| commit | author | age | ||
| 76bbd0 | 1 | ;;; ob-stan.el --- Babel Functions for Stan -*- lexical-binding: t; -*- |
| C | 2 | |
| 3 | ;; Copyright (C) 2015-2018 Free Software Foundation, Inc. | |
| 4 | ||
| 5 | ;; Author: Kyle Meyer | |
| 6 | ;; Keywords: literate programming, reproducible research | |
| 7 | ;; Homepage: https://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 <https://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 | ;; https://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 | Call \"make\" from this directory to compile the Stan block. | |
| 53 | When nil, executing Stan blocks dumps the content to a file." | |
| 54 | :group 'org-babel | |
| 55 | :type '(choice | |
| 56 | (directory :tag "Compilation directory") | |
| 57 | (const :tag "Dump to a file" nil))) | |
| 58 | ||
| 59 | (defvar org-babel-default-header-args:stan | |
| 60 | '((:results . "file"))) | |
| 61 | ||
| 62 | (defun org-babel-execute:stan (body params) | |
| 63 | "Generate Stan file from BODY according to PARAMS. | |
| 64 | A :file header argument must be given. If | |
| 65 | `org-babel-stan-cmdstan-directory' is non-nil and the file name | |
| 66 | does not have a \".stan\" extension, save an intermediate | |
| 67 | \".stan\" file and compile the block to the named file. | |
| 68 | Otherwise, write the Stan code directly to the named file." | |
| 69 | (let ((file (expand-file-name | |
| 70 | (or (cdr (assq :file params)) | |
| 71 | (user-error "Set :file argument to execute Stan blocks"))))) | |
| 72 | (if (or (not org-babel-stan-cmdstan-directory) | |
| 73 | (string-match-p "\\.stan\\'" file)) | |
| 74 | (with-temp-file file (insert body)) | |
| 75 | (with-temp-file (concat file ".stan") (insert body)) | |
| 76 | (let ((default-directory org-babel-stan-cmdstan-directory)) | |
| 77 | (call-process-shell-command (concat "make " file)))) | |
| 78 | nil)) ; Signal that output has been written to file. | |
| 79 | ||
| 80 | (defun org-babel-prep-session:stan (_session _params) | |
| 81 | "Return an error because Stan does not support sessions." | |
| 82 | (user-error "Stan does not support sessions")) | |
| 83 | ||
| 84 | (provide 'ob-stan) | |
| 85 | ;;; ob-stan.el ends here | |
