forked from mirrors/org-mode
moving generalized comint functions to new file org-babel-comint.el
This commit is contained in:
Eric Schulte
parent
a54c27ec91
commit
c5a58ad6aa
93
lisp/org-babel-comint.el
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93
lisp/org-babel-comint.el
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;;; org-babel-comint.el --- org-babel functions for interaction with comint buffers
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;; Copyright (C) 2009 Eric Schulte
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;; Author: Eric Schulte
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;; Keywords: literate programming, reproducible research, comint
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;;; License:
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;; This program 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, or (at your option)
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;; any later version.
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;;
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;; This program 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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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;; This file should provide support for passing commands and results
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;; to and from `comint-mode' buffers.
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;;; Code:
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(require 'org-babel)
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(defun org-babel-comint-initiate-buffer (buffer ignite)
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"If BUFFER does not currently have a process use IGNITE to
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create one."
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(unless (and (buffer-live-p buffer) (get-buffer buffer))
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(save-excursion
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(eval ignite)
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(setf buffer (current-buffer))
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(org-babel-comint-wait-for-output)
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(org-babel-comint-input-command ""))))
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(defun org-babel-comint-command-to-string (buffer command)
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"Send COMMEND to BUFFER's process, and return the results as a string."
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(org-babel-comint-input-command buffer command)
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(org-babel-comint-last-output buffer))
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(defun org-babel-comint-input-command (buffer command)
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"Pass COMMAND to the process running in BUFFER."
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(save-excursion
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(save-match-data
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(set-buffer buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert command)
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(comint-send-input)
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(org-babel-comint-wait-for-output))))
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(defun org-babel-comint-wait-for-output (buffer)
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"Wait until output arrives"
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(save-excursion
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(save-match-data
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(set-buffer buffer)
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(while (progn
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(goto-char comint-last-input-end)
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(not (re-search-forward comint-prompt-regexp nil t)))
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(accept-process-output (get-buffer-process (current-buffer)))))))
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(defun org-babel-comint-last-output (buffer)
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"Return BUFFER's the last output as a string"
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(save-excursion
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(save-match-data
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(set-buffer buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(forward-line 0)
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(let ((raw (buffer-substring comint-last-input-end (- (point) 1)))
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output output-flag)
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(mapconcat
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(lambda (el)
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(if (stringp el)
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(format "%s" el)
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(format "%S" el)))
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(delq nil
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(mapcar
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(lambda (line)
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(unless (string-match "^>" line)
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(and (string-match "\\[[[:digit:]]+\\] *\\(.*\\)$" line)
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(match-string 1 line))))
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;; drop first, because it's the last line of input
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(cdr (split-string raw "[\n\r]")))) "\n")))))
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;;; org-babel-comint.el ends here
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149
org-babel.org
149
org-babel.org
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@ -115,6 +115,84 @@ and the results to be collected in the same table.
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* Tasks [20/32]
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* Tasks [20/32]
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** TODO Create objects in top level (global) environment in R?
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*** initial requirement statement [DED]
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At the moment, objects created by computations performed in the
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code block are evaluated in the scope of the
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code-block-function-body and therefore disappear when the code
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block is evaluated {unless you employ some extra trickery like
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assign('name', object, env=globalenv()) }. I think it will be
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desirable to also allow for a style wherein objects that are
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created in one code block persist in the R global environment and
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can be re-used in a separate block.
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This is what Sweave does, and while I'm not saying we have to be
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the same as Sweave, it wouldn't be hard for us to provide the same
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behaviour in this case; if we don't, we risk undeservedly being
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written off as an oddity by some.
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IOW one aspect of org-babel is that of a sort of functional
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meta-programming language. This is crazy, in a very good
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way. Nevertheless, wrt R I think there's going to be a lot of value
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in providing for a working style in which the objects are stored in
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the R session, rather than elisp/org buffer. This will be a very
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familiar working style to lots of people.
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There are no doubt a number of different ways of accomplishing
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this, the simplest being a hack like adding
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#+begin_src R
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for(objname in ls())
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assign(objname, get(objname), envir=globalenv())
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#+end_src
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to the source code block function body. (Maybe wrap it in an on.exit() call).
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However this may deserve to be thought about more carefully, perhaps
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with a view to having a uniform approach across languages. E.g. shell
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code blocks have the same semantics at the moment (no persistence of
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variables across code blocks), because the body is evaluated in a new
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bash shell process rather than a running shell. And I guess the same
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is true for python. However, in both these cases, you could imagine
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implementing the alternative in which the body is evaluated in a
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persistent interactive session. It's just that it's particularly
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natural for R, seeing as both ESS and org-babel evaluate commands in a
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single persistent R session.
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*** sessions [Eric]
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Thanks for bringing this up. I think you are absolutely correct that we
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should provide support for a persistent environment (maybe called a
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*session*) in which to evaluate code blocks. I think the current setup
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demonstrates my personal bias for a functional style of programming
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which is certainly not ideal in all contexts.
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While the R function you mention does look like an elegant solution, I
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think we should choose an implementation that would be the same across
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all source code types. Specifically I think we should allow the user to
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specify an optional *session* as a header variable (when not present we
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assume a default session for each language). The session name could be
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used to name a comint buffer (like the *R* buffer) in which all
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evaluation would take place (within which variables would retain their
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values --at least once I remove some of the functional method wrappings
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currently in place-- ).
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This would allow multiple environments to be used in the same buffer,
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and once this setup was implemented we should be able to fairly easily
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implement commands for jumping between source code blocks and the
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related session buffers, as well as for dumping the last N commands from
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a session into a new or existing source code block.
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Please let me know if you foresee any problems with this proposed setup,
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or if you think any parts might be confusing for people coming from
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Sweave. I'll hopefully find some time to work on this later in the
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week.
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*** implementation
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in [[file:lisp/org-babel-comint.el][org-babel-comint.el]]
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Currently I've coppied and begun generalizing the functions for
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interacting with R buffers.
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** TODO improve the source-block snippet
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** TODO improve the source-block snippet
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[[file:~/src/emacs-starter-kit/src/snippets/text-mode/rst-mode/chap::name%20Chapter%20title][file:~/src/emacs-starter-kit/src/snippets/text-mode/rst-mode/chap::name Chapter title]]
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[[file:~/src/emacs-starter-kit/src/snippets/text-mode/rst-mode/chap::name%20Chapter%20title][file:~/src/emacs-starter-kit/src/snippets/text-mode/rst-mode/chap::name Chapter title]]
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@ -247,77 +325,6 @@ Another example is in the [[*operations%20in%20on%20tables][grades example]].
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** TODO pass mutliple reference arguments into R
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** TODO pass mutliple reference arguments into R
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Can we do this? I wasn't sure how to supply multiple 'var' header
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Can we do this? I wasn't sure how to supply multiple 'var' header
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args. Just delete this TODO if I'm being dense.
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args. Just delete this TODO if I'm being dense.
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** TODO Create objects in top level (global) environment in R?
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At the moment, objects created by computations performed in the
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code block are evaluated in the scope of the
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code-block-function-body and therefore disappear when the code
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block is evaluated {unless you employ some extra trickery like
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assign('name', object, env=globalenv()) }. I think it will be
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desirable to also allow for a style wherein objects that are
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created in one code block persist in the R global environment and
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can be re-used in a separate block.
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This is what Sweave does, and while I'm not saying we have to be
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the same as Sweave, it wouldn't be hard for us to provide the same
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behaviour in this case; if we don't, we risk undeservedly being
|
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written off as an oddity by some.
|
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IOW one aspect of org-babel is that of a sort of functional
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meta-programming language. This is crazy, in a very good
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way. Nevertheless, wrt R I think there's going to be a lot of value
|
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in providing for a working style in which the objects are stored in
|
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the R session, rather than elisp/org buffer. This will be a very
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familiar working style to lots of people.
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There are no doubt a number of different ways of accomplishing
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this, the simplest being a hack like adding
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#+begin_src R
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for(objname in ls())
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assign(objname, get(objname), envir=globalenv())
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#+end_src
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to the source code block function body. (Maybe wrap it in an on.exit() call).
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However this may deserve to be thought about more carefully, perhaps
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with a view to having a uniform approach across languages. E.g. shell
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code blocks have the same semantics at the moment (no persistence of
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variables across code blocks), because the body is evaluated in a new
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bash shell process rather than a running shell. And I guess the same
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is true for python. However, in both these cases, you could imagine
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implementing the alternative in which the body is evaluated in a
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persistent interactive session. It's just that it's particularly
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natural for R, seeing as both ESS and org-babel evaluate commands in a
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single persistent R session.
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*** sessions [Eric]
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Thanks for bringing this up. I think you are absolutely correct that we
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should provide support for a persistent environment (maybe called a
|
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*session*) in which to evaluate code blocks. I think the current setup
|
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demonstrates my personal bias for a functional style of programming
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which is certainly not ideal in all contexts.
|
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While the R function you mention does look like an elegant solution, I
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think we should choose an implementation that would be the same across
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all source code types. Specifically I think we should allow the user to
|
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specify an optional *session* as a header variable (when not present we
|
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assume a default session for each language). The session name could be
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used to name a comint buffer (like the *R* buffer) in which all
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evaluation would take place (within which variables would retain their
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values --at least once I remove some of the functional method wrappings
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currently in place-- ).
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This would allow multiple environments to be used in the same buffer,
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and once this setup was implemented we should be able to fairly easily
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implement commands for jumping between source code blocks and the
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related session buffers, as well as for dumping the last N commands from
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a session into a new or existing source code block.
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Please let me know if you foresee any problems with this proposed setup,
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or if you think any parts might be confusing for people coming from
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Sweave. I'll hopefully find some time to work on this later in the
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week.
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** PROPOSED support for passing paths to files between source blocks
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** PROPOSED support for passing paths to files between source blocks
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Maybe this should be it's own result type (in addition to scalars and
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Maybe this should be it's own result type (in addition to scalars and
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