From c002f541cad175573b102720e3880ba98d05bf67 Mon Sep 17 00:00:00 2001 From: Pedro Bruel Date: Fri, 24 Sep 2021 16:31:40 -0300 Subject: [PATCH] Include support for evaluating julia code * lisp/ob-julia.el: included from org-contrib * testing/lisp/test-ob-julia.el: start adapting from testing/lisp/test-ob-python.el --- lisp/ob-julia.el | 344 ++++++++++++++++++++++++++++++++++ testing/lisp/test-ob-julia.el | 274 +++++++++++++++++++++++++++ 2 files changed, 618 insertions(+) create mode 100644 lisp/ob-julia.el create mode 100644 testing/lisp/test-ob-julia.el diff --git a/lisp/ob-julia.el b/lisp/ob-julia.el new file mode 100644 index 000000000..cbc58d665 --- /dev/null +++ b/lisp/ob-julia.el @@ -0,0 +1,344 @@ +;;; ob-julia.el --- org-babel functions for julia code evaluation + +;; Copyright (C) 2013, 2014, 2021 G. Jay Kerns +;; Authors: G. Jay Kerns, based on ob-R.el by Eric Schulte and Dan Davison +;; Maintainer: Pedro Bruel +;; Keywords: literate programming, reproducible research, scientific computing +;; Homepage: https://github.com/phrb/ob-julia + +;; 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 of the License, 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 this program. If not, see . + +;;; Commentary: + +;; Org-Babel support for evaluating julia code + +;;; 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 +(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)))) + (rownames-p (unless graphics-file (cdr (assq :rownames 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)) + (or (equal "yes" rownames-p) + (org-babel-pick-name + (cdr (assq :rowname-names params)) rownames-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) + (equal "yes" (cdr (assq :colnames params))) + (equal "yes" (cdr (assq :rownames params))))) + (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 colnames-p rownames-p) + "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))) + (header (if (or (eq (nth 1 value) 'hline) colnames-p) + "TRUE" "FALSE")) + (row-names (if rownames-p "1" "NULL"))) + (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 (boundp 'ess-ask-for-ess-directory) + ess-ask-for-ess-directory + (not (cdr (assq :dir params)))))) + (if (org-babel-comint-buffer-livep session) + session + (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-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)))) + +(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 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." + (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 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." + (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 diff --git a/testing/lisp/test-ob-julia.el b/testing/lisp/test-ob-julia.el new file mode 100644 index 000000000..f6d21726a --- /dev/null +++ b/testing/lisp/test-ob-julia.el @@ -0,0 +1,274 @@ +;;; test-ob-python.el --- tests for ob-python.el + +;; Copyright (c) 2011-2014, 2019, 2021 Eric Schulte +;; Authors: Pedro Bruel, based on test-ob-python.el by Eric Schulte +;; Maintainer: Pedro Bruel + +;; 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 of the License, 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 this program. If not, see . + +;;; Code: +(org-test-for-executable "julia") +(unless (featurep 'ob-julia) + (signal 'missing-test-dependency "Support for julia code blocks")) + +(ert-deftest test-ob-julia/colnames-yes-header-argument () + (should + (equal '(("col") hline ("a") ("b")) + (org-test-with-temp-text "#+name: eg +| col | +|-----| +| a | +| b | + +#+header: :colnames yes +#+header: :var x = eg +#+begin_src julia +return x +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/colnames-yes-header-argument-again () + (should + (equal '(("a") hline ("b*") ("c*")) + (org-test-with-temp-text "#+name: less-cols +| a | +|---| +| b | +| c | + +#+header: :colnames yes +#+begin_src julia :var tab=less-cols + return [[val + '*' for val in row] for row in tab] +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/colnames-nil-header-argument () + (should + (equal '(("col") hline ("a") ("b")) + (org-test-with-temp-text "#+name: eg +| col | +|-----| +| a | +| b | + +#+header: :colnames nil +#+header: :var x = eg +#+begin_src julia +return x +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/colnames-no-header-argument-again () + (should + (equal '(("a*") ("b*") ("c*")) + (org-test-with-temp-text "#+name: less-cols +| a | +|---| +| b | +| c | + +#+header: :colnames no +#+begin_src julia :var tab=less-cols + return [[val + '*' for val in row] for row in tab] +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/colnames-no-header-argument () + (should + (equal '(("col") ("a") ("b")) + (org-test-with-temp-text "#+name: eg +| col | +|-----| +| a | +| b | + +#+header: :colnames no +#+header: :var x = eg +#+begin_src julia +return x +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/session-multiline () + (should + (equal "20" + (org-test-with-temp-text "#+begin_src julia :session :results output + foo = 0 + for _ in range(10): + foo += 1 + + foo += 1 + + print(foo) +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/insert-necessary-blank-line-when-sending-code-to-interpreter () + (should + (equal 2 (org-test-with-temp-text "#+begin_src julia :session :results value +if True: + 1 +2 +#+end_src" + ;; Previously, while adding `:session' to a normal code + ;; block, also need to add extra blank lines to end + ;; indent block or indicate logical sections. Now, the + ;; `org-babel-julia-evaluate-session' can do it + ;; automatically: + ;; + ;; >>> if True: + ;; >>> 1 + ;; >>> + ;; >>> 2 + (org-babel-execute-maybe) + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/if-else-block () + (should + (equal "success" (org-test-with-temp-text "#+begin_src julia :session :results value +value = 'failure' +if False: + pass +else: + value = 'success' +value +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/indent-block-with-blank-lines () + (should + (equal 20 + (org-test-with-temp-text "#+begin_src julia :session :results value + foo = 0 + for i in range(10): + foo += 1 + + foo += 1 + + foo +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/assign-underscore () + (should + (equal "success" + (org-test-with-temp-text "#+begin_src julia :session :results value +_ = 'failure' +'success' +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/multiline-var () + (should + (equal "a\nb\nc" + (org-test-with-temp-text "#+begin_src julia :var text=\"a\\nb\\nc\" +return text +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/multiline-str () + (should + (equal "a\nb\nc" + (org-test-with-temp-text "#+begin_src julia +text=\"a\\nb\\nc\" +return text +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/header-var-assignment () + (should + (equal "success" + (org-test-with-temp-text "#+begin_src julia :var text=\"failure\" +text +text=\"success\" +return text +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/session-value-sleep () + (should + (equal "success" + (org-test-with-temp-text "#+begin_src julia :session :results value +import time +time.sleep(.1) +'success' +#+end_src" + (org-babel-execute-src-block))))) + +(ert-deftest test-ob-julia/async-simple-session-output () + (let ((org-babel-temporary-directory temporary-file-directory) + (org-confirm-babel-evaluate nil)) + (org-test-with-temp-text + "#+begin_src julia :session :async yes :results output +import time +time.sleep(.1) +print('Yep!') +#+end_src\n" + (should (let ((expected "Yep!")) + (and (not (string= expected (org-babel-execute-src-block))) + (string= expected + (progn + (sleep-for 0 200) + (goto-char (org-babel-where-is-src-block-result)) + (org-babel-read-result))))))))) + +(ert-deftest test-ob-julia/async-named-output () + (let (org-confirm-babel-evaluate + (org-babel-temporary-directory temporary-file-directory) + (src-block "#+begin_src julia :async :session :results output +print(\"Yep!\") +#+end_src") + (results-before " + +#+NAME: foobar +#+RESULTS: +: Nope!") + (results-after " + +#+NAME: foobar +#+RESULTS: +: Yep! +")) + (org-test-with-temp-text + (concat src-block results-before) + (should (progn (org-babel-execute-src-block) + (sleep-for 0 200) + (string= (concat src-block results-after) + (buffer-string))))))) + +(ert-deftest test-ob-julia/async-output-drawer () + (let (org-confirm-babel-evaluate + (org-babel-temporary-directory temporary-file-directory) + (src-block "#+begin_src julia :async :session :results output drawer +print(list(range(3))) +#+end_src") + (result " + +#+RESULTS: +:results: +[0, 1, 2] +:end: +")) + (org-test-with-temp-text + src-block + (should (progn (org-babel-execute-src-block) + (sleep-for 0 200) + (string= (concat src-block result) + (buffer-string))))))) + +(provide 'test-ob-julia) + +;;; test-ob-julia.el ends here -- 2.33.0