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+;;; ob-stan.el --- org-babel functions for Stan
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+
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+;; Copyright (C) 2015 Free Software Foundation, Inc.
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+
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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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+
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+;; This file is part of GNU Emacs.
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+
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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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+
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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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+
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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 <http://www.gnu.org/licenses/>.
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+
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+;;; Commentary:
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+
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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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+
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+;;; Code:
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+(require 'ob)
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+(require 'org-compat)
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+
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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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+
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+(defvar org-babel-default-header-args:stan
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+ '((:results . "file")))
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+
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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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+ (org-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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+
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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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+
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+(provide 'ob-stan)
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+;;; ob-stan.el ends here
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Kyle Meyer