From e32a45ed36d6000db4b39171149072d11b77af72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Delafond?= Date: Sun, 13 Jul 2014 13:35:27 +0200 Subject: Imported Upstream version 8.0.7 --- contrib/lisp/ob-julia.el | 302 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 302 insertions(+) create mode 100644 contrib/lisp/ob-julia.el (limited to 'contrib/lisp/ob-julia.el') diff --git a/contrib/lisp/ob-julia.el b/contrib/lisp/ob-julia.el new file mode 100644 index 0000000..3aed818 --- /dev/null +++ b/contrib/lisp/ob-julia.el @@ -0,0 +1,302 @@ +;;; 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 -- cgit v1.2.3