lisp/ob-stan.el

   1 ;;; ob-stan.el --- Babel Functions for Stan          -*- lexical-binding: t; -*-
   2
   3 ;; Copyright (C) 2015-2016 Free Software Foundation, Inc.
   4
   5 ;; Author: Kyle Meyer
   6 ;; Keywords: literate programming, reproducible research
   7 ;; Homepage: http://orgmode.org
   8
   9 ;; This file is part of GNU Emacs.
  10
  11 ;; GNU Emacs is free software: you can redistribute it and/or modify
  12 ;; it under the terms of the GNU General Public License as published by
  13 ;; the Free Software Foundation, either version 3 of the License, or
  14 ;; (at your option) any later version.
  15
  16 ;; GNU Emacs is distributed in the hope that it will be useful,
  17 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
  18 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  19 ;; GNU General Public License for more details.
  20
  21 ;; You should have received a copy of the GNU General Public License
  22 ;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
  23
  24 ;;; Commentary:
  25
  26 ;; Org-Babel support for evaluating Stan [1] source code.
  27 ;;
  28 ;; Evaluating a Stan block can produce two different results.
  29 ;;
  30 ;; 1) Dump the source code contents to a file.
  31 ;;
  32 ;;    This file can then be used as a variable in other blocks, which
  33 ;;    allows interfaces like RStan to use the model.
  34 ;;
  35 ;; 2) Compile the contents to a model file.
  36 ;;
  37 ;;    This provides access to the CmdStan interface.  To use this, set
  38 ;;    `org-babel-stan-cmdstan-directory' and provide a :file argument
  39 ;;    that does not end in ".stan".
  40 ;;
  41 ;; For more information and usage examples, visit
  42 ;; http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-stan.html
  43 ;;
  44 ;; [1] http://mc-stan.org/
  45
  46 ;;; Code:
  47 (require 'ob)
  48 (require 'org-compat)
  49
  50 (defcustom org-babel-stan-cmdstan-directory nil
  51   "CmdStan source directory.
  52 'make' will be called from this directory to compile the Stan
  53 block.  When nil, executing Stan blocks dumps the content to a
  54 plain text file."
  55   :group 'org-babel
  56   :type 'string)
  57
  58 (defvar org-babel-default-header-args:stan
  59   '((:results . "file")))
  60
  61 (defun org-babel-execute:stan (body params)
  62   "Generate Stan file from BODY according to PARAMS.
  63 A :file header argument must be given.  If
  64 `org-babel-stan-cmdstan-directory' is non-nil and the file name
  65 does not have a \".stan\" extension, save an intermediate
  66 \".stan\" file and compile the block to the named file.
  67 Otherwise, write the Stan code directly to the named file."
  68   (let ((file (expand-file-name
  69                (or (cdr (assq :file params))
  70                    (user-error "Set :file argument to execute Stan blocks")))))
  71     (if (or (not org-babel-stan-cmdstan-directory)
  72             (org-string-match-p "\\.stan\\'" file))
  73         (with-temp-file file (insert body))
  74       (with-temp-file (concat file ".stan") (insert body))
  75       (let ((default-directory org-babel-stan-cmdstan-directory))
  76         (call-process-shell-command (concat "make " file))))
  77     nil))               ; Signal that output has been written to file.
  78
  79 (defun org-babel-prep-session:stan (_session _params)
  80   "Return an error because Stan does not support sessions."
  81   (user-error "Stan does not support sessions"))
  82
  83 (provide 'ob-stan)
  84 ;;; ob-stan.el ends here