2018-01-22 20:37:12 -06:00
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;;; ob-jupyter.el --- Jupyter integration with org-mode -*- lexical-binding: t -*-
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;; Copyright (C) 2018 Nathaniel Nicandro
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;; Author: Nathaniel Nicandro <nathanielnicandro@gmail.com>
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;; Created: 21 Jan 2018
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;; Version: 0.0.1
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;; This program is free software; you can redistribute it and/or
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;; modify it under the terms of the GNU General Public License as
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;; published by the Free Software Foundation; either version 2, or (at
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;; your option) any later version.
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;; This program is distributed in the hope that it will be useful, but
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;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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;; General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 59 Temple Place - Suite 330,
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;; Boston, MA 02111-1307, USA.
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;;; Commentary:
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;;
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;;; Code:
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(defgroup ob-jupyter nil
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"Jupyter integration with org-mdoe"
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:group 'jupyter)
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(require 'jupyter)
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(require 'ob)
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(declare-function cddar "cl" (x))
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(declare-function org-element-at-point "org-element")
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(declare-function org-element-property "org-element" (property element))
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(declare-function org-element-type "org-element" (element))
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(declare-function org-element-context "org-element" (&optional element))
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(declare-function org-babel-variable-assignments:python "ob-python" (params))
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(declare-function org-babel-expand-body:generic "ob-core" (body params &optional var-lines))
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(defcustom org-babel-jupyter-resource-directory "./.ob-jupyter/"
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"Directory used to store automatically generated image files.
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See `org-babel-jupyter-file-name'."
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:group 'ob-jupyter)
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(defvar org-babel-jupyter-session-clients (make-hash-table :test #'equal)
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"A hash table mapping session names to `jupyter-repl-client's.")
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(defvar org-babel-header-args:jupyter '((kernel . :any)
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(async . ((yes no))))
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"Available header arguments for Jupter src-blocks.")
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(defvar org-babel-default-header-args:jupyter '((:kernel . "python")
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(:async . "no"))
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"Default header arguments for Jupyter src-blocks.")
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2018-01-23 13:42:10 -06:00
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(defvar org-babel-jupyter-language-regex "^[ \t]*#\\+begin_src[ \t]+jupyter-\\([^ \f\t\n\r\v]+\\)[ \t]*"
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"Regular expression used to extract a source block's language name.")
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(defun org-babel-jupyter--get-src-block-info (&optional light context)
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2018-01-22 20:37:12 -06:00
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"Similar to `org-babel-get-src-block-info', but handle inline-babel-call.
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LIGHT and CONTEXT have the same meaning as in
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`org-babel-get-src-block-info'.
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If CONTEXT corresponds to an inline-babel-call, go to the named
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src block and return its info. Otherwise the behavior is the same
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as `org-babel-get-src-block-info'."
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(or context (setq context (org-element-context)))
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(save-excursion
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(when (eq (org-element-type context) 'inline-babel-call)
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(org-babel-goto-named-src-block
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(org-element-property :call context)))
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(org-babel-get-src-block-info light context)))
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2018-01-23 13:42:10 -06:00
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;; TODO: Handle the case when the kernel changes
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;;
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;; TODO: How to cache results properly? To handle the case when the kernel
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;; argument changes, we are checking for lang every time. Previously we were
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;; adding a text property at the beginning of the block, what we can do instead
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;; is add one as the last character of the kernel argument.
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;;
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;;
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;; FIXME: Parsing with `org-element-at-point' seems to depend on how far away a
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;; source block is from the subtree header line. This is not good if we want
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;; this to be fast, it seems the default value of `org-element-use-cache' is to
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;; blame. In the meantime, do not write large subtrees or large src blocks.
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;; Shouldn't have to anyway.
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(defun org-babel-jupyter-src-block-lang (&optional context)
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"Get the kernel language of a Jupyter src-block.
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CONTEXT should be a src-block org element and and defaults to the
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`org-element-context'."
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(or context (setq context (org-element-context)))
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(let ((type (org-element-type context)))
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(when (and (memq type '(src-block inline-src-block))
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(equal (org-element-property :language context) "jupyter"))
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(let* ((kernel
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(or (alist-get
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:kernel
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(ignore-errors
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(org-babel-parse-header-arguments
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(org-element-property :parameters context))))
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(alist-get
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:kernel
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(ignore-errors
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(apply #'append
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(mapcar #'org-babel-parse-header-arguments
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(org-element-property :header context)))))
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(alist-get
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:kernel
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(ignore-errors
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(org-with-point-at
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(org-element-property :begin context)
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;; FIXME: This looks expensive, but it seems like
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;; having the kernel language be a file local variable
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;; would be common
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(org-babel-params-from-properties "jupyter"))))))
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;; Possibly cache based on the kernel name. Since
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;; `jupyter-find-kernelspecs' matches prefixes, it could
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;; possibly match single letters which is not good.
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(spec (cddar (jupyter-find-kernelspecs kernel))))
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(plist-get spec :language)))))
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;; All calls of `org-src--get-lang-mode' in `org-src' currently have `point' at
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;; the src-block <2018-01-23 Tue>.
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;; (defun org-babel-jupyter--get-lang-mode (orig-fun lang &rest args)
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;; "Identical to `org-src--get-lang-mode' but handle jupyter blocks specially.
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;; This is an advice function for `org-src--get-lang-mode' which
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;; should be passed as the ORIG-FUN argument. Whenever LANG is
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;; \"jupyter\" pass the result of `org-babel-jupyter-src-block-lang'
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;; to ORIG-FUN as its first argument instead of \"jupyter\". ARGS
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;; are any additional arguments to pass to ORIG-FUN. This should be
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;; nil."
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;; (apply orig-fun
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;; (if (equal lang "jupyter")
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;; (org-babel-jupyter-src-block-lang)
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;; lang)
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;; args))
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;; (advice-add 'org-src--get-lang-mode :around #'org-babel-jupyter--get-lang-mode)
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(defun org-babel-variable-assignments:jupyter (params &optional lang)
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"Assign variables in PARAMS according to the Jupyter kernel language.
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Use `org-babel-jupyter-src-block-lang' to get the kernel language
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of the src-block ELEMENT and call the variable assignment
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function for the language. ELEMENT defaults to the
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`org-element-at-point'. So if LANG is the kernel language, then
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call
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org-babel-variable-assignments:LANG
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If the above function doesn't exist or if no kernel langauge can
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be found, fall back to `org-babel-variable-assignments:python'."
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(let* ((lang (or lang
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(save-excursion
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(when (re-search-backward
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org-babel-jupyter-language-regex nil t)
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(match-string 1)))))
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(fun (when lang
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(intern (concat "org-babel-variable-assignments:" lang)))))
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(if (functionp fun) (funcall fun params)
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(org-babel-variable-assignments:python params))))
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2018-01-23 13:42:10 -06:00
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(defun org-babel-expand-body:jupyter (body params &optional var-lines lang)
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"Expand BODY according to PARAMS.
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BODY is the code to expand, PARAMS should be the header arguments
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of the src block with BODY as its code, and VAR-LINES should be
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the list of strings containing the variables to evaluate before
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executing body.
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This function is similar to
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`org-babel-variable-assignments:jupyter' in that it finds the
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kernel language of the src-block ELEMENT, defaulting to the
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`org-element-at-point', to find get the kernel language of BODY.
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So if LANG is the kernel language, call the function
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org-babel-expand-body:LANG
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to expand BODY. If the above function doesn't exist or if no
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kernel langauge can be found fall back to
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`org-babel-expand-body:generic'."
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2018-01-23 13:42:10 -06:00
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(let* ((lang (or lang
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(save-excursion
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(when (re-search-backward
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org-babel-jupyter-language-regex nil t)
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(match-string 1)))))
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2018-01-22 20:37:12 -06:00
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(fun (when lang
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(intern (concat "org-babel-expand-body:" lang)))))
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(if (functionp fun) (funcall fun body params var-lines)
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(org-babel-expand-body:generic body params var-lines))))
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(defun org-babel-edit-prep:jupyter (info)
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"Prepare the edit buffer according to INFO."
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(let* ((params (nth 2 info))
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(session (alist-get :session params)))
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(jupyter-repl-associate-buffer
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(org-babel-jupyter-initiate-session session params))))
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(defun org-babel-prep-session:jupyter (session params &optional no-execute)
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"Prepare a Jupyter SESSION according to PARAMS.
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If optional argument NO-EXECUTE is non-nil, do not execute any of
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the header variables in PARAMS."
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(let ((buffer (org-babel-jupyter-initiate-session session params))
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(var-lines (org-babel-variable-assignments:jupyter params)))
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(with-current-buffer buffer
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(goto-char (point-max))
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(when var-lines
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(jupyter-repl-replace-cell-code
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(mapconcat #'identity var-lines "\n"))
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;; For `org-babel-load-session:jupyter'
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(when no-execute
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(insert "\n")))
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(unless no-execute
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(jupyter-execute-request jupyter-repl-current-client))
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(current-buffer))))
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(defun org-babel-load-session:jupyter (session body params)
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"In a Jupyter SESSION, load BODY according to PARAMS."
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(save-window-excursion
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(let ((buffer (org-babel-prep-session:jupyter session params 'noexecute)))
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(with-current-buffer buffer
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(insert (org-babel-chomp body))
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(current-buffer)))))
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(defun org-babel-jupyter-initiate-session-by-key (session params)
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"Return the `jupyter-repl-client' for SESSION.
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If SESSION does not have a client already, one is created based
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on SESSION and PARAMS. If SESSION ends with \".json\" then
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SESSION is interpreted as a kernel connection file and a new
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kernel connected to SESSION is created. Otherwise a kernel is run
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based on the `:kernel' parameter in PARAMS which should be either
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a valid kernel name or a prefix of one. The first kernel that is
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returned by `jupyter-find-kernelspecs' will be used."
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(let* ((kernel (alist-get :kernel params))
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(key (concat session "-" kernel)))
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(oref (or (gethash key org-babel-jupyter-session-clients)
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(let ((client (if (string-suffix-p ".json" session)
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(connect-jupyter-repl session)
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(run-jupyter-repl kernel))))
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(jupyter-set client 'jupyter-include-other-output nil)
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(with-jupyter-repl-buffer client
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(let ((name (buffer-name)))
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(when (string-match "^\\*\\(.+\\)\\*" name)
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(rename-buffer
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(concat "*" (match-string 1 name) "-" session "*")
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'unique)))
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(add-hook
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'kill-buffer-hook
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(lambda ()
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(remhash key org-babel-jupyter-session-clients))
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nil t))
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(puthash key client org-babel-jupyter-session-clients)))
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buffer)))
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(defun org-babel-jupyter-initiate-session (&optional session params)
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"Initialize a Jupyter SESSION according to PARAMS."
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(if (equal session "none") (error "Need a session to run")
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(org-babel-jupyter-initiate-session-by-key session params)))
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(defun org-babel-jupyter-file-name (info ext)
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"Return a file name based on src-block INFO.
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INFO should be the full list returned by
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`org-babel-get-src-block-info', i.e. the list returned when the
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LIGHT argument is nil. If the src-block that corresponds to INFO
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has a `:file' argument, then just return that. Otherwise, when no
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`:file' argument exists, generate a file name by concatenating
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the following:
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1. `org-babel-jupyter-resource-directory'
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2. The hash returned by `org-babel-sha1-hash' on INFO
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3. .EXT
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Where EXT should be the file extension to give the
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file (excluding the dot)."
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(let ((file (alist-get :file (nth 2 info))))
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(or file
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(let ((dir (prog1 org-babel-jupyter-resource-directory
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(unless (file-directory-p
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org-babel-jupyter-resource-directory)
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(make-directory org-babel-jupyter-resource-directory)))))
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(concat (file-name-as-directory dir)
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(org-babel-sha1-hash info) "." ext)))))
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(defun org-babel-jupyter-render-result (data info)
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"Return the rendered DATA.
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DATA is a plist, (:mimetype1 value1 ...), which is used to render
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a result which can be passed to `org-babel-insert-result'.
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INFO is the list returned by `org-babel-get-src-block-info' for
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the src-block whose results are contained in DATA. Note that INFO
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should be the full src-block info, i.e. the LIGHT argument of
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`org-babel-get-src-block-info' should be nil when obtaining INFO.
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Return a cons cell (RESULT-PARAM . RESULTS) where RESULT-PARAM is
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either a result parameter, i.e. one of the RESULT-PARAMS of
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`org-babel-insert-result', or a key value pair which should be
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added to the ARGUMENTS list of INFO before calling
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`org-babel-insert-result'.
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For example, if DATA only contains the mimetype `:text/markdown',
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the RESULT-PARAM will be
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(:wrap . \"EXPORT markdown\")
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and RESULTS will be the markdown text which should be wrapped in
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an \"EXPORT markdown\" block. See `org-babel-insert-result'.
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Note that INFO is only relevant if the resulting rendered DATA
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ends up being an image and no `:file' argument is found in INFO.
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In this case a file name is automatically generated, see
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`org-babel-jupyter-file-name'."
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(let ((mimetypes (seq-filter #'keywordp data))
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(result-params (alist-get :result-params (nth 2 info)))
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param result)
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(cond
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((memq :text/org mimetypes)
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(setq param "org"
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result (plist-get data :text/org)))
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((memq :text/html mimetypes)
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(let ((html (plist-get data :text/html)))
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(if (string-match "^<img src=\"data:\\(.+\\);base64,\\(.+\\)\"" html)
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(let ((mimetype (intern (concat ":" (match-string 1 html)))))
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(org-babel-jupyter-render-result
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(list mimetype (match-string 2 html)) info))
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(setq param "html"
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result (plist-get data :text/html)))))
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((memq :text/markdown mimetypes)
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(setq param '(:wrap . "EXPORT markdown")
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result (plist-get data :text/markdown)))
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((memq :text/latex mimetypes)
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;; TODO: Handle other cases like this for other mimetypes
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(setq param (unless (member "raw" result-params) "latex")
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result (plist-get data :text/latex)))
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((memq :image/png mimetypes)
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(let ((file (org-babel-jupyter-file-name info "png")))
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(setq param "file"
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result (with-temp-file file
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(let ((buffer-file-coding-system 'binary)
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(require-final-newline nil))
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(insert (plist-get data :image/png))
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(base64-decode-region (point-min) (point-max)))
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file))))
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((memq :image/svg+xml mimetypes)
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(let ((file (org-babel-jupyter-file-name info "svg")))
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(setq param "file"
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result (with-temp-file file
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(let ((require-final-newline nil))
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(insert (plist-get data :image/svg+xml)))
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file))))
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((memq :text/plain mimetypes)
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(setq result (plist-get data :text/plain)))
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(t (warn "No supported mimetype found %s" mimetypes)))
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(list param result)))
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;; TODO: Properly handle the execution-state and execution-count of the REPL
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;; buffer. I don't think ob-jupyter should be responsible for updating the
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;; state of the REPL buffer. What I really want to do is to be able to silence
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;; any output generated by the REPL due to execute requests of a jupyter
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;; src-block. Since a jupyter src-block already handles all of the output
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;; anyways it doesn't seem necessary. It seems that there should be an option
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;; to prevent output in the REPL buffer and just send off execute requests
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;; without displaying any results and this should have the option of being
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;; configured for every request since you would still like to show the output
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;; when sending requests directly from the REPL buffer.
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(defun org-babel-execute:jupyter (body params)
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"Execute BODY according to PARAMS.
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BODY is the code to execute for the current Jupyter `:session' of
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PARAMS."
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(let* ((session (alist-get :session params))
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(repl-buffer (org-babel-jupyter-initiate-session session params))
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;; TODO: Figure out if the current context is always a source block
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;; context for the various commands that can execute code blocks.
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;; Since this function is only given a body and params, I am assuming
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;; it should be written to not depend on a context.
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(element (org-element-at-point))
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(context (org-element-context element))
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(block-info (org-babel-jupyter--get-src-block-info nil context))
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(code (org-babel-expand-body:jupyter
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body params (org-babel-variable-assignments:jupyter
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params element)
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element))
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(req (with-current-buffer repl-buffer
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(goto-char (point-max))
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(jupyter-repl-replace-cell-code code)
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;; TODO: Should handlers be inhbited? They are inhibited to
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;; prevent output from going into the REPL buffer when it is
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;; redirected to the output of a Jupyter src block. It
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;; doesn't seem to make sense to insert output in the REPL
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;; buffer when it is redirected somewhere else.
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(prog1 (let ((jupyter-inhibit-handlers t))
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(jupyter-execute-request jupyter-repl-current-client))
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(when (get-buffer-window)
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(set-window-point (get-buffer-window) (point)))))))
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;; Setup callbacks for the request
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(let* ((result-type (alist-get :result-type params))
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(result-params (alist-get :result-params params))
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(async (equal (alist-get :async params) "yes"))
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(block-beginning
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(copy-marker org-babel-current-src-block-location))
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(finalize-execution
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(lambda (result)
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;; Unmark the REPL cell as busy. This is needed since we set
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;; `jupyter-inhibit-handlers' to t before executing a jupyter
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;; src-block which means that the handler which unmark's the cell
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;; is not run. The cell is marked as busy in
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;; `jupyter-execute-request' for a `jupyter-repl-client'.
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|
(with-current-buffer repl-buffer
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|
|
(save-excursion
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(jupyter-repl-goto-cell req)
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|
(jupyter-repl-cell-unmark-busy)))
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|
|
(when async
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|
|
(org-with-point-at block-beginning
|
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|
|
(let ((lang (org-babel-jupyter-src-block-lang)))
|
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|
|
(org-babel-insert-result
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|
result result-params block-info nil lang))))
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|
(set-marker block-beginning nil)))
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|
result output)
|
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|
|
(jupyter-add-callback req
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|
:stream
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|
(lambda (msg)
|
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|
|
(and (eq result-type 'output)
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|
(equal (jupyter-message-get msg :name) "stdout")
|
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|
|
(push (ansi-color-apply (jupyter-message-get msg :text))
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|
output)))
|
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|
|
;; FIXME: finalize-execution should be called when the status goes idle
|
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|
|
;; so that in the case of result-type output, all of the output is
|
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|
|
;; captured. See
|
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|
|
;; http://jupyter-client.readthedocs.io/en/stable/messaging.html#request-reply
|
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|
|
;;
|
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|
|
;; The reason this is not done is due to the Julia kernel not sending
|
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|
|
;; the idle message when multiple execute requests are queued. It seems
|
|
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|
|
;; to mangle the parent message id when this is the case so that
|
|
|
|
|
;; multiple idle messages are received for the same request instead of
|
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|
|
;; one for each queued request. <2018-01-22 Mon>
|
|
|
|
|
:execute-reply
|
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|
|
(lambda (msg)
|
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|
|
|
(cl-destructuring-bind (&key status ename evalue traceback
|
|
|
|
|
&allow-other-keys)
|
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|
|
(jupyter-message-content msg)
|
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|
|
(if (equal status "ok")
|
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|
|
;; See the execute-result callback for when result-type is
|
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|
|
;; value
|
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|
|
(when (eq result-type 'output)
|
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|
(setq result (mapconcat #'identity (nreverse output) "\n")))
|
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|
(if (eq result-type 'value)
|
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|
|
(setq result (format "%s: %s" ename (ansi-color-apply evalue)))
|
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|
|
(push (mapconcat #'ansi-color-apply traceback "\n") output)
|
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|
|
(setq result (mapconcat #'identity (nreverse output) "\n"))))
|
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|
|
(funcall finalize-execution result)))
|
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|
|
:execute-result
|
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|
|
|
(lambda (msg)
|
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|
|
|
(unless (eq result-type 'output)
|
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|
|
|
(cl-destructuring-bind (render-param res)
|
|
|
|
|
(org-babel-jupyter-render-result
|
|
|
|
|
(jupyter-message-get msg :data) block-info)
|
|
|
|
|
;; Update params/result-params for `org-babel-insert-result' This
|
|
|
|
|
;; gives a way to insert the results based on its mimetype.
|
|
|
|
|
;;
|
|
|
|
|
;; NOTE: This relies on the semantics of
|
|
|
|
|
;; `org-babel-insert-result' which prioritizes the various values
|
|
|
|
|
;; of result-params. So if a user species different result-params
|
|
|
|
|
;; locally to a block, the settings here may override the user's
|
|
|
|
|
;; setting and vice versa.
|
|
|
|
|
;;
|
|
|
|
|
;; NOTE: This modifies the lists contained in params so that
|
|
|
|
|
;; synchronous evaluation will work. This seems to be the only
|
|
|
|
|
;; way to handle both cases of async and synchronous execution.
|
|
|
|
|
(cond
|
|
|
|
|
((consp render-param)
|
|
|
|
|
(nconc params (list render-param))
|
|
|
|
|
;; Since async results are inserted using block-info
|
|
|
|
|
(cl-callf org-babel-merge-params (nth 2 block-info)
|
|
|
|
|
(list render-param)))
|
|
|
|
|
((stringp render-param)
|
|
|
|
|
(nconc result-params (list render-param))))
|
|
|
|
|
(setq result res)))))
|
|
|
|
|
(if async (format "%s%s"
|
|
|
|
|
(if (member "raw" result-params) ": " "")
|
|
|
|
|
(jupyter-request-id req))
|
|
|
|
|
(jupyter-wait-until-received :execute-reply req most-positive-fixnum)
|
|
|
|
|
result))))
|
|
|
|
|
|
2018-01-23 13:42:10 -06:00
|
|
|
(defun org-babel-jupyter-make-language-alias (lang)
|
|
|
|
|
"Simimilar to `org-babel-make-language-alias' except do not
|
|
|
|
|
make an alias for the header args and set the OLD LANG as
|
|
|
|
|
jupyter."
|
|
|
|
|
(dolist (fn '("execute" "expand-body" "prep-session" "edit-prep"
|
|
|
|
|
"variable-assignments" "load-session"))
|
|
|
|
|
(let ((sym (intern-soft (concat "org-babel-" fn ":jupyter"))))
|
|
|
|
|
(when (and sym (fboundp sym))
|
|
|
|
|
(defalias (intern (concat "org-babel-" fn ":" lang)) sym))))
|
|
|
|
|
(defalias (intern (concat "org-babel-header-args:" lang))
|
|
|
|
|
'org-babel-header-args:jupyter)
|
|
|
|
|
(defalias (intern (concat "org-babel-" lang "-initiate-session"))
|
|
|
|
|
'org-babel-jupyter-initiate-session))
|
|
|
|
|
|
|
|
|
|
(cl-loop
|
|
|
|
|
for (kernel . (_dir . spec)) in (jupyter-available-kernelspecs)
|
|
|
|
|
for lang = (plist-get spec :language)
|
|
|
|
|
for jupyter-lang = (concat "jupyter-" lang)
|
|
|
|
|
do
|
|
|
|
|
(org-babel-jupyter-make-language-alias jupyter-lang)
|
|
|
|
|
(add-to-list 'org-src-lang-modes
|
|
|
|
|
(cons jupyter-lang
|
|
|
|
|
(intern (or (cdr (assoc lang org-src-lang-modes))
|
|
|
|
|
(replace-regexp-in-string
|
|
|
|
|
"[0-9]*" "" lang)))))
|
|
|
|
|
;; (add-to-list 'org-babel-tangle-lang-exts
|
|
|
|
|
;; (cons (concat "jupyter-" lang) file_extension))
|
|
|
|
|
(set (intern (concat "org-babel-default-header-args:" jupyter-lang))
|
|
|
|
|
`((:kernel . ,kernel)
|
|
|
|
|
(:async . "no"))))
|
|
|
|
|
|
2018-01-22 20:37:12 -06:00
|
|
|
(provide 'ob-jupyter)
|
|
|
|
|
|
|
|
|
|
;;; ob-jupyter.el ends here
|
