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authorSebastien Delafond <seb@debian.org>2013-08-11 16:27:56 +0200
committerS├ębastien Delafond <sdelafond@gmail.com>2014-07-13 13:35:27 +0200
commit53b246b7d66bfa03ab9bcf47d4647913b401e3d6 (patch)
treeb5ea4e732c2219456d13048feb05b37b22a76391 /contrib/lisp/ob-julia.el
parent8606e2621fc00fd8b334a06924aeef3aab7a2e4d (diff)
parente32a45ed36d6000db4b39171149072d11b77af72 (diff)
Imported Debian patch 8.0.7-1
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+;;; ob-julia.el --- org-babel functions for julia code evaluation
+
+;; Copyright (C) 2013 G. Jay Kerns
+;; Author: G. Jay Kerns, based on ob-R.el by Eric Schulte and Dan Davison
+
+;; This file is not part of GNU Emacs.
+
+;; This program 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, or (at your option)
+;; any later version.
+;;
+;; This program 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; see the file COPYING. If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+
+;; The file provides Org-Babel support for evaluating julia code.
+;;
+;; See https://github.com/gjkerns/ob-julia/blob/master/ob-julia-doc.org
+;; for detailed instructions on how to get started. The git repository
+;; contains more documentation: git://github.com/gjkerns/ob-julia.git
+
+;;; Code:
+(require 'ob)
+(eval-when-compile (require 'cl))
+
+(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 org-number-sequence "org-compat" (from &optional to inc))
+(declare-function org-remove-if-not "org" (predicate seq))
+
+(defconst 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 inferior-julia-program-name
+ "Name of command to use for executing julia code."
+ :group 'org-babel
+ :version "24.4"
+ :package-version '(Org . "8.0")
+ :type 'string)
+
+(defvar ess-local-process-name) ; dynamically scoped
+(defun org-babel-edit-prep:julia (info)
+ (let ((session (cdr (assoc :session (nth 2 info)))))
+ (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
+ (save-match-data (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."
+ (let ((graphics-file
+ (or graphics-file (org-babel-julia-graphical-output-file params))))
+ (mapconcat
+ #'identity
+ ((lambda (inside)
+ (if graphics-file
+ inside
+ inside))
+ (append (org-babel-variable-assignments:julia params)
+ (list body))) "\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 (assoc :result-params params)))
+ (result-type (cdr (assoc :result-type params)))
+ (session (org-babel-julia-initiate-session
+ (cdr (assoc :session params)) params))
+ (colnames-p (cdr (assoc :colnames params)))
+ (rownames-p (cdr (assoc :rownames params)))
+ (graphics-file (org-babel-julia-graphical-output-file 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 (assoc :colname-names params)) colnames-p))
+ (or (equal "yes" rownames-p)
+ (org-babel-pick-name
+ (cdr (assoc :rowname-names params)) rownames-p)))))
+ (if graphics-file nil 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 (mapcar #'cdr (org-babel-get-header params :var))))
+ (mapcar
+ (lambda (pair)
+ (org-babel-julia-assign-elisp
+ (car pair) (cdr pair)
+ (equal "yes" (cdr (assoc :colnames params)))
+ (equal "yes" (cdr (assoc :rownames params)))))
+ (mapcar
+ (lambda (i)
+ (cons (car (nth i vars))
+ (org-babel-reassemble-table
+ (cdr (nth i vars))
+ (cdr (nth i (cdr (assoc :colname-names params))))
+ (cdr (nth i (cdr (assoc :rowname-names params)))))))
+ (org-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 colnames-p rownames-p)
+ "Construct julia code assigning the elisp VALUE to a variable named NAME."
+ (if (listp value)
+ (let ((max (apply #'max (mapcar #'length (org-remove-if-not
+ #'sequencep value))))
+ (min (apply #'min (mapcar #'length (org-remove-if-not
+ #'sequencep value))))
+ (transition-file (org-babel-temp-file "julia-import-")))
+ ;; ensure VALUE has an orgtbl structure (depth of at least 2)
+ (unless (listp (car value)) (setq value (list value)))
+ (with-temp-file transition-file
+ (insert
+ (orgtbl-to-csv value '(:fmt org-babel-julia-quote-csv-field))
+ "\n"))
+ (let ((file (org-babel-process-file-name transition-file 'noquote))
+ (header (if (or (eq (nth 1 value) 'hline) colnames-p)
+ "TRUE" "FALSE"))
+ (row-names (if rownames-p "1" "NULL")))
+ (if (= max min)
+ (format "%s = readcsv(\"%s\")" name file)
+ (format "%s = readcsv(\"%s\")"
+ 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 (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
+ (not (cdr (assoc :dir params))))))
+ (if (org-babel-comint-buffer-livep session)
+ session
+ (save-window-excursion
+ (require 'ess) (julia)
+ (rename-buffer
+ (if (bufferp session)
+ (buffer-name session)
+ (if (stringp session)
+ session
+ (buffer-name))))
+ (current-buffer))))))
+
+(defun org-babel-julia-associate-session (session)
+ "Associate julia code buffer with a julia session.
+Make SESSION be the inferior ESS process associated with the
+current code buffer."
+ (setq ess-local-process-name
+ (process-name (get-buffer-process session)))
+ (ess-make-buffer-current))
+
+(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))))
+
+(defvar org-babel-julia-eoe-indicator "print(\"org_babel_julia_eoe\")")
+(defvar org-babel-julia-eoe-output "org_babel_julia_eoe")
+
+(defvar org-babel-julia-write-object-command "writecsv(\"%s\",%s)")
+
+;; The following was a very complicated write object command
+;; The replacement needs to add error catching
+;(defvar org-babel-julia-write-object-command "{function(object,transfer.file){object;invisible(if(inherits(try({tfile<-tempfile();write.table(object,file=tfile,sep=\"\\t\",na=\"nil\",row.names=%s,col.names=%s,quote=FALSE);file.rename(tfile,transfer.file)},silent=TRUE),\"try-error\")){if(!file.exists(transfer.file))file.create(transfer.file)})}}(object=%s,transfer.file=\"%s\")")
+
+(defun org-babel-julia-evaluate
+ (session body result-type result-params column-names-p row-names-p)
+ "Evaluate julia code in BODY."
+ (if session
+ (org-babel-julia-evaluate-session
+ session body result-type result-params column-names-p row-names-p)
+ (org-babel-julia-evaluate-external-process
+ body result-type result-params column-names-p row-names-p)))
+
+(defun org-babel-julia-evaluate-external-process
+ (body result-type result-params column-names-p row-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."
+ (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
+ (org-babel-process-file-name tmp-file 'noquote)
+ (format "begin\n%s\nend" body)))
+ (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 row-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."
+ (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
+ (org-babel-process-file-name tmp-file 'noquote) "ans"))
+ (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
+ "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
+ (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