1 ;;; ob-julia.el --- org-babel functions for julia code evaluation
3 ;; Copyright (C) 2013, 2014 G. Jay Kerns
4 ;; Author: G. Jay Kerns, based on ob-R.el by Eric Schulte and Dan Davison
6 ;; This file is not part of GNU Emacs.
8 ;; This program is free software; you can redistribute it and/or modify
9 ;; it under the terms of the GNU General Public License as published by
10 ;; the Free Software Foundation; either version 3, or (at your option)
13 ;; This program is distributed in the hope that it will be useful,
14 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
15 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 ;; GNU General Public License for more details.
18 ;; You should have received a copy of the GNU General Public License
19 ;; along with GNU Emacs; see the file COPYING. If not, write to the
20 ;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
21 ;; Boston, MA 02110-1301, USA.
25 ;; The file provides Org-Babel support for evaluating julia code.
27 ;; See https://github.com/gjkerns/ob-julia/blob/master/ob-julia-doc.org
28 ;; for detailed instructions on how to get started. The git repository
29 ;; contains more documentation: git://github.com/gjkerns/ob-julia.git
35 (declare-function orgtbl-to-csv
"org-table" (table params
))
36 (declare-function julia
"ext:ess-julia" (&optional start-args
))
37 (declare-function inferior-ess-send-input
"ext:ess-inf" ())
38 (declare-function ess-make-buffer-current
"ext:ess-inf" ())
39 (declare-function ess-eval-buffer
"ext:ess-inf" (vis))
40 (declare-function org-number-sequence
"org-compat" (from &optional to inc
))
42 (defconst org-babel-header-args
:julia
45 (results .
((file list vector table scalar verbatim
)
46 (raw org html latex code pp wrap
)
47 (replace silent append prepend
)
48 (output value graphics
))))
49 "julia-specific header arguments.")
51 (add-to-list 'org-babel-tangle-lang-exts
'("julia" .
"jl"))
53 (defvar org-babel-default-header-args
:julia
'())
55 (defcustom org-babel-julia-command inferior-julia-program-name
56 "Name of command to use for executing julia code."
59 :package-version
'(Org .
"8.0")
62 (defvar ess-local-process-name
) ; dynamically scoped
63 (defun org-babel-edit-prep:julia
(info)
64 (let ((session (cdr (assq :session
(nth 2 info
)))))
65 (when (and session
(string-match "^\\*\\(.+?\\)\\*$" session
))
66 (save-match-data (org-babel-julia-initiate-session session nil
)))))
68 (defun org-babel-expand-body:julia
(body params
&optional graphics-file
)
69 "Expand BODY according to PARAMS, return the expanded body."
71 (or graphics-file
(org-babel-julia-graphical-output-file params
))))
78 (append (org-babel-variable-assignments:julia params
)
81 (defun org-babel-execute:julia
(body params
)
82 "Execute a block of julia code.
83 This function is called by `org-babel-execute-src-block'."
85 (let* ((result-params (cdr (assq :result-params params
)))
86 (result-type (cdr (assq :result-type params
)))
87 (session (org-babel-julia-initiate-session
88 (cdr (assq :session params
)) params
))
89 (colnames-p (cdr (assq :colnames params
)))
90 (rownames-p (cdr (assq :rownames params
)))
91 (graphics-file (org-babel-julia-graphical-output-file params
))
92 (full-body (org-babel-expand-body:julia body params graphics-file
))
94 (org-babel-julia-evaluate
95 session full-body result-type result-params
96 (or (equal "yes" colnames-p
)
98 (cdr (assq :colname-names params
)) colnames-p
))
99 (or (equal "yes" rownames-p
)
101 (cdr (assq :rowname-names params
)) rownames-p
)))))
102 (if graphics-file nil result
))))
104 (defun org-babel-prep-session:julia
(session params
)
105 "Prepare SESSION according to the header arguments specified in PARAMS."
106 (let* ((session (org-babel-julia-initiate-session session params
))
107 (var-lines (org-babel-variable-assignments:julia params
)))
108 (org-babel-comint-in-buffer session
110 (end-of-line 1) (insert var
) (comint-send-input nil t
)
111 (org-babel-comint-wait-for-output session
)) var-lines
))
114 (defun org-babel-load-session:julia
(session body params
)
115 "Load BODY into SESSION."
116 (save-window-excursion
117 (let ((buffer (org-babel-prep-session:julia session params
)))
118 (with-current-buffer buffer
119 (goto-char (process-mark (get-buffer-process (current-buffer))))
120 (insert (org-babel-chomp body
)))
125 (defun org-babel-variable-assignments:julia
(params)
126 "Return list of julia statements assigning the block's variables."
127 (let ((vars (org-babel--get-vars params
)))
130 (org-babel-julia-assign-elisp
131 (car pair
) (cdr pair
)
132 (equal "yes" (cdr (assq :colnames params
)))
133 (equal "yes" (cdr (assq :rownames params
)))))
136 (cons (car (nth i vars
))
137 (org-babel-reassemble-table
139 (cdr (nth i
(cdr (assq :colname-names params
))))
140 (cdr (nth i
(cdr (assq :rowname-names params
)))))))
141 (org-number-sequence 0 (1- (length vars
)))))))
143 (defun org-babel-julia-quote-csv-field (s)
144 "Quote field S for export to julia."
146 (concat "\"" (mapconcat 'identity
(split-string s
"\"") "\"\"") "\"")
149 (defun org-babel-julia-assign-elisp (name value colnames-p rownames-p
)
150 "Construct julia code assigning the elisp VALUE to a variable named NAME."
152 (let ((max (apply #'max
(mapcar #'length
(cl-remove-if-not
153 #'sequencep value
))))
154 (min (apply #'min
(mapcar #'length
(cl-remove-if-not
155 #'sequencep value
))))
156 (transition-file (org-babel-temp-file "julia-import-")))
157 ;; ensure VALUE has an orgtbl structure (depth of at least 2)
158 (unless (listp (car value
)) (setq value
(list value
)))
159 (with-temp-file transition-file
161 (orgtbl-to-csv value
'(:fmt org-babel-julia-quote-csv-field
))
163 (let ((file (org-babel-process-file-name transition-file
'noquote
))
164 (header (if (or (eq (nth 1 value
) 'hline
) colnames-p
)
166 (row-names (if rownames-p
"1" "NULL")))
168 (format "%s = readcsv(\"%s\")" name file
)
169 (format "%s = readcsv(\"%s\")"
171 (format "%s = %s" name
(org-babel-julia-quote-csv-field value
))))
173 (defvar ess-ask-for-ess-directory
) ; dynamically scoped
175 (defun org-babel-julia-initiate-session (session params
)
176 "If there is not a current julia process then create one."
177 (unless (string= session
"none")
178 (let ((session (or session
"*julia*"))
179 (ess-ask-for-ess-directory
180 (and (and (boundp 'ess-ask-for-ess-directory
) ess-ask-for-ess-directory
)
181 (not (cdr (assq :dir params
))))))
182 (if (org-babel-comint-buffer-livep session
)
184 (save-window-excursion
185 (require 'ess
) (julia)
187 (if (bufferp session
)
188 (buffer-name session
)
189 (if (stringp session
)
192 (current-buffer))))))
194 (defun org-babel-julia-associate-session (session)
195 "Associate julia code buffer with a julia session.
196 Make SESSION be the inferior ESS process associated with the
197 current code buffer."
198 (setq ess-local-process-name
199 (process-name (get-buffer-process session
)))
200 (ess-make-buffer-current))
202 (defun org-babel-julia-graphical-output-file (params)
203 "Name of file to which julia should send graphical output."
204 (and (member "graphics" (cdr (assq :result-params params
)))
205 (cdr (assq :file params
))))
207 (defvar org-babel-julia-eoe-indicator
"print(\"org_babel_julia_eoe\")")
208 (defvar org-babel-julia-eoe-output
"org_babel_julia_eoe")
210 (defvar org-babel-julia-write-object-command
"writecsv(\"%s\",%s)")
212 ;; The following was a very complicated write object command
213 ;; The replacement needs to add error catching
214 ;(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\")")
216 (defun org-babel-julia-evaluate
217 (session body result-type result-params column-names-p row-names-p
)
218 "Evaluate julia code in BODY."
220 (org-babel-julia-evaluate-session
221 session body result-type result-params column-names-p row-names-p
)
222 (org-babel-julia-evaluate-external-process
223 body result-type result-params column-names-p row-names-p
)))
225 (defun org-babel-julia-evaluate-external-process
226 (body result-type result-params column-names-p row-names-p
)
227 "Evaluate BODY in external julia process.
228 If RESULT-TYPE equals 'output then return standard output as a
229 string. If RESULT-TYPE equals 'value then return the value of the
230 last statement in BODY, as elisp."
233 (let ((tmp-file (org-babel-temp-file "julia-")))
234 (org-babel-eval org-babel-julia-command
235 (format org-babel-julia-write-object-command
236 (org-babel-process-file-name tmp-file
'noquote
)
237 (format "begin\n%s\nend" body
)))
238 (org-babel-julia-process-value-result
239 (org-babel-result-cond result-params
241 (insert-file-contents tmp-file
)
243 (org-babel-import-elisp-from-file tmp-file
'(4)))
245 (output (org-babel-eval org-babel-julia-command body
))))
247 (defun org-babel-julia-evaluate-session
248 (session body result-type result-params column-names-p row-names-p
)
249 "Evaluate BODY in SESSION.
250 If RESULT-TYPE equals 'output then return standard output as a
251 string. If RESULT-TYPE equals 'value then return the value of the
252 last statement in BODY, as elisp."
256 (insert (org-babel-chomp body
))
257 (let ((ess-local-process-name
258 (process-name (get-buffer-process session
)))
259 (ess-eval-visibly-p nil
))
260 (ess-eval-buffer nil
)))
261 (let ((tmp-file (org-babel-temp-file "julia-")))
262 (org-babel-comint-eval-invisibly-and-wait-for-file
264 (format org-babel-julia-write-object-command
265 (org-babel-process-file-name tmp-file
'noquote
) "ans"))
266 (org-babel-julia-process-value-result
267 (org-babel-result-cond result-params
269 (insert-file-contents tmp-file
)
271 (org-babel-import-elisp-from-file tmp-file
'(4)))
279 (lambda (line) (when (> (length line
) 0) line
))
281 (lambda (line) ;; cleanup extra prompts left in output
283 "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line
)
284 (substring line
(match-end 1))
286 (org-babel-comint-with-output (session org-babel-julia-eoe-output
)
287 (insert (mapconcat #'org-babel-chomp
288 (list body org-babel-julia-eoe-indicator
)
290 (inferior-ess-send-input)))))) "\n"))))
292 (defun org-babel-julia-process-value-result (result column-names-p
)
293 "julia-specific processing of return value.
294 Insert hline if column names in output have been requested."
296 (cons (car result
) (cons 'hline
(cdr result
)))
301 ;;; ob-julia.el ends here