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;;; ob-stan.el --- Babel Functions for Stan -*- lexical-binding: t; -*-
;; Copyright (C) 2015-2016 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)
(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
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