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Most of this change is to boilerplate commentary such as license URLs. This change was prompted by ftp://ftp.gnu.org's going-away party, planned for November. Change these FTP URLs to https://ftp.gnu.org instead. Make similar changes for URLs to other organizations moving away from FTP. Also, change HTTP to HTTPS for URLs to gnu.org and fsf.org when this works, as this will further help defend against man-in-the-middle attacks (for this part I omitted the MS-DOS and MS-Windows sources and the test tarballs to keep the workload down). HTTPS is not fully working to lists.gnu.org so I left those URLs alone for now.
85 lines
3.0 KiB
EmacsLisp
85 lines
3.0 KiB
EmacsLisp
;;; ob-stan.el --- Babel Functions for Stan -*- lexical-binding: t; -*-
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;; Copyright (C) 2015-2017 Free Software Foundation, Inc.
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;; Author: Kyle Meyer
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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;; This file is part of GNU Emacs.
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;; GNU Emacs 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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;; GNU Emacs 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 GNU Emacs. If not, see <https://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Org-Babel support for evaluating Stan [1] source code.
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;;
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;; Evaluating a Stan block can produce two different results.
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;;
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;; 1) Dump the source code contents to a file.
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;;
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;; This file can then be used as a variable in other blocks, which
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;; allows interfaces like RStan to use the model.
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;;
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;; 2) Compile the contents to a model file.
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;;
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;; This provides access to the CmdStan interface. To use this, set
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;; `org-babel-stan-cmdstan-directory' and provide a :file argument
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;; that does not end in ".stan".
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;;
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;; For more information and usage examples, visit
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;; http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-stan.html
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;;
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;; [1] http://mc-stan.org/
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;;; Code:
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(require 'ob)
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(require 'org-compat)
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(defcustom org-babel-stan-cmdstan-directory nil
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"CmdStan source directory.
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'make' will be called from this directory to compile the Stan
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block. When nil, executing Stan blocks dumps the content to a
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plain text file."
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:group 'org-babel
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:type 'string)
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(defvar org-babel-default-header-args:stan
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'((:results . "file")))
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(defun org-babel-execute:stan (body params)
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"Generate Stan file from BODY according to PARAMS.
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A :file header argument must be given. If
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`org-babel-stan-cmdstan-directory' is non-nil and the file name
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does not have a \".stan\" extension, save an intermediate
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\".stan\" file and compile the block to the named file.
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Otherwise, write the Stan code directly to the named file."
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(let ((file (expand-file-name
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(or (cdr (assq :file params))
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(user-error "Set :file argument to execute Stan blocks")))))
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(if (or (not org-babel-stan-cmdstan-directory)
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(string-match-p "\\.stan\\'" file))
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(with-temp-file file (insert body))
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(with-temp-file (concat file ".stan") (insert body))
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(let ((default-directory org-babel-stan-cmdstan-directory))
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(call-process-shell-command (concat "make " file))))
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nil)) ; Signal that output has been written to file.
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(defun org-babel-prep-session:stan (_session _params)
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"Return an error because Stan does not support sessions."
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(user-error "Stan does not support sessions"))
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(provide 'ob-stan)
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;;; ob-stan.el ends here
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