mirror of
https://git.savannah.gnu.org/git/emacs/org-mode.git
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ac73e594c9
* lisp/ob-R.el (org-babel-R-associate-session):
* lisp/ob-clojure.el (ob-clojure-nbb-command, ob-clojure-cli-command):
* lisp/ob-core.el (org-babel-execute-src-block):
* lisp/ob-exp.el (org-babel-exp-code):
* lisp/ob-julia.el (org-babel-julia-associate-session):
* lisp/ob-python.el
(org-babel-python--python-util-comint-end-of-output-p):
* lisp/ol.el (org-insert-link):
* lisp/org-attach.el (org-attach):
* lisp/org-clock.el (org-clock-select-task):
* lisp/org-compat.el (fboundp):
* lisp/org-element-ast.el (org-element-property-raw)
(org-element-put-property, org-element-copy):
* lisp/org-element.el (org-element-timestamp-interpreter)
(org-element--cache-key):
* lisp/org-goto.el (org-goto-location):
* lisp/org-lint.el (org-lint-suspicious-language-in-src-block)
(org-lint-export-option-keywords):
* lisp/org-macs.el (org-mks):
* lisp/org-persist.el: (org-persist-write:elisp):
* lisp/org-table.el (org-table-fedit-finish):
* lisp/org.el (org-entry-get-with-inheritance):
* lisp/ox-html.el (org-html--reference, org-html--build-mathjax-config)
(org-html-example-block):
* lisp/ox-latex.el (org-latex-table-row):
* lisp/ox.el (org-export--prune-tree)
(org-export--blindly-expand-include):
* testing/lisp/test-duplicates-detector.el
(test-duplicates-detector--find-duplicates):
* testing/lisp/test-ob-haskell-ghci.el
(test-ob-haskell-ghci-checking-buffers):
* testing/lisp/test-ob-python.el
(test-ob-python/async-local-python-shell):
* testing/lisp/test-ob-shell.el (test-ob-shell/bash-uses-assoc-arrays)
(test-ob-shell/bash-uses-assoc-arrays-with-lists)
(test-ob-shell/remote-with-stdin-or-cmdline):
Replace use of if-let and when-let, obsolete in Emacs 31.0.50.
(cherry picked from commit bc7033f2d1)
352 lines
13 KiB
EmacsLisp
352 lines
13 KiB
EmacsLisp
;;; ob-julia.el --- org-babel functions for julia code evaluation -*- lexical-binding: t; -*-
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;; Copyright (C) 2013-2024 Free Software Foundation, Inc.
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;; Authors: G. Jay Kerns
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;; Maintainer: Pedro Bruel <pedro.bruel@gmail.com>
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;; Keywords: literate programming, reproducible research, scientific computing
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;; URL: https://github.com/phrb/ob-julia
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;; This file is part of GNU Emacs.
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;; GNU Emacs is free software: you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; GNU Emacs is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU 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. If not, see <https://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Org-Babel support for evaluating julia code
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;;
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;; Based on ob-R.el by Eric Schulte and Dan Davison.
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;;
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;; Session support requires the installation of the DataFrames and CSV
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;; Julia packages.
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;;; Code:
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(require 'org-macs)
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(org-assert-version)
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(require 'cl-lib)
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(require 'ob)
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(declare-function orgtbl-to-csv "org-table" (table params))
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(declare-function julia "ext:ess-julia" (&optional start-args))
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(declare-function inferior-ess-send-input "ext:ess-inf" ())
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(declare-function ess-make-buffer-current "ext:ess-inf" ())
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(declare-function ess-eval-buffer "ext:ess-inf" (vis))
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(declare-function ess-wait-for-process "ext:ess-inf"
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(&optional proc sec-prompt wait force-redisplay))
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(defvar ess-current-process-name) ; ess-custom.el
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(defvar ess-local-process-name) ; ess-custom.el
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(defvar ess-eval-visibly) ; ess-custom.el
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(defvar ess-local-customize-alist); ess-custom.el
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(defvar ess-gen-proc-buffer-name-function) ; ess-custom.el
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(defvar ess-ask-for-ess-directory) ; ess-custom.el
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(defvar ess-directory-function) ; ess-custom.el
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(defvar ess-directory) ; ess-custom.el
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(defvar org-babel-header-args:julia
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'((width . :any)
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(horizontal . :any)
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(results . ((file list vector table scalar verbatim)
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(raw org html latex code pp wrap)
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(replace silent append prepend)
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(output value graphics))))
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"Julia-specific header arguments.")
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(add-to-list 'org-babel-tangle-lang-exts '("julia" . "jl"))
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(defvar org-babel-default-header-args:julia '())
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(defcustom org-babel-julia-command "julia"
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"Name of command to use for executing julia code."
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:version "24.3"
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:package-version '(Org . "8.0")
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:group 'org-babel
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:type 'string)
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(defun org-babel-julia-associate-session (session)
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"Associate R code buffer with an R session.
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Make SESSION be the inferior ESS process associated with the
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current code buffer."
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(when-let* ((process (get-buffer-process session)))
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(setq ess-local-process-name (process-name process))
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(ess-make-buffer-current))
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(setq-local ess-gen-proc-buffer-name-function (lambda (_) session)))
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(defun org-babel-expand-body:julia (body params &optional _graphics-file)
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"Expand BODY according to PARAMS, return the expanded body."
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(mapconcat #'identity
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(append
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(when (cdr (assq :prologue params))
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(list (cdr (assq :prologue params))))
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(org-babel-variable-assignments:julia params)
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(list body)
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(when (cdr (assq :epilogue params))
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(list (cdr (assq :epilogue params)))))
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"\n"))
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(defun org-babel-execute:julia (body params)
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"Execute a block of julia code.
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This function is called by `org-babel-execute-src-block'."
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(save-excursion
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(let* ((result-params (cdr (assq :result-params params)))
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(result-type (cdr (assq :result-type params)))
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(session (org-babel-julia-initiate-session
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(cdr (assq :session params)) params))
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(graphics-file (and (member "graphics" (assq :result-params params))
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(org-babel-graphical-output-file params)))
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(colnames-p (unless graphics-file (cdr (assq :colnames params))))
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(full-body (org-babel-expand-body:julia body params graphics-file))
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(result
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(org-babel-julia-evaluate
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session full-body result-type result-params
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(or (equal "yes" colnames-p)
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(org-babel-pick-name
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(cdr (assq :colname-names params)) colnames-p)))))
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(if graphics-file nil result))))
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(defun org-babel-normalize-newline (result)
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(replace-regexp-in-string
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"\\(\n\r?\\)\\{2,\\}"
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"\n"
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result))
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(defun org-babel-prep-session:julia (session params)
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"Prepare SESSION according to the header arguments specified in PARAMS."
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(let* ((session (org-babel-julia-initiate-session session params))
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(var-lines (org-babel-variable-assignments:julia params)))
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(org-babel-comint-in-buffer session
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(mapc (lambda (var)
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(end-of-line 1) (insert var) (comint-send-input nil t)
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(org-babel-comint-wait-for-output session)) var-lines))
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session))
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(defun org-babel-load-session:julia (session body params)
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"Load BODY into SESSION."
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(save-window-excursion
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(let ((buffer (org-babel-prep-session:julia session params)))
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(with-current-buffer buffer
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert (org-babel-chomp body)))
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buffer)))
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;; helper functions
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(defun org-babel-variable-assignments:julia (params)
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"Return list of julia statements assigning the block's variables."
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(let ((vars (org-babel--get-vars params)))
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(mapcar
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(lambda (pair) (org-babel-julia-assign-elisp (car pair) (cdr pair)))
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(mapcar
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(lambda (i)
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(cons (car (nth i vars))
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(org-babel-reassemble-table
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(cdr (nth i vars))
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(cdr (nth i (cdr (assq :colname-names params))))
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(cdr (nth i (cdr (assq :rowname-names params)))))))
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(number-sequence 0 (1- (length vars)))))))
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(defun org-babel-julia-quote-csv-field (s)
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"Quote field S for export to julia."
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(if (stringp s)
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(concat "\"" (mapconcat #'identity (split-string s "\"") "\"\"") "\"")
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(format "%S" s)))
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(defun org-babel-julia-assign-elisp (name value)
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"Construct julia code assigning the elisp VALUE to a variable named NAME."
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(if (listp value)
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(let* ((lengths (mapcar #'length (cl-remove-if-not #'sequencep value)))
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(max (if lengths (apply #'max lengths) 0))
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(min (if lengths (apply #'min lengths) 0)))
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;; Ensure VALUE has an orgtbl structure (depth of at least 2).
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(unless (listp (car value)) (setq value (list value)))
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(let ((file (orgtbl-to-csv value '(:fmt org-babel-julia-quote-csv-field))))
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(if (= max min)
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(format "%s = begin
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using CSV
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CSV.read(\"%s\")
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end" name file)
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(format "%s = begin
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using CSV
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CSV.read(\"%s\")
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end"
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name file))))
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(format "%s = %s" name (org-babel-julia-quote-csv-field value))))
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(defvar ess-ask-for-ess-directory) ; dynamically scoped
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(defun org-babel-julia-initiate-session (session _params)
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"If there is not a current julia process then create one."
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(unless (string= session "none")
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(let* ((session (or session "*Julia*"))
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;; Force using `default-directory', as we promise in the
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;; manual. The caller should have taken care about setting
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;; it according to :dir if necessary.
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;; https://ess.r-project.org/Manual/ess.html#Changing-the-startup-actions
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(ess-ask-for-ess-directory nil)
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(ess-directory-function nil)
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(ess-directory nil)
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;; Make ESS name the process buffer as SESSION.
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(ess-gen-proc-buffer-name-function
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(lambda (_) session)))
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(if (org-babel-comint-buffer-livep session)
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session
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;; FIXME: Depending on `display-buffer-alist', (julia) may end up
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;; popping up a new frame which `save-window-excursion' won't be able
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;; to "undo", so we really should call a kind of
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;; `julia-no-select' instead so we don't need to undo any
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;; window-changes afterwards.
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(save-window-excursion
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(when (get-buffer session)
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;; Session buffer exists, but with dead process
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(set-buffer session))
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(org-require-package 'ess "ESS")
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(set-buffer (julia))
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(current-buffer))))))
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(defun org-babel-julia-graphical-output-file (params)
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"Name of file to which julia should send graphical output."
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(and (member "graphics" (cdr (assq :result-params params)))
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(cdr (assq :file params))))
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(defconst org-babel-julia-eoe-indicator "print(\"org_babel_julia_eoe\")")
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(defconst org-babel-julia-eoe-output "org_babel_julia_eoe")
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(defconst org-babel-julia-write-object-command "begin
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local p_ans = %s
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local p_tmp_file = \"%s\"
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try
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using CSV, DataFrames
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if typeof(p_ans) <: DataFrame
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p_ans_df = p_ans
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else
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p_ans_df = DataFrame(:ans => p_ans)
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end
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CSV.write(p_tmp_file,
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p_ans_df,
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writeheader = %s,
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transform = (col, val) -> something(val, missing),
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missingstring = \"nil\",
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quotestrings = false)
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p_ans
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catch e
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err_msg = \"Source block evaluation failed. $e\"
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CSV.write(p_tmp_file,
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DataFrame(:ans => err_msg),
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writeheader = false,
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transform = (col, val) -> something(val, missing),
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missingstring = \"nil\",
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quotestrings = false)
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err_msg
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end
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end")
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(defun org-babel-julia-evaluate
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(session body result-type result-params column-names-p)
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"Evaluate julia code in BODY."
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(if session
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(org-babel-julia-evaluate-session
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session body result-type result-params column-names-p)
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(org-babel-julia-evaluate-external-process
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body result-type result-params column-names-p)))
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(defun org-babel-julia-evaluate-external-process
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(body result-type result-params column-names-p)
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"Evaluate BODY in external julia process.
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If RESULT-TYPE equals `output' then return standard output as a
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string. If RESULT-TYPE equals `value' then return the value of the
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last statement in BODY, as elisp."
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(cl-case result-type
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(value
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(let ((tmp-file (org-babel-temp-file "julia-")))
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(org-babel-eval org-babel-julia-command
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(format org-babel-julia-write-object-command
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(format "begin %s end" body)
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(org-babel-process-file-name tmp-file 'noquote)
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(if column-names-p "true" "false")
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))
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(org-babel-julia-process-value-result
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(org-babel-result-cond result-params
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(with-temp-buffer
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(insert-file-contents tmp-file)
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(buffer-string))
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(org-babel-import-elisp-from-file tmp-file '(4)))
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column-names-p)))
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(output (org-babel-eval org-babel-julia-command body))))
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(defun org-babel-julia-evaluate-session
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(session body result-type result-params column-names-p)
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"Evaluate BODY in SESSION.
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If RESULT-TYPE equals `output' then return standard output as a
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string. If RESULT-TYPE equals `value' then return the value of the
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last statement in BODY, as elisp."
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(cl-case result-type
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(value
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(with-temp-buffer
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(insert (org-babel-chomp body))
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(let ((ess-local-customize-alist t)
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(ess-local-process-name
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(process-name (get-buffer-process session)))
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(ess-eval-visibly nil))
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(ess-eval-buffer nil)))
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(let ((tmp-file (org-babel-temp-file "julia-")))
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(org-babel-comint-eval-invisibly-and-wait-for-file
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session tmp-file
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(format org-babel-julia-write-object-command
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"ans"
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(org-babel-process-file-name tmp-file 'noquote)
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(if column-names-p "true" "false")
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))
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(org-babel-julia-process-value-result
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(org-babel-result-cond result-params
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(with-temp-buffer
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(insert-file-contents tmp-file)
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(buffer-string))
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(org-babel-import-elisp-from-file tmp-file '(4)))
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column-names-p)))
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(output
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(mapconcat
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#'org-babel-chomp
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(butlast
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(delq nil
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(mapcar
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(lambda (line) (when (> (length line) 0) line))
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(mapcar
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(lambda (line) ;; cleanup extra prompts left in output
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(if (string-match
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"^\\([>+.]\\([ ][>.+]\\)*[ ]\\)"
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(car (split-string line "\n")))
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(substring line (match-end 1))
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line))
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(org-babel-comint-with-output (session org-babel-julia-eoe-output)
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(insert (mapconcat #'org-babel-chomp
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(list body org-babel-julia-eoe-indicator)
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"\n"))
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(inferior-ess-send-input))))))
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"\n"))))
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(defun org-babel-julia-process-value-result (result column-names-p)
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"Julia-specific processing of return value.
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Insert hline if column names in output have been requested."
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(if column-names-p
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(cons (car result) (cons 'hline (cdr result)))
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result))
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(provide 'ob-julia)
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;;; ob-julia.el ends here
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