match "^\\[.+\\]$" results)
|
|
|
|
(string-match "^(.+)$" results))
|
2009-06-12 15:46:00 +00:00
|
|
|
(org-babel-read
|
2010-04-10 21:14:27 +00:00
|
|
|
(concat "'"
|
|
|
|
(replace-regexp-in-string
|
|
|
|
"\\[" "(" (replace-regexp-in-string
|
|
|
|
"\\]" ")" (replace-regexp-in-string
|
|
|
|
", " " " (replace-regexp-in-string
|
|
|
|
"'" "\"" results))))))
|
2009-06-12 15:46:00 +00:00
|
|
|
results)))
|
|
|
|
|
2009-06-12 21:48:40 +00:00
|
|
|
(defvar org-babel-python-buffers '(:default . nil))
|
|
|
|
|
|
|
|
(defun org-babel-python-session-buffer (session)
|
2010-06-12 00:12:15 +00:00
|
|
|
"Return the buffer associated with SESSION."
|
2009-06-12 21:48:40 +00:00
|
|
|
(cdr (assoc session org-babel-python-buffers)))
|
|
|
|
|
2009-06-14 18:34:06 +00:00
|
|
|
(defun org-babel-python-initiate-session-by-key (&optional session)
|
2009-06-12 15:46:00 +00:00
|
|
|
"If there is not a current inferior-process-buffer in SESSION
|
|
|
|
then create. Return the initialized session."
|
2009-06-12 21:48:40 +00:00
|
|
|
(save-window-excursion
|
|
|
|
(let* ((session (if session (intern session) :default))
|
|
|
|
(python-buffer (org-babel-python-session-buffer session)))
|
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
|
|
|
(cond
|
|
|
|
((fboundp 'run-python) ; python.el
|
|
|
|
(run-python))
|
|
|
|
((fboundp 'py-shell) ; python-mode.el
|
|
|
|
;; `py-shell' creates a buffer whose name is the value of
|
|
|
|
;; `py-which-bufname' with '*'s at the beginning and end
|
|
|
|
(let* ((bufname (if python-buffer
|
|
|
|
(replace-regexp-in-string "^\\*\\([^*]+\\)\\*$" "\\1" python-buffer) ; zap surrounding *
|
|
|
|
(concat "Python-" (symbol-name session))))
|
|
|
|
(py-which-bufname bufname)) ; avoid making a mess with buffer-local
|
|
|
|
(py-shell)
|
|
|
|
(setq python-buffer (concat "*" bufname "*"))))
|
|
|
|
(t
|
|
|
|
(error "No function available for running an inferior python.")))
|
|
|
|
|
2009-07-12 03:59:04 +00:00
|
|
|
(setq org-babel-python-buffers (cons (cons session python-buffer)
|
|
|
|
(assq-delete-all session org-babel-python-buffers)))
|
2009-06-12 21:48:40 +00:00
|
|
|
session)))
|
2009-06-12 15:46:00 +00:00
|
|
|
|
2010-03-13 17:59:41 +00:00
|
|
|
(defun org-babel-python-initiate-session (&optional session params)
|
2010-06-12 00:12:15 +00:00
|
|
|
"Create a session named SESSION according to PARAMS."
|
2009-06-15 18:14:32 +00:00
|
|
|
(unless (string= session "none")
|
|
|
|
(org-babel-python-session-buffer (org-babel-python-initiate-session-by-key session))))
|
2009-06-14 18:34:06 +00:00
|
|
|
|
2009-06-12 15:46:00 +00:00
|
|
|
(defvar org-babel-python-last-value-eval "_"
|
|
|
|
"When evaluated by Python this returns the return value of the last statement.")
|
2009-10-18 19:14:39 +00:00
|
|
|
(defvar org-babel-python-pp-last-value-eval
|
|
|
|
'("results = _"
|
|
|
|
"import pprint"
|
|
|
|
"org_babel_pp = pprint.PrettyPrinter()"
|
|
|
|
"org_babel_pp.pprint(results)")
|
|
|
|
"When evaluated by Python this pretty prints the value of the last statement.")
|
2009-06-12 15:46:00 +00:00
|
|
|
(defvar org-babel-python-eoe-indicator "'org_babel_python_eoe'"
|
|
|
|
"Used to indicate that evaluation is has completed.")
|
2009-06-15 18:14:32 +00:00
|
|
|
(defvar org-babel-python-wrapper-method
|
|
|
|
"
|
|
|
|
def main():
|
|
|
|
%s
|
|
|
|
|
|
|
|
open('%s', 'w').write( str(main()) )")
|
2009-10-18 19:14:39 +00:00
|
|
|
(defvar org-babel-python-pp-wrapper-method
|
|
|
|
"
|
|
|
|
import pprint
|
|
|
|
def main():
|
|
|
|
%s
|
|
|
|
|
|
|
|
open('%s', 'w').write( pprint.pformat(main()) )")
|
2009-06-12 15:46:00 +00:00
|
|
|
|
|
|
|
(defun org-babel-python-evaluate (buffer body &optional result-type)
|
|
|
|
"Pass BODY to the Python process in BUFFER. If RESULT-TYPE equals
|
|
|
|
'output then return a list of the outputs of the statements in
|
|
|
|
BODY, if RESULT-TYPE equals 'value then return the value of the
|
2009-07-06 01:23:17 +00:00
|
|
|
last statement in BODY, as elisp."
|
2009-06-15 18:14:32 +00:00
|
|
|
(if (not session)
|
|
|
|
;; external process evaluation
|
2010-03-05 11:29:30 +00:00
|
|
|
(save-excursion
|
2009-06-15 18:14:32 +00:00
|
|
|
(case result-type
|
|
|
|
(output
|
|
|
|
(with-temp-buffer
|
|
|
|
(insert body)
|
|
|
|
;; (message "buffer=%s" (buffer-string)) ;; debugging
|
2010-03-04 16:38:58 +00:00
|
|
|
(org-babel-shell-command-on-region (point-min) (point-max) "python" 'current-buffer 'replace)
|
2009-06-15 18:14:32 +00:00
|
|
|
(buffer-string)))
|
|
|
|
(value
|
2010-03-05 11:29:30 +00:00
|
|
|
(let* ((tmp-file (make-temp-file "org-babel-python-results-")) exit-code
|
|
|
|
(stderr
|
|
|
|
(with-temp-buffer
|
|
|
|
(insert
|
|
|
|
(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")
|
|
|
|
tmp-file))
|
|
|
|
;; (message "buffer=%s" (buffer-string)) ;; debugging
|
|
|
|
(setq exit-code (org-babel-shell-command-on-region
|
|
|
|
(point-min) (point-max) "python" nil 'replace (current-buffer)))
|
|
|
|
(buffer-string))))
|
|
|
|
(if (> exit-code 0) (org-babel-error-notify exit-code stderr))
|
2010-02-21 05:43:53 +00:00
|
|
|
(let ((raw (with-temp-buffer
|
2010-02-23 16:10:11 +00:00
|
|
|
(insert-file-contents (org-babel-maybe-remote-file tmp-file))
|
2010-02-21 05:43:53 +00:00
|
|
|
(buffer-string))))
|
2009-10-18 19:14:39 +00:00
|
|
|
(if (or (member "code" result-params) (member "pp" result-params))
|
2009-10-16 22:51:46 +00:00
|
|
|
raw
|
|
|
|
(org-babel-python-table-or-string raw)))))))
|
2009-06-15 18:14:32 +00:00
|
|
|
;; comint session evaluation
|
|
|
|
(org-babel-comint-in-buffer buffer
|
2010-06-12 22:57:38 +00:00
|
|
|
(let* ((raw (org-babel-comint-with-output
|
2010-06-15 00:00:49 +00:00
|
|
|
(buffer org-babel-python-eoe-indicator t full-body)
|
2009-06-15 18:14:32 +00:00
|
|
|
;; for some reason python is fussy, and likes enters after every input
|
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
|
|
|
(let ((comint-process-echoes nil))
|
|
|
|
(mapc (lambda (statement) (insert statement) (comint-send-input))
|
|
|
|
(split-string (org-babel-trim body) "[\r\n]+"))
|
|
|
|
(comint-send-input) (comint-send-input)
|
|
|
|
(if (member "pp" result-params)
|
|
|
|
(mapc (lambda (statement) (insert statement) (comint-send-input))
|
|
|
|
org-babel-python-pp-last-value-eval)
|
|
|
|
(insert org-babel-python-last-value-eval))
|
|
|
|
(comint-send-input) (comint-send-input)
|
|
|
|
(insert org-babel-python-eoe-indicator)
|
|
|
|
(comint-send-input))))
|
|
|
|
(raw (apply #'append ; split further
|
|
|
|
(mapcar #'(lambda (r)
|
|
|
|
(split-string r "[\r\n]+"))
|
|
|
|
raw)))
|
2009-06-15 18:14:32 +00:00
|
|
|
(results (delete org-babel-python-eoe-indicator
|
|
|
|
(cdr (member org-babel-python-eoe-indicator
|
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
|
|
|
(mapcar #'org-babel-trim raw))))))
|
2009-10-18 19:14:39 +00:00
|
|
|
(unless (or (member "code" result-params) (member "pp" result-params))
|
|
|
|
(setq results (mapcar #'org-babel-python-read-string results)))
|
2009-07-05 23:16:08 +00:00
|
|
|
(case result-type
|
|
|
|
(output (org-babel-trim (mapconcat #'identity (reverse (cdr results)) "\n")))
|
2009-10-16 22:51:46 +00:00
|
|
|
(value
|
2009-10-18 19:14:39 +00:00
|
|
|
(if (or (member "code" result-params) (member "pp" result-params))
|
2009-10-16 22:51:46 +00:00
|
|
|
(car results)
|
|
|
|
(org-babel-python-table-or-string (org-babel-trim (car results))))))))))
|
2009-06-12 15:46:00 +00:00
|
|
|
|
2009-06-12 23:23:28 +00:00
|
|
|
(defun org-babel-python-read-string (string)
|
2010-02-19 16:34:16 +00:00
|
|
|
"Strip 's from around python string"
|
|
|
|
(if (string-match "^'\\([^\000]+\\)'$" string)
|
2009-06-12 23:23:28 +00:00
|
|
|
(match-string 1 string)
|
|
|
|
string))
|
|
|
|
|
2010-06-11 23:02:42 +00:00
|
|
|
(provide 'ob-python)
|
|
|
|
;;; ob-python.el ends here
|