org-mode/lisp/ob-python.el

571 lines
22 KiB
EmacsLisp

;;; ob-python.el --- Babel Functions for Python -*- lexical-binding: t; -*-
;; Copyright (C) 2009-2024 Free Software Foundation, Inc.
;; Authors: Eric Schulte
;; Dan Davison
;; Maintainer: Jack Kamm <jackkamm@gmail.com>
;; Keywords: literate programming, reproducible research
;; URL: https://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 <https://www.gnu.org/licenses/>.
;;; Commentary:
;; Org-Babel support for evaluating python source code.
;;; Code:
(require 'org-macs)
(org-assert-version)
(require 'ob)
(require 'org-macs)
(require 'python)
(require 'subr-x) ; For `string-trim-right', Emacs < 28
(defvar org-babel-tangle-lang-exts)
(add-to-list 'org-babel-tangle-lang-exts '("python" . "py"))
(defvar org-babel-default-header-args:python '())
(defconst org-babel-header-args:python
'((return . :any)
(python . :any)
(async . ((yes no))))
"Python-specific header arguments.")
(defcustom org-babel-python-command 'auto
"Command (including arguments) for interactive and non-interactive Python code.
When not `auto', it overrides `org-babel-python-command-session'
and `org-babel-python-command-nonsession'."
:package-version '(Org . "9.7")
:group 'org-babel
:type '(choice string (const auto)))
(defcustom org-babel-python-command-session 'auto
"Command (including arguments) for starting interactive Python sessions.
If `auto' (the default), uses the values from
`python-shell-interpreter' and `python-shell-interpreter-args'.
If `org-babel-python-command' is set, then it overrides this
option."
:package-version '(Org . "9.7")
:group 'org-babel
:type '(choice string (const auto)))
(defcustom org-babel-python-command-nonsession "python"
"Command (including arguments) for executing non-interactive Python code.
If `org-babel-python-command' is set, then it overrides this option."
:package-version '(Org . "9.7")
:group 'org-babel
:type 'string)
(defcustom org-babel-python-hline-to "None"
"Replace hlines in incoming tables with this when translating to python."
:group 'org-babel
:package-version '(Org . "8.0")
:type 'string)
(defcustom org-babel-python-None-to 'hline
"Replace `None' in python tables with this before returning."
:group 'org-babel
:package-version '(Org . "8.0")
:type 'symbol)
(defun org-babel-python-associate-session (session)
"Associate Python code buffer with an Python session.
Make SESSION without earmuffs be the Python buffer name."
(setq-local python-shell-buffer-name
(org-babel-python-without-earmuffs session)))
(defun org-babel-execute:python (body params)
"Execute Python BODY according to PARAMS.
This function is called by `org-babel-execute-src-block'."
(let* ((org-babel-python-command
(or (cdr (assq :python params))
org-babel-python-command))
(session (org-babel-python-initiate-session
(cdr (assq :session params))))
(graphics-file (and (member "graphics" (assq :result-params params))
(org-babel-graphical-output-file params)))
(result-params (cdr (assq :result-params params)))
(result-type (cdr (assq :result-type params)))
(return-val (when (eq result-type 'value)
(cdr (assq :return params))))
(preamble (cdr (assq :preamble params)))
(async (org-babel-comint-use-async params))
(full-body
(concat
(org-babel-expand-body:generic
body params
(org-babel-variable-assignments:python params))
(when return-val
(format (if session "\n%s" "\nreturn %s") return-val))))
(result (org-babel-python-evaluate
session full-body result-type
result-params preamble async graphics-file)))
(org-babel-reassemble-table
result
(org-babel-pick-name (cdr (assq :colname-names params))
(cdr (assq :colnames params)))
(org-babel-pick-name (cdr (assq :rowname-names params))
(cdr (assq :rownames params))))))
(defun org-babel-prep-session:python (session params)
"Prepare SESSION according to the header arguments in PARAMS.
VARS contains resolved variable references."
(let* ((session (org-babel-python-initiate-session session))
(var-lines
(org-babel-variable-assignments:python params)))
(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)))
;; helper functions
(defconst org-babel-python--output-graphics-wrapper "\
import matplotlib.pyplot
matplotlib.pyplot.gcf().clear()
%s
matplotlib.pyplot.savefig('%s')"
"Format string for saving Python graphical output.
Has two %s escapes, for the Python code to be evaluated, and the
file to save the graphics to.")
(defconst org-babel-python--def-format-value "\
def __org_babel_python_format_value(result, result_file, result_params):
with open(result_file, 'w') as f:
if 'graphics' in result_params:
result.savefig(result_file)
elif 'pp' in result_params:
import pprint
f.write(pprint.pformat(result))
elif 'list' in result_params and isinstance(result, dict):
f.write(str(['{} :: {}'.format(k, v) for k, v in result.items()]))
else:
if not set(result_params).intersection(\
['scalar', 'verbatim', 'raw']):
def dict2table(res):
if isinstance(res, dict):
return [(k, dict2table(v)) for k, v in res.items()]
elif isinstance(res, list) or isinstance(res, tuple):
return [dict2table(x) for x in res]
else:
return res
if 'table' in result_params:
result = dict2table(result)
try:
import pandas
except ImportError:
pass
else:
if isinstance(result, pandas.DataFrame) and 'table' in result_params:
result = [[result.index.name or ''] + list(result.columns)] + \
[None] + [[i] + list(row) for i, row in result.iterrows()]
elif isinstance(result, pandas.Series) and 'table' in result_params:
result = list(result.items())
try:
import numpy
except ImportError:
pass
else:
if isinstance(result, numpy.ndarray):
if 'table' in result_params:
result = result.tolist()
else:
result = repr(result)
f.write(str(result))"
"Python function to format value result and save it to file.")
(defun org-babel-variable-assignments:python (params)
"Return a list of Python statements assigning the block's variables.
The assignments are defined in PARAMS."
(mapcar
(lambda (pair)
(format "%s=%s"
(car pair)
(org-babel-python-var-to-python (cdr pair))))
(org-babel--get-vars params)))
(defun org-babel-python-var-to-python (var)
"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 (eq var 'hline)
org-babel-python-hline-to
(format
(if (and (stringp var) (string-match "[\n\r]" var)) "\"\"%S\"\"" "%S")
(if (stringp var) (substring-no-properties var) var)))))
(defun org-babel-python-table-or-string (results)
"Convert RESULTS into an appropriate elisp value.
If the results look like a list or tuple (but not a dict), then
convert them into an Emacs-lisp table. Otherwise return the
results as a string."
(let ((res (if (and (> (length results) 0)
(string-equal "{" (substring results 0 1)))
results ;don't convert dicts to elisp
(org-babel-script-escape results))))
(if (listp res)
(mapcar (lambda (el) (if (eq el 'None)
org-babel-python-None-to el))
res)
res)))
(defvar org-babel-python-buffers '((:default . "*Python*")))
(defun org-babel-python-session-buffer (session)
"Return the buffer associated with SESSION."
(cdr (assoc session org-babel-python-buffers)))
(defun org-babel-python-with-earmuffs (session)
"Return SESSION name as string, ensuring *...* around."
(let ((name (if (stringp session) session (format "%s" session))))
(if (and (string= "*" (substring name 0 1))
(string= "*" (substring name (- (length name) 1))))
name
(format "*%s*" name))))
(defun org-babel-python-without-earmuffs (session)
"Return SESSION name as string, without *...* around."
(let ((name (if (stringp session) session (format "%s" session))))
(if (and (string= "*" (substring name 0 1))
(string= "*" (substring name (- (length name) 1))))
(substring name 1 (- (length name) 1))
name)))
(defun org-babel-session-buffer:python (session &optional _)
"Return session buffer name for SESSION."
(or (org-babel-python-session-buffer session)
(org-babel-python-with-earmuffs session)))
(defun org-babel-python--python-util-comint-end-of-output-p ()
"Return non-nil if the last prompt matches input prompt.
Backport of `python-util-comint-end-of-output-p' to emacs28. To
be removed after minimum supported version reaches emacs29."
(when-let* ((prompt (python-util-comint-last-prompt)))
(python-shell-comint-end-of-output-p
(buffer-substring-no-properties
(car prompt) (cdr prompt)))))
(defun org-babel-python--command (is-session)
"Helper function to return the Python command.
This checks `org-babel-python-command', and then
`org-babel-python-command-session' (if IS-SESSION) or
`org-babel-python-command-nonsession' (if not IS-SESSION). If
IS-SESSION, this might return nil, which means to use
`python-shell-calculate-command'."
(or (unless (eq org-babel-python-command 'auto)
org-babel-python-command)
(if is-session
(unless (eq org-babel-python-command-session 'auto)
org-babel-python-command-session)
org-babel-python-command-nonsession)))
(defvar-local org-babel-python--initialized nil
"Flag used to mark that python session has been initialized.")
(defun org-babel-python--setup-session ()
"Babel Python session setup code, to be run once per session.
Function should be run from within the Python session buffer.
This is often run as a part of `python-shell-first-prompt-hook',
unless the Python session was created outside Org."
(python-shell-send-string-no-output org-babel-python--def-format-value)
(setq-local org-babel-python--initialized t))
(defun org-babel-python-initiate-session-by-key (&optional session)
"Initiate a python session.
If there is not a current inferior-process-buffer matching
SESSION then create it. If inferior process already
exists (e.g. if it was manually started with `run-python'), make
sure it's configured to work with ob-python. If session has
already been configured as such, do nothing. Return the
initialized session."
(save-window-excursion
(let* ((session (if session (intern session) :default))
(py-buffer (org-babel-session-buffer:python session))
(python-shell-buffer-name
(org-babel-python-without-earmuffs py-buffer))
(existing-session-p (comint-check-proc py-buffer))
(cmd (org-babel-python--command t)))
(if cmd
(let* ((cmd-split (split-string-and-unquote cmd))
(python-shell-interpreter (car cmd-split))
(python-shell-interpreter-args
(combine-and-quote-strings
(append (cdr cmd-split)
(when (member system-type
'(cygwin windows-nt ms-dos))
(list "-i"))))))
(run-python))
(run-python))
(with-current-buffer py-buffer
(if existing-session-p
;; Session was created outside Org. Assume first prompt
;; already happened; run session setup code directly
(unless org-babel-python--initialized
;; Ensure first prompt. Based on python-tests.el
;; (`python-tests-shell-wait-for-prompt')
(while (not (org-babel-python--python-util-comint-end-of-output-p))
(sit-for 0.1))
(org-babel-python--setup-session))
;; Adding to `python-shell-first-prompt-hook' immediately
;; after `run-python' should be safe from race conditions,
;; because subprocess output only arrives when Emacs is
;; waiting (see elisp manual, "Output from Processes")
(add-hook
'python-shell-first-prompt-hook
#'org-babel-python--setup-session
nil 'local)))
;; Wait until Python initializes
;; This is more reliable compared to
;; `org-babel-comint-wait-for-output' as python may emit
;; multiple prompts during initialization.
(with-current-buffer py-buffer
(while (not org-babel-python--initialized)
(sleep-for 0.010)))
(setq org-babel-python-buffers
(cons (cons session py-buffer)
(assq-delete-all session org-babel-python-buffers)))
session)))
(defun org-babel-python-initiate-session (&optional session _params)
"Initiate Python session named SESSION according to PARAMS.
If there is not a current inferior-process-buffer matching
SESSION then create it. If inferior process already
exists (e.g. if it was manually started with `run-python'), make
sure it's configured to work with ob-python. If session has
already been configured as such, do nothing."
(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"
"A string to indicate that evaluation has completed.")
(defun org-babel-python-format-session-value
(src-file result-file result-params)
"Return Python code to evaluate SRC-FILE and write result to RESULT-FILE.
RESULT-PARAMS defines the result type."
(format "\
import ast
with open('%s') as __org_babel_python_tmpfile:
__org_babel_python_ast = ast.parse(__org_babel_python_tmpfile.read())
__org_babel_python_final = __org_babel_python_ast.body[-1]
if isinstance(__org_babel_python_final, ast.Expr):
__org_babel_python_ast.body = __org_babel_python_ast.body[:-1]
exec(compile(__org_babel_python_ast, '<string>', 'exec'))
__org_babel_python_final = eval(compile(ast.Expression(
__org_babel_python_final.value), '<string>', 'eval'))
else:
exec(compile(__org_babel_python_ast, '<string>', 'exec'))
__org_babel_python_final = None
__org_babel_python_format_value(__org_babel_python_final, '%s', %s)"
(org-babel-process-file-name src-file 'noquote)
(org-babel-process-file-name result-file 'noquote)
(org-babel-python-var-to-python result-params)))
(defun org-babel-python-evaluate
(session body &optional result-type result-params preamble async graphics-file)
"Evaluate BODY as Python code."
(if session
(if async
(org-babel-python-async-evaluate-session
session body result-type result-params graphics-file)
(org-babel-python-evaluate-session
session body result-type result-params graphics-file))
(org-babel-python-evaluate-external-process
body result-type result-params preamble graphics-file)))
(defun org-babel-python--shift-right (body &optional count)
(with-temp-buffer
(python-mode)
(insert body)
(goto-char (point-min))
(while (not (eobp))
(unless (python-syntax-context 'string)
(python-indent-shift-right (line-beginning-position)
(line-end-position)
count))
(forward-line 1))
(buffer-string)))
(defun org-babel-python-evaluate-external-process
(body &optional result-type result-params preamble graphics-file)
"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. If GRAPHICS-FILE is
non-nil, then save graphical results to that file instead."
(let ((raw
(pcase result-type
(`output (org-babel-eval (org-babel-python--command nil)
(concat preamble (and preamble "\n")
(if graphics-file
(format org-babel-python--output-graphics-wrapper
body graphics-file)
body))))
(`value (let ((results-file (or graphics-file
(org-babel-temp-file "python-"))))
(org-babel-eval (org-babel-python--command nil)
(concat
preamble (and preamble "\n")
(format
(concat org-babel-python--def-format-value "
def main():
%s
__org_babel_python_format_value(main(), '%s', %s)")
(org-babel-python--shift-right body)
(org-babel-process-file-name results-file 'noquote)
(org-babel-python-var-to-python result-params))))
(org-babel-eval-read-file results-file))))))
(org-babel-result-cond result-params
raw
(org-babel-python-table-or-string raw))))
(defun org-babel-python-send-string (session body)
"Pass BODY to the Python process in SESSION.
Return output."
(org-babel-chomp
(string-trim-right
(org-babel-comint-with-output
((org-babel-session-buffer:python session)
org-babel-python-eoe-indicator
nil nil 'disable-prompt-filtering)
(python-shell-send-string (format "\
try:
%s
except:
raise
finally:
print('%s')"
(org-babel-python--shift-right body 4)
org-babel-python-eoe-indicator)))
(rx (literal org-babel-python-eoe-indicator) (zero-or-more anychar)))))
(defun org-babel-python-evaluate-session
(session body &optional result-type result-params graphics-file)
"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. If GRAPHICS-FILE is
non-nil, then save graphical results to that file instead."
(let* ((tmp-src-file (org-babel-temp-file "python-"))
(results
(progn
(with-temp-file tmp-src-file
(insert (if (and graphics-file (eq result-type 'output))
(format org-babel-python--output-graphics-wrapper
body graphics-file)
body)))
(pcase result-type
(`output
(let ((body (format "\
with open('%s') as f:
exec(compile(f.read(), f.name, 'exec'))"
(org-babel-process-file-name
tmp-src-file 'noquote))))
(org-babel-python-send-string session body)))
(`value
(let* ((results-file (or graphics-file
(org-babel-temp-file "python-")))
(body (org-babel-python-format-session-value
tmp-src-file results-file result-params)))
(org-babel-python-send-string session body)
(sleep-for 0.010)
(org-babel-eval-read-file results-file)))))))
(org-babel-result-cond result-params
results
(org-babel-python-table-or-string results))))
(defun org-babel-python-read-string (string)
"Strip \\='s from around Python STRING."
(if (and (string-prefix-p "'" string)
(string-suffix-p "'" string))
(substring string 1 -1)
string))
;; Async session eval
(defconst org-babel-python-async-indicator "print ('ob_comint_async_python_%s_%s')")
(defun org-babel-python-async-value-callback (params tmp-file)
(let ((result-params (cdr (assq :result-params params)))
(results (org-babel-eval-read-file tmp-file)))
(org-babel-result-cond result-params
results
(org-babel-python-table-or-string results))))
(defun org-babel-python-async-evaluate-session
(session body &optional result-type result-params graphics-file)
"Asynchronously evaluate BODY in SESSION.
Returns a placeholder string for insertion, to later be replaced
by `org-babel-comint-async-filter'."
(org-babel-comint-async-register
session (current-buffer)
"ob_comint_async_python_\\(start\\|end\\|file\\)_\\(.+\\)"
'org-babel-chomp 'org-babel-python-async-value-callback
'disable-prompt-filtering)
(pcase result-type
(`output
(let ((uuid (org-id-uuid)))
(with-temp-buffer
(insert (format org-babel-python-async-indicator "start" uuid))
(insert "\n")
(insert (if graphics-file
(format org-babel-python--output-graphics-wrapper
body graphics-file)
body))
(insert "\n")
(insert (format org-babel-python-async-indicator "end" uuid))
(let ((python-shell-buffer-name
(org-babel-python-without-earmuffs session)))
(python-shell-send-buffer)))
uuid))
(`value
(let ((results-file (or graphics-file
(org-babel-temp-file "python-")))
(tmp-src-file (org-babel-temp-file "python-")))
(with-temp-file tmp-src-file (insert body))
(with-temp-buffer
(insert (org-babel-python-format-session-value
tmp-src-file results-file result-params))
(insert "\n")
(unless graphics-file
(insert (format org-babel-python-async-indicator "file" results-file)))
(let ((python-shell-buffer-name
(org-babel-python-without-earmuffs session)))
(python-shell-send-buffer)))
results-file))))
(provide 'ob-python)
;;; ob-python.el ends here