~bzg/org-contrib

f5edcb4de2c8a19f9a6c56fe93d219bbe87f96d5 — Bastien Guerry 2 months ago cdc1962
Move ob-stan.el here from Org's core
3 files changed, 128 insertions(+), 40 deletions(-)

M README.md
M README.org
A lisp/ob-stan.el
M README.md => README.md +21 -20
@@ 34,22 34,22 @@ later version.  See [COPYING](COPYING).
These files are maintained in a separate repository, which you can
find after the "Homepage:" keyword in the files themselves:

-   **ob-arduino.el:** Org-mode Babel support for Arduino
-   **ob-clojure-literate.el:** Clojure's Org-mode Literate Programming
-   **ob-mathematica.el:** org-babel functions for Mathematica evaluation
-   **org-link-edit.el:** Slurp and barf with Org links
-   **ol-notmuch.el:** Links to notmuch messages
-   **org-notify.el:** Notifications for Org-mode
-   **org-mac-link.el:** Insert org-mode links to items selected in various Mac apps
-   **org-passwords.el:** org derived mode for managing passwords
-   **ob-php.el:** Execute PHP within org-mode blocks
-   **ob-redis.el:** Execute Redis queries within org-mode blocks
-   **ob-arduino.el:** Org-mode Babel support for Arduino
-   **ob-spice.el:** org-babel functions for spice evaluation
-   **ob-sclang.el:** SCLang support for Org-mode Babel
-   **ob-smiles.el:** Org-mode Babel support for SMILES
-   **ob-clojure-literate.el:** Clojure's Org-mode Literate Programming
-   **ox-rss.el:** RSS 2.0 Back-End for Org Export Engine
-   **ob-spice.el:** org-babel functions for spice evaluation
-   **ol-notmuch.el:** Links to notmuch messages
-   **org-attach-embedded-images.el:** Transmute images to attachments
-   **org-link-edit.el:** Slurp and barf with Org links
-   **org-mac-link.el:** Insert org-mode links to items selected in various Mac apps
-   **org-notify.el:** Notifications for Org-mode
-   **org-passwords.el:** org derived mode for managing passwords
-   **org-velocity.el:** something like Notational Velocity for Org
-   **ox-rss.el:** RSS 2.0 Back-End for Org Export Engine


# Other files


@@ 68,8 68,8 @@ find after the "Homepage:" keyword in the files themselves:
-   **org-depend.el:** TODO dependencies for Org-mode
-   **org-effectiveness.el:** Measuring your personal effectiveness
-   **org-eldoc.el:** Eldoc documentation for SRC blocks
-   **org-eval-light.el:** Evaluate in-buffer code on demand
-   **org-eval.el:** The <lisp> tag, adapted from Muse
-   **org-eval-light.el:** Evaluate in-buffer code on demand
-   **org-expiry.el:** Expiry mechanism for Org entries
-   **org-git-link.el:** Provide org links to specific file version
-   **org-interactive-query.el:** Interactive modification of tags query


@@ 122,32 122,33 @@ find after the "Homepage:" keyword in the files themselves:

## Org Babel languages

-   **ob-J.el:** Org-mode Babel Functions for J
-   **ob-abc.el:** Org-mode Babel Functions for ABC
-   **ob-arduino.el:** Org-mode Babel Functions for Arduino
-   **ob-asymptote.el:** Org-mode Babel Functions for Asymptote
-   **ob-clojure-literate.el:** Clojure's Org-mode Literate Programming
-   **ob-coq.el:** Org-mode Babel Functions for Coq
-   **ob-csharp.el:** Org-mode Babel Functions for csharp evaluation
-   **ob-ebnf.el:** Org-mode Babel Functions for EBNF
-   **ob-eukleides.el:** Org-mode Babel Functions for eukleides evaluation
-   **ob-fomus.el:** Org-mode Babel Functions for fomus evaluation
-   **ob-hledger.el:** Org-mode Babel Functions for hledger
-   **ob-io.el:** Org-mode Babel Functions for Io
-   **ob-J.el:** Org-mode Babel Functions for J
-   **ob-ledger.el:** Org-mode Babel Functions for Ledger
-   **ob-mscgen.el:** Org-mode Babel Functions for Mscgen
-   **ob-picolisp.el:** Org-mode Babel Functions for Picolisp
-   **ob-shen.el:** Org-mode Babel Functions for Shen
-   **ob-vala.el:** Org-mode Babel Functions for Vala
-   **ob-arduino.el:** Org-mode Babel Functions for Arduino
-   **ob-clojure-literate.el:** Clojure's Org-mode Literate Programming
-   **ob-csharp.el:** Org-mode Babel Functions for csharp evaluation
-   **ob-eukleides.el:** Org-mode Babel Functions for eukleides evaluation
-   **ob-fomus.el:** Org-mode Babel Functions for fomus evaluation
-   **ob-mathematica.el:** Org-mode Babel Functions for Mathematica evaluation
-   **ob-mathomatic.el:** Org-mode Babel Functions for mathomatic evaluation
-   **ob-mscgen.el:** Org-mode Babel Functions for Mscgen
-   **ob-oz.el:** Org-mode Babel Functions for Oz evaluation
-   **ob-php.el:** Execute PHP within org-mode blocks
-   **ob-picolisp.el:** Org-mode Babel Functions for Picolisp
-   **ob-redis.el:** Execute Redis queries within org-mode blocks
-   **ob-sclang.el:** SCLang support for Org-mode Babel
-   **ob-shen.el:** Org-mode Babel Functions for Shen
-   **ob-smiles.el:** Org-mode Babel support for SMILES
-   **ob-spice.el:** Org-mode Babel Functions for spice evaluation
-   **ob-stan.el:** Babel Functions for Stan
-   **ob-stata.el:** Org-mode Babel Functions for Stata evaluation
-   **ob-tcl.el:** Org-mode Babel Functions for tcl evaluation
-   **ob-vala.el:** Org-mode Babel Functions for Vala
-   **ob-vbnet.el:** Org-mode Babel Functions for VB.Net evaluation


M README.org => README.org +21 -20
@@ 31,22 31,22 @@ later version.  See [[file:COPYING][COPYING]].
These files are maintained in a separate repository, which you can
find after the "Homepage:" keyword in the files themselves:

- ob-arduino.el :: Org-mode Babel support for Arduino
- ob-clojure-literate.el :: Clojure's Org-mode Literate Programming
- ob-mathematica.el :: org-babel functions for Mathematica evaluation
- org-link-edit.el :: Slurp and barf with Org links
- ol-notmuch.el :: Links to notmuch messages
- org-notify.el :: Notifications for Org-mode
- org-mac-link.el :: Insert org-mode links to items selected in various Mac apps
- org-passwords.el :: org derived mode for managing passwords
- ob-php.el :: Execute PHP within org-mode blocks
- ob-redis.el :: Execute Redis queries within org-mode blocks
- ob-arduino.el :: Org-mode Babel support for Arduino
- ob-spice.el :: org-babel functions for spice evaluation
- ob-sclang.el :: SCLang support for Org-mode Babel
- ob-smiles.el :: Org-mode Babel support for SMILES
- ob-clojure-literate.el :: Clojure's Org-mode Literate Programming
- ox-rss.el :: RSS 2.0 Back-End for Org Export Engine
- ob-spice.el :: org-babel functions for spice evaluation
- ol-notmuch.el :: Links to notmuch messages
- org-attach-embedded-images.el :: Transmute images to attachments
- org-link-edit.el :: Slurp and barf with Org links
- org-mac-link.el :: Insert org-mode links to items selected in various Mac apps
- org-notify.el :: Notifications for Org-mode
- org-passwords.el :: org derived mode for managing passwords
- org-velocity.el :: something like Notational Velocity for Org
- ox-rss.el :: RSS 2.0 Back-End for Org Export Engine

** Other files
*** Org utils


@@ 62,8 62,8 @@ find after the "Homepage:" keyword in the files themselves:
- org-depend.el :: TODO dependencies for Org-mode
- org-effectiveness.el :: Measuring your personal effectiveness
- org-eldoc.el :: Eldoc documentation for SRC blocks
- org-eval-light.el :: Evaluate in-buffer code on demand
- org-eval.el :: The <lisp> tag, adapted from Muse
- org-eval-light.el :: Evaluate in-buffer code on demand
- org-expiry.el :: Expiry mechanism for Org entries
- org-git-link.el :: Provide org links to specific file version
- org-interactive-query.el :: Interactive modification of tags query


@@ 113,31 113,32 @@ find after the "Homepage:" keyword in the files themselves:

*** Org Babel languages

- ob-J.el :: Org-mode Babel Functions for J
- ob-abc.el :: Org-mode Babel Functions for ABC
- ob-arduino.el :: Org-mode Babel Functions for Arduino
- ob-asymptote.el :: Org-mode Babel Functions for Asymptote
- ob-clojure-literate.el :: Clojure's Org-mode Literate Programming
- ob-coq.el :: Org-mode Babel Functions for Coq
- ob-csharp.el :: Org-mode Babel Functions for csharp evaluation
- ob-ebnf.el :: Org-mode Babel Functions for EBNF
- ob-eukleides.el :: Org-mode Babel Functions for eukleides evaluation
- ob-fomus.el :: Org-mode Babel Functions for fomus evaluation
- ob-hledger.el :: Org-mode Babel Functions for hledger
- ob-io.el :: Org-mode Babel Functions for Io
- ob-J.el :: Org-mode Babel Functions for J
- ob-ledger.el :: Org-mode Babel Functions for Ledger
- ob-mscgen.el :: Org-mode Babel Functions for Mscgen
- ob-picolisp.el :: Org-mode Babel Functions for Picolisp
- ob-shen.el :: Org-mode Babel Functions for Shen
- ob-vala.el :: Org-mode Babel Functions for Vala
- ob-arduino.el :: Org-mode Babel Functions for Arduino
- ob-clojure-literate.el :: Clojure's Org-mode Literate Programming
- ob-csharp.el :: Org-mode Babel Functions for csharp evaluation
- ob-eukleides.el :: Org-mode Babel Functions for eukleides evaluation
- ob-fomus.el :: Org-mode Babel Functions for fomus evaluation
- ob-mathematica.el :: Org-mode Babel Functions for Mathematica evaluation
- ob-mathomatic.el :: Org-mode Babel Functions for mathomatic evaluation
- ob-mscgen.el :: Org-mode Babel Functions for Mscgen
- ob-oz.el :: Org-mode Babel Functions for Oz evaluation
- ob-php.el :: Execute PHP within org-mode blocks
- ob-picolisp.el :: Org-mode Babel Functions for Picolisp
- ob-redis.el :: Execute Redis queries within org-mode blocks
- ob-sclang.el :: SCLang support for Org-mode Babel
- ob-shen.el :: Org-mode Babel Functions for Shen
- ob-smiles.el :: Org-mode Babel support for SMILES
- ob-spice.el :: Org-mode Babel Functions for spice evaluation
- ob-stan.el :: Babel Functions for Stan
- ob-stata.el :: Org-mode Babel Functions for Stata evaluation
- ob-tcl.el :: Org-mode Babel Functions for tcl evaluation
- ob-vala.el :: Org-mode Babel Functions for Vala
- ob-vbnet.el :: Org-mode Babel Functions for VB.Net evaluation

A lisp/ob-stan.el => lisp/ob-stan.el +86 -0
@@ 0,0 1,86 @@
;;; ob-stan.el --- Babel Functions for Stan          -*- lexical-binding: t; -*-

;; Copyright (C) 2015-2021 Free Software Foundation, Inc.

;; Author: Kyle Meyer
;; Keywords: literate programming, reproducible research
;; Homepage: https://git.kyleam.com/ob-stan

;; This file is not 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 <https://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
;; https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-stan.html
;;
;; [1] https://mc-stan.org/

;;; Code:
(require 'ob)
(require 'org-compat)

(defcustom org-babel-stan-cmdstan-directory nil
  "CmdStan source directory.
Call \"make\" from this directory to compile the Stan block.
When nil, executing Stan blocks dumps the content to a file."
  :group 'org-babel
  :type '(choice
	  (directory :tag "Compilation directory")
	  (const :tag "Dump to a file" nil)))

(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