forked from mirrors/org-mode
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
This commit is contained in:
Pedro Bruel
Bastien
parent
45a5f17add
commit
bf1c4c7575
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@ -0,0 +1,344 @@
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;;; ob-julia.el --- org-babel functions for julia code evaluation
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;; Copyright (C) 2013, 2014, 2021 G. Jay Kerns
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;; Authors: G. Jay Kerns, based on ob-R.el by Eric Schulte and Dan Davison
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;; Maintainer: Pedro Bruel <pedro.bruel@gmail.com>
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;; Keywords: literate programming, reproducible research, scientific computing
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;; Homepage: https://github.com/phrb/ob-julia
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;; This file is not part of GNU Emacs.
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with this program. If not, see <https://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Org-Babel support for evaluating julia code
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;;; Code:
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(require 'cl-lib)
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(require 'ob)
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(declare-function orgtbl-to-csv "org-table" (table params))
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(declare-function julia "ext:ess-julia" (&optional start-args))
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(declare-function inferior-ess-send-input "ext:ess-inf" ())
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(declare-function ess-make-buffer-current "ext:ess-inf" ())
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(declare-function ess-eval-buffer "ext:ess-inf" (vis))
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(declare-function ess-wait-for-process "ext:ess-inf"
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(&optional proc sec-prompt wait force-redisplay))
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(defvar org-babel-header-args:julia
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'((width . :any)
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(horizontal . :any)
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(results . ((file list vector table scalar verbatim)
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(raw org html latex code pp wrap)
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(replace silent append prepend)
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(output value graphics))))
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"julia-specific header arguments.")
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(add-to-list 'org-babel-tangle-lang-exts '("julia" . "jl"))
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(defvar org-babel-default-header-args:julia '())
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(defcustom org-babel-julia-command "julia"
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"Name of command to use for executing julia code."
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:version "24.3"
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:package-version '(Org . "8.0")
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:group 'org-babel
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:type 'string)
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(defvar ess-current-process-name) ; dynamically scoped
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(defvar ess-local-process-name) ; dynamically scoped
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(defun org-babel-edit-prep:julia (info)
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(let ((session (cdr (assq :session (nth 2 info)))))
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(when (and session
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(string-prefix-p "*" session)
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(string-suffix-p "*" session))
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(org-babel-julia-initiate-session session nil))))
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(defun org-babel-expand-body:julia (body params &optional _graphics-file)
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"Expand BODY according to PARAMS, return the expanded body."
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(mapconcat 'identity
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(append
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(when (cdr (assq :prologue params))
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(list (cdr (assq :prologue params))))
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(org-babel-variable-assignments:julia params)
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(list body)
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(when (cdr (assq :epilogue params))
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(list (cdr (assq :epilogue params)))))
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"\n"))
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(defun org-babel-execute:julia (body params)
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"Execute a block of julia code.
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This function is called by `org-babel-execute-src-block'."
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(save-excursion
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(let* ((result-params (cdr (assq :result-params params)))
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(result-type (cdr (assq :result-type params)))
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(session (org-babel-julia-initiate-session
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(cdr (assq :session params)) params))
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(graphics-file (and (member "graphics" (assq :result-params params))
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(org-babel-graphical-output-file params)))
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(colnames-p (unless graphics-file (cdr (assq :colnames params))))
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(rownames-p (unless graphics-file (cdr (assq :rownames params))))
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(full-body (org-babel-expand-body:julia body params graphics-file))
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(result
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(org-babel-julia-evaluate
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session full-body result-type result-params
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(or (equal "yes" colnames-p)
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(org-babel-pick-name
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(cdr (assq :colname-names params)) colnames-p))
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(or (equal "yes" rownames-p)
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(org-babel-pick-name
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(cdr (assq :rowname-names params)) rownames-p)))))
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(if graphics-file nil result))))
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(defun org-babel-normalize-newline (result)
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(replace-regexp-in-string
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"\\(\n\r?\\)\\{2,\\}"
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"\n"
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result))
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(defun org-babel-prep-session:julia (session params)
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"Prepare SESSION according to the header arguments specified in PARAMS."
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(let* ((session (org-babel-julia-initiate-session session params))
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(var-lines (org-babel-variable-assignments:julia params)))
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(org-babel-comint-in-buffer session
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(mapc (lambda (var)
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(end-of-line 1) (insert var) (comint-send-input nil t)
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(org-babel-comint-wait-for-output session)) var-lines))
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session))
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(defun org-babel-load-session:julia (session body params)
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"Load BODY into SESSION."
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(save-window-excursion
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(let ((buffer (org-babel-prep-session:julia session params)))
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(with-current-buffer buffer
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert (org-babel-chomp body)))
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buffer)))
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;; helper functions
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(defun org-babel-variable-assignments:julia (params)
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"Return list of julia statements assigning the block's variables."
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(let ((vars (org-babel--get-vars params)))
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(mapcar
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(lambda (pair)
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(org-babel-julia-assign-elisp
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(car pair) (cdr pair)
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(equal "yes" (cdr (assq :colnames params)))
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(equal "yes" (cdr (assq :rownames params)))))
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(mapcar
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(lambda (i)
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(cons (car (nth i vars))
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(org-babel-reassemble-table
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(cdr (nth i vars))
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(cdr (nth i (cdr (assq :colname-names params))))
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(cdr (nth i (cdr (assq :rowname-names params)))))))
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(number-sequence 0 (1- (length vars)))))))
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(defun org-babel-julia-quote-csv-field (s)
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"Quote field S for export to julia."
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(if (stringp s)
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(concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
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(format "%S" s)))
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(defun org-babel-julia-assign-elisp (name value colnames-p rownames-p)
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"Construct julia code assigning the elisp VALUE to a variable named NAME."
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(if (listp value)
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(let* ((lengths (mapcar 'length (cl-remove-if-not 'sequencep value)))
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(max (if lengths (apply 'max lengths) 0))
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(min (if lengths (apply 'min lengths) 0)))
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;; Ensure VALUE has an orgtbl structure (depth of at least 2).
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(unless (listp (car value)) (setq value (list value)))
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(let ((file (orgtbl-to-csv value '(:fmt org-babel-julia-quote-csv-field)))
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(header (if (or (eq (nth 1 value) 'hline) colnames-p)
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"TRUE" "FALSE"))
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(row-names (if rownames-p "1" "NULL")))
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(if (= max min)
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(format "%s = begin
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using CSV
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CSV.read(\"%s\")
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end" name file)
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(format "%s = begin
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using CSV
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CSV.read(\"%s\")
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end"
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name file))))
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(format "%s = %s" name (org-babel-julia-quote-csv-field value))))
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(defvar ess-ask-for-ess-directory) ; dynamically scoped
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(defun org-babel-julia-initiate-session (session params)
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"If there is not a current julia process then create one."
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(unless (string= session "none")
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(let ((session (or session "*Julia*"))
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(ess-ask-for-ess-directory
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(and (boundp 'ess-ask-for-ess-directory)
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ess-ask-for-ess-directory
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(not (cdr (assq :dir params))))))
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(if (org-babel-comint-buffer-livep session)
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session
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(save-window-excursion
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(when (get-buffer session)
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;; Session buffer exists, but with dead process
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(set-buffer session))
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(require 'ess) (set-buffer (julia))
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(rename-buffer
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(if (bufferp session)
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(buffer-name session)
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(if (stringp session)
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session
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(buffer-name))))
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(current-buffer))))))
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; (defun org-babel-julia-associate-session (session)
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; "Associate julia code buffer with a julia session.
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; Make SESSION be the inferior ESS process associated with the
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; current code buffer."
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; (setq ess-local-process-name
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; (process-name (get-buffer-process session)))
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; (ess-make-buffer-current))
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(defun org-babel-julia-graphical-output-file (params)
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"Name of file to which julia should send graphical output."
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(and (member "graphics" (cdr (assq :result-params params)))
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(cdr (assq :file params))))
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(defconst org-babel-julia-eoe-indicator "print(\"org_babel_julia_eoe\")")
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(defconst org-babel-julia-eoe-output "org_babel_julia_eoe")
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(defconst org-babel-julia-write-object-command "begin
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local p_ans = %s
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local p_tmp_file = \"%s\"
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try
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using CSV, DataFrames
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if typeof(p_ans) <: DataFrame
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p_ans_df = p_ans
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else
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p_ans_df = DataFrame(:ans => p_ans)
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end
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CSV.write(p_tmp_file,
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p_ans_df,
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writeheader = %s,
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transform = (col, val) -> something(val, missing),
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missingstring = \"nil\",
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quotestrings = false)
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p_ans
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catch e
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err_msg = \"Source block evaluation failed. $e\"
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CSV.write(p_tmp_file,
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DataFrame(:ans => err_msg),
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writeheader = false,
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transform = (col, val) -> something(val, missing),
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missingstring = \"nil\",
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quotestrings = false)
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err_msg
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end
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end")
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(defun org-babel-julia-evaluate
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(session body result-type result-params column-names-p row-names-p)
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"Evaluate julia code in BODY."
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(if session
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(org-babel-julia-evaluate-session
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session body result-type result-params column-names-p row-names-p)
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(org-babel-julia-evaluate-external-process
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body result-type result-params column-names-p row-names-p)))
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(defun org-babel-julia-evaluate-external-process
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(body result-type result-params column-names-p row-names-p)
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"Evaluate BODY in external julia process.
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If RESULT-TYPE equals 'output then return standard output as a
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string. If RESULT-TYPE equals 'value then return the value of the
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last statement in BODY, as elisp."
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(cl-case result-type
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(value
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(let ((tmp-file (org-babel-temp-file "julia-")))
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(org-babel-eval org-babel-julia-command
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(format org-babel-julia-write-object-command
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(format "begin %s end" body)
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(org-babel-process-file-name tmp-file 'noquote)
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(if column-names-p "true" "false")
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))
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(org-babel-julia-process-value-result
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(org-babel-result-cond result-params
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(with-temp-buffer
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(insert-file-contents tmp-file)
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(buffer-string))
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(org-babel-import-elisp-from-file tmp-file '(4)))
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column-names-p)))
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(output (org-babel-eval org-babel-julia-command body))))
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(defun org-babel-julia-evaluate-session
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(session body result-type result-params column-names-p row-names-p)
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"Evaluate BODY in SESSION.
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If RESULT-TYPE equals 'output then return standard output as a
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string. If RESULT-TYPE equals 'value then return the value of the
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last statement in BODY, as elisp."
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(cl-case result-type
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(value
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(with-temp-buffer
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(insert (org-babel-chomp body))
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(let ((ess-local-process-name
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(process-name (get-buffer-process session)))
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(ess-eval-visibly-p nil))
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(ess-eval-buffer nil)))
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(let ((tmp-file (org-babel-temp-file "julia-")))
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(org-babel-comint-eval-invisibly-and-wait-for-file
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session tmp-file
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(format org-babel-julia-write-object-command
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"ans"
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(org-babel-process-file-name tmp-file 'noquote)
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(if column-names-p "true" "false")
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))
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(org-babel-julia-process-value-result
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(org-babel-result-cond result-params
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(with-temp-buffer
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(insert-file-contents tmp-file)
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(buffer-string))
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(org-babel-import-elisp-from-file tmp-file '(4)))
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column-names-p)))
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(output
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(mapconcat
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'org-babel-chomp
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(butlast
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(delq nil
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(mapcar
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(lambda (line) (when (> (length line) 0) line))
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(mapcar
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(lambda (line) ;; cleanup extra prompts left in output
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(if (string-match
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"^\\([>+.]\\([ ][>.+]\\)*[ ]\\)"
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(car (split-string line "\n")))
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(substring line (match-end 1))
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line))
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(org-babel-comint-with-output (session org-babel-julia-eoe-output)
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(insert (mapconcat 'org-babel-chomp
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(list body org-babel-julia-eoe-indicator)
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"\n"))
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(inferior-ess-send-input)))))) "\n"))))
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(defun org-babel-julia-process-value-result (result column-names-p)
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"julia-specific processing of return value.
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Insert hline if column names in output have been requested."
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(if column-names-p
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(cons (car result) (cons 'hline (cdr result)))
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result))
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(provide 'ob-julia)
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;;; ob-julia.el ends here
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@ -0,0 +1,274 @@
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;;; test-ob-python.el --- tests for ob-python.el
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;; Copyright (c) 2011-2014, 2019, 2021 Eric Schulte
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;; Authors: Pedro Bruel, based on test-ob-python.el by Eric Schulte
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;; Maintainer: Pedro Bruel <pedro.bruel@gmail.com>
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;; This file is not part of GNU Emacs.
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with this program. If not, see <https://www.gnu.org/licenses/>.
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;;; Code:
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(org-test-for-executable "julia")
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(unless (featurep 'ob-julia)
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(signal 'missing-test-dependency "Support for julia code blocks"))
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(ert-deftest test-ob-julia/colnames-yes-header-argument ()
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(should
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(equal '(("col") hline ("a") ("b"))
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(org-test-with-temp-text "#+name: eg
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| col |
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|-----|
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| a |
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| b |
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#+header: :colnames yes
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#+header: :var x = eg
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<point>#+begin_src julia
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return x
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#+end_src"
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(org-babel-execute-src-block)))))
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(ert-deftest test-ob-julia/colnames-yes-header-argument-again ()
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(should
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(equal '(("a") hline ("b*") ("c*"))
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(org-test-with-temp-text "#+name: less-cols
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| a |
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|---|
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| b |
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| c |
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#+header: :colnames yes
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<point>#+begin_src julia :var tab=less-cols
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return [[val + '*' for val in row] for row in tab]
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#+end_src"
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(org-babel-execute-src-block)))))
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(ert-deftest test-ob-julia/colnames-nil-header-argument ()
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(should
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(equal '(("col") hline ("a") ("b"))
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(org-test-with-temp-text "#+name: eg
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| col |
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|-----|
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| a |
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| b |
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#+header: :colnames nil
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#+header: :var x = eg
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<point>#+begin_src julia
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return x
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#+end_src"
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(org-babel-execute-src-block)))))
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(ert-deftest test-ob-julia/colnames-no-header-argument-again ()
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(should
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(equal '(("a*") ("b*") ("c*"))
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(org-test-with-temp-text "#+name: less-cols
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| a |
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|---|
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| b |
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| c |
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#+header: :colnames no
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<point>#+begin_src julia :var tab=less-cols
|
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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
|
||||
<point>#+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
|
||||
;; >>> <insert_blank_line_here>
|
||||
;; >>> 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
|
||||
Loading…
Reference in New Issue