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* lisp/ox.el (org-export-table-dimensions): * lisp/ox-texinfo.el (org-texinfo-template): * lisp/ox-md.el (org-md-link): * lisp/ox-icalendar.el (org-icalendar-use-UTC-date-time-p): * lisp/ox-ascii.el (org-ascii-fixed-width): * lisp/org.el (org-context): * lisp/org-table.el (org-table-eval-formula) (org-table-export): * lisp/org-refile.el: * lisp/org-plot.el (org-plot/gnuplot-to-grid-data): * lisp/org-num.el (org-num): * lisp/org-mouse.el (org-mouse-popup-global-menu) (org-mouse-context-menu): * lisp/org-macro.el (org-macro): * lisp/org-lint.el (org-lint): * lisp/org-keys.el (org-keys): * lisp/org-duration.el: * lisp/org-clock.el (org-clock-get-last-clock-out-time) (org-clock-update-mode-line, org-find-open-clocks): * lisp/org-agenda.el (org-diary) (org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item) (org-agenda-highlight-todo, org-cmp-alpha) (org-agenda-filter-by-category): * lisp/ol.el (org-link-expand-abbrev, ol): * lisp/ol-docview.el (ol-docview): * lisp/ol-bibtex.el (org-execute-file-search-in-bibtex) (org-bibtex, org-bibtex-read): * lisp/ol-bbdb.el (org-bbdb-anniversary-description): * lisp/ob-tangle.el (org-babel-tangle-jump-to-org): * lisp/ob-table.el (org-babel-table-truncate-at-newline): * lisp/ob-stan.el: * lisp/ob-sqlite.el (org-babel-sqlite-table-or-scalar): * lisp/ob-sql.el: * lisp/ob-shen.el: * lisp/ob-shell.el (org-babel-prep-session:shell) (org-babel-prep-session:shell): * lisp/ob-sed.el (org-babel-execute:sed) (org-babel-execute:sed): * lisp/ob-screen.el: * lisp/ob-sass.el: * lisp/ob-ruby.el (org-babel-prep-session:ruby) (org-babel-prep-session:ruby): * lisp/ob-ref.el (org-babel-ref-resolve, ob-ref): * lisp/ob-python.el (org-babel-prep-session:python) (org-babel-prep-session:python): * lisp/ob-plantuml.el: * lisp/ob-picolisp.el: * lisp/ob-perl.el: * lisp/ob-org.el: * lisp/ob-octave.el (org-babel-prep-session:octave) (org-babel-prep-session:octave) (org-babel-octave-evaluate-session): * lisp/ob-ocaml.el: * lisp/ob-mscgen.el (org-babel-execute:mscgen) (org-babel-execute:mscgen): * lisp/ob-maxima.el: (ob-maxima): * lisp/ob-matlab.el: * lisp/ob-makefile.el: * lisp/ob-lua.el (org-babel-prep-session:lua) (org-babel-prep-session:lua): * lisp/ob-lisp.el: * lisp/ob-ledger.el: * lisp/ob-latex.el (org-babel-expand-body:latex) (org-babel-expand-body:latex, ob-latex): * lisp/ob-js.el: * lisp/ob-java.el: * lisp/ob-io.el (org-babel-prep-session:io) (org-babel-prep-session:io): * lisp/ob-hledger.el: * lisp/ob-haskell.el: * lisp/ob-groovy.el (org-babel-groovy-wrapper-method) (org-babel-groovy-evaluate): * lisp/ob-gnuplot.el: * lisp/ob-fortran.el (org-babel-expand-body:fortran) (org-babel-expand-body:fortran): * lisp/ob-forth.el (org-babel-forth-session-execute): * lisp/ob-exp.el (ob-exp): * lisp/ob-eval.el: * lisp/ob-emacs-lisp.el: * lisp/ob-ebnf.el: * lisp/ob-dot.el: * lisp/ob-ditaa.el: * lisp/ob-css.el: * lisp/ob-core.el (org-babel-put-rownames): * lisp/ob-coq.el: * lisp/ob-comint.el: * lisp/ob-calc.el: * lisp/ob-awk.el: * lisp/ob-asymptote.el: * lisp/ob-abc.el: * lisp/ob-R.el (org-babel-prep-session:R): Formatting fixes.
87 lines
3.1 KiB
EmacsLisp
87 lines
3.1 KiB
EmacsLisp
;;; ob-stan.el --- Babel Functions for Stan -*- lexical-binding: t; -*-
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;; Copyright (C) 2015-2020 Free Software Foundation, Inc.
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;; Author: Kyle Meyer
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;; Keywords: literate programming, reproducible research
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;; Homepage: https://orgmode.org
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;; This file is part of GNU Emacs.
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;; GNU Emacs is free software: you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; GNU Emacs is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs. If not, see <https://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Org-Babel support for evaluating Stan [1] source code.
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;;
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;; Evaluating a Stan block can produce two different results.
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;;
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;; 1) Dump the source code contents to a file.
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;;
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;; This file can then be used as a variable in other blocks, which
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;; allows interfaces like RStan to use the model.
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;;
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;; 2) Compile the contents to a model file.
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;;
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;; This provides access to the CmdStan interface. To use this, set
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;; `org-babel-stan-cmdstan-directory' and provide a :file argument
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;; that does not end in ".stan".
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;;
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;; For more information and usage examples, visit
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;; https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-stan.html
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;;
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;; [1] http://mc-stan.org/
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;;; Code:
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(require 'ob)
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(require 'org-compat)
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(defcustom org-babel-stan-cmdstan-directory nil
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"CmdStan source directory.
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Call \"make\" from this directory to compile the Stan block.
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When nil, executing Stan blocks dumps the content to a file."
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:group 'org-babel
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:type '(choice
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(directory :tag "Compilation directory")
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(const :tag "Dump to a file" nil)))
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(defvar org-babel-default-header-args:stan
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'((:results . "file")))
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(defun org-babel-execute:stan (body params)
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"Generate Stan file from BODY according to PARAMS.
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A :file header argument must be given. If
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`org-babel-stan-cmdstan-directory' is non-nil and the file name
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does not have a \".stan\" extension, save an intermediate
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\".stan\" file and compile the block to the named file.
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Otherwise, write the Stan code directly to the named file."
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(let ((file (expand-file-name
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(or (cdr (assq :file params))
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(user-error "Set :file argument to execute Stan blocks")))))
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(if (or (not org-babel-stan-cmdstan-directory)
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(string-match-p "\\.stan\\'" file))
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(with-temp-file file (insert body))
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(with-temp-file (concat file ".stan") (insert body))
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(let ((default-directory org-babel-stan-cmdstan-directory))
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(call-process-shell-command (concat "make " file))))
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nil)) ; Signal that output has been written to file.
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(defun org-babel-prep-session:stan (_session _params)
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"Return an error because Stan does not support sessions."
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(user-error "Stan does not support sessions"))
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(provide 'ob-stan)
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;;; ob-stan.el ends here
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