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Diffstat (limited to 'elpa/org-9.5.2/ob-julia.el')
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diff --git a/elpa/org-9.5.2/ob-julia.el b/elpa/org-9.5.2/ob-julia.el new file mode 100644 index 0000000..3176baf --- /dev/null +++ b/elpa/org-9.5.2/ob-julia.el @@ -0,0 +1,333 @@ +;;; 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 |