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Add Babel support for Stan

* lisp/ob-stan.el: New file.
* lisp/org.el (org-babel-load-languages): Add Stan.
Kyle Meyer 4 years ago
parent
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7ab1874a93
2 changed files with 85 additions and 0 deletions
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      lisp/ob-stan.el
  2. 1 0
      lisp/org.el

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lisp/ob-stan.el

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+;;; ob-stan.el --- org-babel functions for Stan
+
+;; Copyright (C) 2015 Free Software Foundation, Inc.
+
+;; Author: Kyle Meyer
+;; Keywords: literate programming, reproducible research
+;; Homepage: http://orgmode.org
+
+;; 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 <http://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;; Org-Babel support for evaluating Stan [1] source code.
+;;
+;; Evaluating a Stan block can produce two different results.
+;;
+;; 1) Dump the source code contents to a file.
+;;
+;;    This file can then be used as a variable in other blocks, which
+;;    allows interfaces like RStan to use the model.
+;;
+;; 2) Compile the contents to a model file.
+;;
+;;    This provides access to the CmdStan interface.  To use this, set
+;;    `org-babel-stan-cmdstan-directory' and provide a :file argument
+;;    that does not end in ".stan".
+;;
+;; For more information and usage examples, visit
+;; http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-stan.html
+;;
+;; [1] http://mc-stan.org/
+
+;;; Code:
+(require 'ob)
+(require 'org-compat)
+
+(defcustom org-babel-stan-cmdstan-directory nil
+  "CmdStan source directory.
+'make' will be called from this directory to compile the Stan
+block.  When nil, executing Stan blocks dumps the content to a
+plain text file."
+  :group 'org-babel
+  :type 'string)
+
+(defvar org-babel-default-header-args:stan
+  '((:results . "file")))
+
+(defun org-babel-execute:stan (body params)
+  "Generate Stan file from BODY according to PARAMS.
+A :file header argument must be given.  If
+`org-babel-stan-cmdstan-directory' is non-nil and the file name
+does not have a \".stan\" extension, save an intermediate
+\".stan\" file and compile the block to the named file.
+Otherwise, write the Stan code directly to the named file."
+  (let ((file (expand-file-name
+	       (or (cdr (assq :file params))
+		   (user-error "Set :file argument to execute Stan blocks")))))
+    (if (or (not org-babel-stan-cmdstan-directory)
+	    (org-string-match-p "\\.stan\\'" file))
+	(with-temp-file file (insert body))
+      (with-temp-file (concat file ".stan") (insert body))
+      (let ((default-directory org-babel-stan-cmdstan-directory))
+	(call-process-shell-command (concat "make " file))))
+    nil))		; Signal that output has been written to file.
+
+(defun org-babel-prep-session:stan (session params)
+  "Return an error because Stan does not support sessions."
+  (user-error "Stan does not support sessions"))
+
+(provide 'ob-stan)
+;;; ob-stan.el ends here

+ 1 - 0
lisp/org.el

@@ -300,6 +300,7 @@ requirements) is loaded."
 		 (const :tag "Shen" shen)
 		 (const :tag "Sql" sql)
 		 (const :tag "Sqlite" sqlite)
+		 (const :tag "Stan" stan)
 		 (const :tag "ebnf2ps" ebnf2ps))
 		:value-type (boolean :tag "Activate" :value t)))