;;; ob-python.el --- Babel Functions for Python -*- lexical-binding: t; -*-
;; Copyright (C) 2009-2020 Free Software Foundation, Inc.
;; Authors: Eric Schulte
;; Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: 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 .
;;; Commentary:
;; Org-Babel support for evaluating python source code.
;;; Code:
(require 'ob)
(require 'org-macs)
(require 'python)
(declare-function py-shell "ext:python-mode" (&rest args))
(declare-function py-toggle-shells "ext:python-mode" (arg))
(declare-function py-shell-send-string "ext:python-mode" (strg &optional process))
(declare-function py-send-string-no-output "ext:python-mode" (strg &optional process buffer-name))
(defvar org-babel-tangle-lang-exts)
(add-to-list 'org-babel-tangle-lang-exts '("python" . "py"))
(defvar org-babel-default-header-args:python '())
(defcustom org-babel-python-command "python"
"Name of the command for executing Python code."
:version "24.4"
:package-version '(Org . "8.0")
:group 'org-babel
:type 'string)
(defcustom org-babel-python-mode
(if (featurep 'python-mode) 'python-mode 'python)
"Preferred python mode for use in running python interactively.
This will typically be either `python' or `python-mode'."
:group 'org-babel
:version "24.4"
:package-version '(Org . "8.0")
:type 'symbol)
(defcustom org-babel-python-hline-to "None"
"Replace hlines in incoming tables with this when translating to python."
:group 'org-babel
:version "24.4"
: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
:version "24.4"
:package-version '(Org . "8.0")
:type 'symbol)
(defun org-babel-execute:python (body params)
"Execute a block of Python code with Babel.
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 (and (eq result-type 'value) (not session))
(cdr (assq :return params))))
(preamble (cdr (assq :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
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
(defun org-babel-variable-assignments:python (params)
"Return a 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))))
(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, then convert them into an
Emacs-lisp table, otherwise return the results as a string."
(let ((res (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)
(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)
(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)))
(defvar py-default-interpreter)
(defvar py-which-bufname)
(defvar python-shell-buffer-name)
(defun org-babel-python-initiate-session-by-key (&optional session)
"Initiate a python session.
If there is not a current inferior-process-buffer in SESSION
then create. Return the initialized session."
(save-window-excursion
(let* ((session (if session (intern session) :default))
(py-buffer (org-babel-python-session-buffer session))
(cmd (if (member system-type '(cygwin windows-nt ms-dos))
(concat org-babel-python-command " -i")
org-babel-python-command)))
(cond
((and (eq 'python org-babel-python-mode)
(fboundp 'run-python)) ; python.el
(if (not (version< "24.1" emacs-version))
(run-python cmd)
(unless py-buffer
(setq py-buffer (org-babel-python-with-earmuffs session)))
(let ((python-shell-buffer-name
(org-babel-python-without-earmuffs py-buffer)))
(run-python cmd))))
((and (eq 'python-mode org-babel-python-mode)
(fboundp 'py-shell)) ; python-mode.el
(require 'python-mode)
;; 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 py-buffer (buffer-live-p py-buffer))
(replace-regexp-in-string ;; zap surrounding *
"^\\*\\([^*]+\\)\\*$" "\\1" py-buffer)
(concat "Python-" (symbol-name session))))
(py-which-bufname bufname))
(setq py-buffer (org-babel-python-with-earmuffs bufname))
(py-shell nil nil t org-babel-python-command py-buffer nil nil t nil)))
(t
(error "No function available for running an inferior Python")))
(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)
"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))))
(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))
else:
if not set(result_params).intersection(\
['scalar', 'verbatim', 'raw']):
def dict2alist(res):
if isinstance(res, dict):
return [(k, dict2alist(v)) for k, v in res.items()]
elif isinstance(res, list) or isinstance(res, tuple):
return [dict2alist(x) for x in res]
else:
return res
result = dict2alist(result)
try:
import pandas as pd
except ImportError:
pass
else:
if isinstance(result, pd.DataFrame):
result = [[''] + list(result.columns), None] + \
[[i] + list(row) for i, row in result.iterrows()]
elif isinstance(result, pd.Series):
result = list(result.items())
try:
import numpy as np
except ImportError:
pass
else:
if isinstance(result, np.ndarray):
result = result.tolist()
f.write(str(result))")
(defun org-babel-python--output-graphics-wrapper
(body graphics-file)
"Wrap BODY to plot to GRAPHICS-FILE if it is non-nil."
(if graphics-file
(format "\
import matplotlib.pyplot as __org_babel_python_plt
__org_babel_python_plt.gcf().clear()
%s
__org_babel_python_plt.savefig('%s')" body graphics-file)
body))
(defconst org-babel-python--nonsession-value-wrapper
(concat org-babel-python--def-format-value "
def main():
%s
__org_babel_python_format_value(main(), '%s', %s)")
"TODO")
(defconst org-babel-python--session-output-wrapper "\
with open('%s') as f:
exec(compile(f.read(), f.name, 'exec'))"
"Wrapper for session block with output results.
Has a single %s escape, the tempfile containing the source code
to evaluate.")
(defconst org-babel-python--session-value-wrapper
(concat org-babel-python--def-format-value "
import ast
with open('%s') as f:
__org_babel_python_ast = ast.parse(f.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, '', 'exec'))
__org_babel_python_final = eval(compile(ast.Expression(
__org_babel_python_final.value), '', 'eval'))
else:
exec(compile(__org_babel_python_ast, '', 'exec'))
__org_babel_python_final = None
__org_babel_python_format_value(__org_babel_python_final, '%s', %s)")
"Wrapper for session block with value results.
Has three %s escapes to be filled in:
1. Tempfile containing source to evaluate.
2. Tempfile to write results to.
3. result-params, converted from lisp to Python list.")
(defun org-babel-python-evaluate
(session body &optional result-type result-params preamble graphics-file)
"Evaluate BODY as Python code."
(if session
(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-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."
(let ((raw
(pcase result-type
(`output (org-babel-eval org-babel-python-command
(concat preamble (and preamble "\n")
(org-babel-python--output-graphics-wrapper
body graphics-file))))
(`value (let ((results-file (or graphics-file
(org-babel-temp-file "python-"))))
(org-babel-eval
org-babel-python-command
(concat
preamble (and preamble "\n")
(format
org-babel-python--nonsession-value-wrapper
(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)))
(forward-line 1))
(buffer-string))
(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 (org-trim raw)))))
(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."
(require org-babel-python-mode)
(let* ((python-shell-buffer-name (org-babel-python-without-earmuffs session))
(tmp-src-file (org-babel-temp-file "python-"))
(results
(progn
(with-temp-file tmp-src-file (insert body))
(pcase result-type
(`output
(let ((src-str (org-babel-python--output-graphics-wrapper
(format org-babel-python--session-output-wrapper
(org-babel-process-file-name
tmp-src-file 'noquote))
graphics-file)))
(if (eq 'python-mode org-babel-python-mode)
(py-send-string-no-output
src-str (get-buffer-process session) session)
(python-shell-send-string-no-output src-str))))
(`value
(let* ((results-file (or graphics-file
(org-babel-temp-file "python-")))
(src-str (format
org-babel-python--session-value-wrapper
(org-babel-process-file-name tmp-src-file 'noquote)
(org-babel-process-file-name results-file 'noquote)
(org-babel-python-var-to-python result-params))))
(if (eq 'python-mode org-babel-python-mode)
(py-shell-send-string src-str (get-buffer-process session))
(python-shell-send-string src-str))
(sleep-for 0 10)
(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))
(provide 'ob-python)
;;; ob-python.el ends here