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-;;; ob-julia.el --- org-babel functions for julia code evaluation  -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2013-2021 Free Software Foundation, Inc.
-;; Authors: G. Jay Kerns
-;; Maintainer: Pedro Bruel <pedro.bruel@gmail.com>
-;; Keywords: literate programming, reproducible research, scientific computing
-;; Homepage: https://github.com/phrb/ob-julia
-
-;; 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 julia code
-;;
-;; Based on ob-R.el by Eric Schulte and Dan Davison.
-
-;;; Code:
-(require 'cl-lib)
-(require 'ob)
-
-(declare-function orgtbl-to-csv "org-table" (table params))
-(declare-function julia "ext:ess-julia" (&optional start-args))
-(declare-function inferior-ess-send-input "ext:ess-inf" ())
-(declare-function ess-make-buffer-current "ext:ess-inf" ())
-(declare-function ess-eval-buffer "ext:ess-inf" (vis))
-(declare-function ess-wait-for-process "ext:ess-inf"
-		  (&optional proc sec-prompt wait force-redisplay))
-
-(defvar org-babel-header-args:julia
-  '((width		 . :any)
-    (horizontal		 . :any)
-    (results             . ((file list vector table scalar verbatim)
-			    (raw org html latex code pp wrap)
-			    (replace silent append prepend)
-			    (output value graphics))))
-  "Julia-specific header arguments.")
-
-(add-to-list 'org-babel-tangle-lang-exts '("julia" . "jl"))
-
-(defvar org-babel-default-header-args:julia '())
-
-(defcustom org-babel-julia-command "julia"
-  "Name of command to use for executing julia code."
-  :version "24.3"
-  :package-version '(Org . "8.0")
-  :group 'org-babel
-  :type 'string)
-
-(defvar ess-current-process-name) ; dynamically scoped
-(defvar ess-local-process-name)   ; dynamically scoped
-(defvar ess-eval-visibly-p)       ; dynamically scoped
-(defun org-babel-edit-prep:julia (info)
-  (let ((session (cdr (assq :session (nth 2 info)))))
-    (when (and session
-	       (string-prefix-p "*"  session)
-	       (string-suffix-p "*" session))
-      (org-babel-julia-initiate-session session nil))))
-
-(defun org-babel-expand-body:julia (body params &optional _graphics-file)
-  "Expand BODY according to PARAMS, return the expanded body."
-  (mapconcat #'identity
-	     (append
-	      (when (cdr (assq :prologue params))
-		(list (cdr (assq :prologue params))))
-	      (org-babel-variable-assignments:julia params)
-	      (list body)
-	      (when (cdr (assq :epilogue params))
-		(list (cdr (assq :epilogue params)))))
-	     "\n"))
-
-(defun org-babel-execute:julia (body params)
-  "Execute a block of julia code.
-This function is called by `org-babel-execute-src-block'."
-  (save-excursion
-    (let* ((result-params (cdr (assq :result-params params)))
-	   (result-type (cdr (assq :result-type params)))
-           (session (org-babel-julia-initiate-session
-		     (cdr (assq :session params)) params))
-	   (graphics-file (and (member "graphics" (assq :result-params params))
-			       (org-babel-graphical-output-file params)))
-	   (colnames-p (unless graphics-file (cdr (assq :colnames params))))
-	   (full-body (org-babel-expand-body:julia body params graphics-file))
-	   (result
-	    (org-babel-julia-evaluate
-	     session full-body result-type result-params
-	     (or (equal "yes" colnames-p)
-		 (org-babel-pick-name
-		  (cdr (assq :colname-names params)) colnames-p)))))
-      (if graphics-file nil result))))
-
-(defun org-babel-normalize-newline (result)
-  (replace-regexp-in-string
-   "\\(\n\r?\\)\\{2,\\}"
-   "\n"
-   result))
-
-(defun org-babel-prep-session:julia (session params)
-  "Prepare SESSION according to the header arguments specified in PARAMS."
-  (let* ((session (org-babel-julia-initiate-session session params))
-	 (var-lines (org-babel-variable-assignments:julia params)))
-    (org-babel-comint-in-buffer session
-      (mapc (lambda (var)
-              (end-of-line 1) (insert var) (comint-send-input nil t)
-              (org-babel-comint-wait-for-output session)) var-lines))
-    session))
-
-(defun org-babel-load-session:julia (session body params)
-  "Load BODY into SESSION."
-  (save-window-excursion
-    (let ((buffer (org-babel-prep-session:julia 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:julia (params)
-  "Return list of julia statements assigning the block's variables."
-  (let ((vars (org-babel--get-vars params)))
-    (mapcar
-     (lambda (pair) (org-babel-julia-assign-elisp (car pair) (cdr pair)))
-     (mapcar
-      (lambda (i)
-	(cons (car (nth i vars))
-	      (org-babel-reassemble-table
-	       (cdr (nth i vars))
-	       (cdr (nth i (cdr (assq :colname-names params))))
-	       (cdr (nth i (cdr (assq :rowname-names params)))))))
-      (number-sequence 0 (1- (length vars)))))))
-
-(defun org-babel-julia-quote-csv-field (s)
-  "Quote field S for export to julia."
-  (if (stringp s)
-      (concat "\"" (mapconcat #'identity (split-string s "\"") "\"\"") "\"")
-    (format "%S" s)))
-
-(defun org-babel-julia-assign-elisp (name value)
-  "Construct julia code assigning the elisp VALUE to a variable named NAME."
-  (if (listp value)
-      (let* ((lengths (mapcar #'length (cl-remove-if-not #'sequencep value)))
-             (max (if lengths (apply #'max lengths) 0))
-             (min (if lengths (apply #'min lengths) 0)))
-        ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
-        (unless (listp (car value)) (setq value (list value)))
-        (let ((file (orgtbl-to-csv value '(:fmt org-babel-julia-quote-csv-field))))
-          (if (= max min)
-              (format "%s = begin
-    using CSV
-    CSV.read(\"%s\")
-end" name file)
-            (format "%s = begin
-    using CSV
-    CSV.read(\"%s\")
-end"
-                    name file))))
-    (format "%s = %s" name (org-babel-julia-quote-csv-field value))))
-
-(defvar ess-ask-for-ess-directory) ; dynamically scoped
-(defun org-babel-julia-initiate-session (session params)
-  "If there is not a current julia process then create one."
-  (unless (string= session "none")
-    (let ((session (or session "*Julia*"))
-	  (ess-ask-for-ess-directory
-	   (and (bound-and-true-p ess-ask-for-ess-directory)
-                (not (cdr (assq :dir params))))))
-      (if (org-babel-comint-buffer-livep session)
-	  session
-	;; FIXME: Depending on `display-buffer-alist', (julia) may end up
-        ;; popping up a new frame which `save-window-excursion' won't be able
-        ;; to "undo", so we really should call a kind of
-        ;; `julia-no-select' instead so we don't need to undo any
-        ;; window-changes afterwards.
-	(save-window-excursion
-	  (when (get-buffer session)
-	    ;; Session buffer exists, but with dead process
-	    (set-buffer session))
-          (require 'ess) (set-buffer (julia))
-	  (rename-buffer
-	   (if (bufferp session)
-	       (buffer-name session)
-	     (if (stringp session)
-		 session
-	       (buffer-name))))
-	  (current-buffer))))))
-
-(defun org-babel-julia-graphical-output-file (params)
-  "Name of file to which julia should send graphical output."
-  (and (member "graphics" (cdr (assq :result-params params)))
-       (cdr (assq :file params))))
-
-(defconst org-babel-julia-eoe-indicator "print(\"org_babel_julia_eoe\")")
-(defconst org-babel-julia-eoe-output "org_babel_julia_eoe")
-
-(defconst org-babel-julia-write-object-command "begin
-    local p_ans = %s
-    local p_tmp_file = \"%s\"
-
-    try
-        using CSV, DataFrames
-
-        if typeof(p_ans) <: DataFrame
-           p_ans_df = p_ans
-        else
-            p_ans_df = DataFrame(:ans => p_ans)
-        end
-
-        CSV.write(p_tmp_file,
-                  p_ans_df,
-                  writeheader = %s,
-                  transform = (col, val) -> something(val, missing),
-                  missingstring = \"nil\",
-                  quotestrings = false)
-        p_ans
-    catch e
-        err_msg = \"Source block evaluation failed. $e\"
-        CSV.write(p_tmp_file,
-                  DataFrame(:ans => err_msg),
-                  writeheader = false,
-                  transform = (col, val) -> something(val, missing),
-                  missingstring = \"nil\",
-                  quotestrings = false)
-
-        err_msg
-    end
-end")
-
-(defun org-babel-julia-evaluate
-    (session body result-type result-params column-names-p)
-  "Evaluate julia code in BODY."
-  (if session
-      (org-babel-julia-evaluate-session
-       session body result-type result-params column-names-p)
-    (org-babel-julia-evaluate-external-process
-     body result-type result-params column-names-p)))
-
-(defun org-babel-julia-evaluate-external-process
-    (body result-type result-params column-names-p)
-  "Evaluate BODY in external julia 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."
-  (cl-case result-type
-    (value
-     (let ((tmp-file (org-babel-temp-file "julia-")))
-       (org-babel-eval org-babel-julia-command
-		       (format org-babel-julia-write-object-command
-			       (format "begin %s end" body)
-			       (org-babel-process-file-name tmp-file 'noquote)
-                               (if column-names-p "true" "false")
-                               ))
-       (org-babel-julia-process-value-result
-	(org-babel-result-cond result-params
-	  (with-temp-buffer
-	    (insert-file-contents tmp-file)
-	    (buffer-string))
-	  (org-babel-import-elisp-from-file tmp-file '(4)))
-	column-names-p)))
-    (output (org-babel-eval org-babel-julia-command body))))
-
-(defun org-babel-julia-evaluate-session
-    (session body result-type result-params column-names-p)
-  "Evaluate BODY 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."
-  (cl-case result-type
-    (value
-     (with-temp-buffer
-       (insert (org-babel-chomp body))
-       (let ((ess-local-process-name
-	      (process-name (get-buffer-process session)))
-	     (ess-eval-visibly-p nil))
-	 (ess-eval-buffer nil)))
-     (let ((tmp-file (org-babel-temp-file "julia-")))
-       (org-babel-comint-eval-invisibly-and-wait-for-file
-	session tmp-file
-	(format org-babel-julia-write-object-command
-                "ans"
-		(org-babel-process-file-name tmp-file 'noquote)
-                (if column-names-p "true" "false")
-                ))
-       (org-babel-julia-process-value-result
-	(org-babel-result-cond result-params
-	  (with-temp-buffer
-	    (insert-file-contents tmp-file)
-	    (buffer-string))
-	  (org-babel-import-elisp-from-file tmp-file '(4)))
-	column-names-p)))
-    (output
-     (mapconcat
-      #'org-babel-chomp
-      (butlast
-       (delq nil
-	     (mapcar
-	      (lambda (line) (when (> (length line) 0) line))
-	      (mapcar
-	       (lambda (line) ;; cleanup extra prompts left in output
-		 (if (string-match
-		      "^\\([>+.]\\([ ][>.+]\\)*[ ]\\)"
-		      (car (split-string line "\n")))
-		     (substring line (match-end 1))
-		   line))
-	       (org-babel-comint-with-output (session org-babel-julia-eoe-output)
-		 (insert (mapconcat #'org-babel-chomp
-				    (list body org-babel-julia-eoe-indicator)
-				    "\n"))
-                 (inferior-ess-send-input))))))
-      "\n"))))
-
-(defun org-babel-julia-process-value-result (result column-names-p)
-  "Julia-specific processing of return value.
-Insert hline if column names in output have been requested."
-  (if column-names-p
-      (cons (car result) (cons 'hline (cdr result)))
-    result))
-
-(provide 'ob-julia)
-
-;;; ob-julia.el ends here