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author | Kyle Meyer <kyle@kyleam.com> | 2015-09-02 01:34:15 -0400 |
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committer | Kyle Meyer <kyle@kyleam.com> | 2015-09-03 00:30:09 -0400 |
commit | 7ab1874a93a89f5b9c509a2f15bbe4381b25c73f (patch) | |
tree | 94d826ee5cf3179814a34b36fc70d4a63518bfb4 | |
parent | a2d0cd922e5b4367114feeefa8cef0d621914162 (diff) | |
download | org-mode-7ab1874a93a89f5b9c509a2f15bbe4381b25c73f.tar.gz |
Add Babel support for Stan
* lisp/ob-stan.el: New file.
* lisp/org.el (org-babel-load-languages): Add Stan.
-rw-r--r-- | lisp/ob-stan.el | 84 | ||||
-rwxr-xr-x | lisp/org.el | 1 |
2 files changed, 85 insertions, 0 deletions
diff --git a/lisp/ob-stan.el b/lisp/ob-stan.el new file mode 100644 index 0000000..7891600 --- /dev/null +++ b/lisp/ob-stan.el @@ -0,0 +1,84 @@ +;;; 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 diff --git a/lisp/org.el b/lisp/org.el index 82c42c2..6fddb69 100755 --- a/lisp/org.el +++ b/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))) |