org-mode/lisp/ob-julia.el

;;; ob-julia.el --- org-babel functions for julia code evaluation  -*- lexical-binding: t; -*-

;; Copyright (C) 2013-2022 Free Software Foundation, Inc.
;; Authors: G. Jay Kerns
;; Maintainer: Pedro Bruel <pedro.bruel@gmail.com>
;; Keywords: literate programming, reproducible research, scientific computing
;; URL: 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.
;;
;; Session support requires the installation of the DataFrames and CSV
;; Julia packages.

;;; 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
(defvar ess-local-customize-alist); 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-customize-alist t)
             (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