* lisp/ob.el (org-babel-result-end): end position is end of current
sublist instead of bottom point, as results might be inserted in a
list themselves.
* lisp/org.el (org-skip-over-state-notes,org-store-log-note): use new
accessors.
* list/ob.el (org-babel-result-end): use new accessors.
* list/org-exp.el (org-export-mark-list-ending): use new accessors.
* lisp/ob.el (org-babel-src-block-names): Don't strip text properties from search hits
(org-babel-result-names): Don't strip text properties from search hits
* lisp/ob.el (org-babel-script-escape): Use `substring' comparison
instead of regexp matching
Workaround for regexp limitation, e.g.
(string-match
"^\\[.+\\]$"
(concat
"["
(mapconcat (lambda (i) "x") (number-sequence 1 33500) "")
"]"))
gives "Stack overflow in regexp matcher" in several current builds.
* lisp/org-src.el (org-edit-src-persistent-message): Change docstring.
(org-edit-src-code): Get rid of help message in echo area.
* lisp/ob.el (org-babel-do-in-edit-buffer): Do not pass 'quietly
argument to org-edit-src-code as this has been removed
* lisp/ob-exp.el (org-babel-exp-inline-src-blocks): Simplified
exportation of inline code blocks using normal code block execution
mechanism to insert results.
(org-babel-exp-results): Results exportation mechanism is unified
for both inline and regular code blocks.
* lisp/ob.el (org-babel-where-is-src-block-result): Returns the point
after an inline code block for inline code blocks.
* lisp/ob.el (org-babel-insert-result): Special handling of the
position of results of inline code blocks.
(org-babel-examplize-region): Now able to comment inline regions.
* lisp/ob.el (org-babel-map-inline-src-blocks): Macro for executing
code in each inline code block.
(org-babel-execute-buffer): Executes inline code blocks as well as
regular code blocks.
* lisp/ob-tangle.el (org-babel-spec-to-string): Adding "noweb" as a
linking comment type
(org-babel-tangle-comment-links): Returns comment links for the
source code block at point
* lisp/ob.el (org-babel-expand-noweb-references): When :comments is
set to "noweb" then wrap noweb references in comment links.
Thanks to Leo Alekseyev for bringing this bug to my attention
* lisp/ob.el (org-babel-open-src-block-result): Must collect result
*before* jumping to the result buffer.
* lisp/ob.el (org-babel-temp-file): Ensure that
org-babel-temporary-directory is bound before using.
(org-babel-remove-temporary-directory): Safer error throwing.
* lisp/ob.el (org-babel-script-escape): Replace commas with spaces for
better list reading when list items are packed with commas,
e.g. Haskell list output.
Thanks to Vladimir Alexiev for submitting this patch
* lisp/ob.el (org-babel-confirm-evaluate): Fix for the case when
org-confirm-babel-evaluate is a function (used to always ask no matter
what the function returns).
* doc/org.texi (Code evaluation security): Add example for using a
function.
* lisp/ob.el (org-babel-format-result): New function to format results
of src block execution.
(org-babel-execute-src-block): Use `org-babel-format-result' when
writing to file.
(org-babel-open-src-block-result): Use `org-babel-format-result' when
displaying results in a buffer; name results buffer differently.
* org.el: remove spurious linebreak introduced by earlier patch
* ob.el, ob-ref.el: remove double fix of the same problem
Achim Gratz <Stromeko@Stromeko.DE> wrote:
> this patch had already been partially applied by Carsten and Eric (in
> slightly a different way than I suggested). The changes to ob.el and
> ob-ref.el (the require statements) are therefore superfluous and should
> probably be backed out. There was also a superfluous whitespace change
> in org.el (a closing paren that was broken onto the next line). Patch
> to this effect is attached. You've already cleaned up org-agenda.el and
> the conditions in org-macs...
* lisp/ob.el (org-babel-remove-temporary-directory): Handle exception
with message informing of failure to remove directory.
Thanks to Antti Kaihola for the bug report:
http://thread.gmane.org/gmane.emacs.orgmode/34394
From: Antti Kaihola <akaihola <at> gmail.com>
Subject: Can't close Emacs+org-mode if /tmp and /home on different partitions
Newsgroups: gmane.emacs.orgmode
Date: 2010-12-02 08:33:28 GMT (6 days, 1 hour and 22 minutes ago)
I have /tmp on my root partition and a separate partition for /home.
When trying to close an Emacs session which is using org-mode, I get
this error:
move-file-to-trash: Non-regular file: Is a directory, /tmp/babel-XXXXXXX
(where XXXXXXX are random characters).
I tracked down the problem to org-babel-remove-temporary-directory
which ob.el adds to kill-emacs-hook. It tries to remove the temporary
directory using delete-directory, which in turn tries to move the
directory (by renaming) into trash, which is in my home directory.
I added this to my ~/.emacs.d/init.el:
(custom-set-variables '(temporary-file-directory "/home/akaihola/tmp/"))
and closing Emacs works correctly again. However, since my init.el is
part of emacs-starter-kit which I update frequently, I'd prefer not to
modify that file. Unfortunately the customization hook
emacs-starter-kit provides (~/.emacs.d/custom.el) is loaded too late
to affect the temporary directory.
I'm running emacs-snapshot 1:20090909-1 in Ubuntu 10.10. Looks like
this is really an Emacs bug and is already fixed:
http://groups.google.com/group/gnu.emacs.bug/browse_thread/thread/0446b8684a8ef504
* lisp/ob.el (org-babel-insert-result): Responds to new "wrap" header
argument.
(org-babel-merge-params): Includes new "wrap" header argument in
one of the results header argument exclusive groups.
* lisp/org.el (org-additional-option-like-keywords): Fontify begin and
and results lines as comments.
Thanks to Charles C. Berry for insisting on this issues existence
This change is now secured with a unit test
* lisp/ob.el (org-babel-parse-header-arguments): Stripping trailing
spaces off of header arguments (even the first one).
* lisp/ob-eval.el (org-babel-error-buffer-name): Define new variable.
(org-babel-eval-error-notify): Use new variable `org-babel-error-buffer-name'
(org-babel-eval): Make temp error buffer invisible to the user with
initial space in name.
(org-babel-eval-wipe-error-buffer): New function to wipe the error message buffer.
* lisp/ob-exp.el (org-babel-eval-wipe-error-buffer): Declare external function
`org-babel-eval-wipe-error-buffer'.
(org-babel-exp-results): Wipe error buffer clean at outset of execution
* lisp/ob.el (org-babel-execute-src-block-maybe): Wipe error buffer clean at
outset of execution
(org-babel-eval-wipe-error-buffer): Declare external function
`org-babel-eval-wipe-error-buffer'.
* lisp/ob-python.el (org-babel-python-table-or-string): Using
`org-babel-script-escape' for reading string input from scripting
languages.
* lisp/ob-ruby.el (org-babel-ruby-table-or-string): Using
`org-babel-script-escape' for reading string input from scripting
languages.
* lisp/ob.el (org-babel-script-escape): Using
`org-babel-script-escape' for reading string input from scripting
languages.
* lisp/ob-haskell.el (org-babel-haskell-table-or-string): Using
`org-babel-script-escape' for reading string input from scripting
languages.
Thanks to Nicolas Goaziou for pointing this out
* lisp/ob-ref.el (org-babel-ref-at-ref-p): Use higher level function
for testing list membership.
* lisp/ob.el (org-babel-read-result): Use higher level function for
testing list membership.
(org-babel-result-end): Use higher level function for testing list
membership.
* lisp/ob-ref.el (org-babel-ref-resolve): Recognize `list' as a unique
type of data
(org-babel-ref-at-ref-p): Recognize `list' as a unique type of data
* lisp/ob.el (org-babel-read-result): Recognize `list' as a unique
type of data
(org-babel-read-list): A function to read a textual Org-mode list
into an emacs-lisp list.
(org-babel-insert-result): Recognizes the "list" result param to
insert data as an Org-mode list.
(org-babel-result-end): Find the end of an Org-mode list.
(org-babel-merge-params): Add "list" as a result param.
* doc/org.texi (results): Documentation of the new "list" results
header argument.
* lisp/ob-lob.el (org-babel-lob-get-info): including pass-through
header arguments in results variable header argument string
* lisp/ob.el (org-babel-execute-src-block): working with new header
argument setup
(org-babel-parse-header-arguments): only split header argument
strings when []'s are balanced
* lisp/ob.el (org-babel-execute-src-block): If ":results file" is in
effect, then ensure that the value of :file is returned as the result;
don't rely on language files for this.
Examples of languages that were not honouring :file are sh and
emacs-lisp.
* lisp/ob-tangle.el (org-babel-update-block-body): declaring function
for updating code block bodies
(org-babel-spec-to-string):
(org-babel-detangle): detangle all tangled and commented code blocks
in the current file back to org
(org-babel-tangle-jump-to-org): jump from a tangled and commented
file back to the originating org-mode code block
ob-tangle: detangle changes in code files back to the original org files
* lisp/ob-tangle.el (org-babel-update-block-body): declaring function
for updating code block bodies
(org-babel-spec-to-string):
(org-babel-detangle): detangle all tangled and commented code blocks
in the current file back to org
(org-babel-tangle-jump-to-org): jump from a tangled and commented
file back to the originating org-mode code block
* lisp/ob.el (org-babel-sha1-hash): now handles more complex types in
params
* testing/examples/babel.org: whitespace
* testing/lisp/test-ob.el (test-org-babel/sha1-hash): new test for
babel hashing
* lisp/ob.el (org-babel-execute-src-block): generally using the new
more informative params
(org-babel-process-params): don't forget the :var portion of
variable assignments
* ob.el (org-babel-expand-src-block): Supply variable
assignment lines to generic expansion function
(org-babel-expand-body:generic): Prepend body with optional
variable assignment lines
* lisp/ob-exp.el (org-babel-exp-results): replaced old function call
* lisp/ob-lob.el (org-babel-lob-execute): replaced old function call
* lisp/ob-ref.el (org-babel-ref-parse): removed obsolete optional
params argument, also no longer chokes when handed an
already-resolved reference
(org-babel-ref-resolve): removed obsolete optional params argument
* lisp/ob.el (org-babel-ref-parse): updated function declaration
(org-babel-get-src-block-info): replaced old function call
(org-babel-header-arg-names): indentation
(org-babel-execute-src-block): now expanding all parameters using
the newly combined org-babel-process-params
(org-babel-switch-to-session-with-code): indentation
(org-mode-hook): indentation
(org-babel-process-params): now packages all results into the
parameter alist and does variable expansion, this should no longer
be called from inside of language functions
(org-babel-expand-noweb-references): updated function call for newly
removed obsolete function parameter
* lisp/ob-lob.el (org-babel-lob-execute): now expanding variable
references before execution
* lisp/ob.el (org-babel-merge-params): better indentation, and finally
sorted out the proper replacement of conflicting variable
definitions
ob-get-src-block-info wasn't correctly returning the name of the
code block
* lisp/ob-lob.el (org-babel-lob-ingest): now returns the count of
ingested code blocks
* lisp/ob.el (org-babel-get-src-block-info): walks up possible
additional header arg lines before checking for the code block name
(org-babel-merge-params): can now handle empty variables gracefully
includes a simple export test
* lisp/ob-exp.el (org-babel-exp-in-export-file): wrapper for
collecting information from within the original export file
(org-babel-exp-src-blocks): simplified through use of the above
macro
(org-babel-exp-code): simplified through the use of new functions
for parsing header arguments
(org-babel-exp-results): simpler high-level organization, also this
is now where the expansion of variable references takes place during
export
* lisp/ob.el (org-babel-expand-variables): broke variable replacement
in a parameter list into it's own function
(org-babel-get-src-block-info): now using the above function
for example, from the test of this functionality
* multi-line header arguments
:PROPERTIES:
:ID: b77c8857-6c76-4ea9-8a61-ddc2648d96c4
:END:
(map 'list #'list numbers letters)
| 1 | a |
| 2 | b |
| 3 | c |
| 4 | d |
| 5 | e |
| 6 | f |
| 7 | g |
* lisp/ob.el (org-babel-multi-line-header-regexp): new variable for
matching header lines preceding code blocks
(org-babel-src-name-w-name-regexp): now includes possible header
lines between source name and code block
(org-babel-get-src-block-info): now also collecting header arguments
from preceding header lines
(org-babel-src-block-names): updated match-string to reflect new
value of org-babel-src-name-w-name-regexp
(org-babel-merge-params): fixed error in variable string regexp
* ob.el (org-babel-mark-block): New function to mark the body
of a src block in the style of `mark-defun'.
* ob-keys.el (org-babel-key-bindings): Bind
`org-babel-mark-block' to C-c C-v C-M-h
* lisp/org-compat.el (org-number-sequence): New function.
* lisp/ob-R.el (org-babel-expand-body:R): Use `org-number-sequence'.
* lisp/ob.el (org-babel-where-is-src-block-result): Use `org-number-sequence'.
(org-babel-current-buffer-properties): Fix variable definition.
* lisp/ob-ref.el (org-babel-ref-index-list): Use `org-number-sequence'.
* lisp/ob-latex.el (org-babel-latex-tex-to-pdf): Use the 2-argument version
of `shell-command'.
* lisp/org-latex.el (org-export-as-pdf): Use the 2-argument version
of `shell-command'.
Thanks to Achim Gratz
* lisp/ob.el (or): don't create org-babel-temporary-directory in batch
as it won't be removed by emacs-kill-hook
(org-babel-remove-temporary-directory): only try to remove this
directory if it exists
We had stopped using this because users noticed that temporary
directories were accumulating in their /tmp directory. I believe this
was due to repeatedly evaluating the ob.el emacs-lisp file, which
repeatedly re-defined the `org-babel-temporary-directory' variable
creating multiple directories. This problem should be fixed by
wrapping the defvar holding this form in (unless (boundp org...)).
* lisp/ob.el (boundp): uncommenting defvar form for
org-babel-temporary-directory
(org-babel-temp-file): now using the org-babel-temporary-directory
for holding new babel temporary files
(org-babel-remove-temporary-directory): removes the babel temp dir
when Emacs shutsdown
(kill-emacs-hook): now removing the babel temp dir on Emacs shutdown
* ob.el (org-babel-process-file-name): New function
(org-babel-maybe-remote-file): Delete function
* ob-sql.el (org-babel-execute:sql):
Use org-babel-process-file-name
* ob-scheme.el (org-babel-execute:scheme):
Use org-babel-process-file-name
* ob-sass.el (org-babel-execute:sass):
Use org-babel-process-file-name
* ob-ruby.el (org-babel-ruby-evaluate):
Use org-babel-process-file-name
* ob-python.el (org-babel-python-evaluate-external-process):
Use org-babel-process-file-name
(org-babel-python-evaluate-session):
Use org-babel-process-file-name
* ob-plantuml.el (org-babel-execute:plantuml):
Use org-babel-process-file-name
* ob-perl.el (org-babel-perl-evaluate):
Use org-babel-process-file-name
* ob-octave.el (org-babel-octave-evaluate-external-process):
Use org-babel-process-file-name
(org-babel-octave-evaluate-session):
Use org-babel-process-file-name,
don't use org-babel-maybe-remote-file
* ob-lisp.el (org-babel-execute:lisp):
Use org-babel-process-file-name
* ob-ledger.el (org-babel-execute:ledger):
Use org-babel-process-file-name
* ob-js.el (org-babel-execute:js):
Use org-babel-process-file-name
* ob-haskell.el (org-babel-haskell-export-to-lhs):
Use org-babel-process-file-name
* ob-gnuplot.el (org-babel-execute:gnuplot):
Use org-babel-process-file-name
* ob-eval.el (org-babel-eval-read-file): Don't use
org-babel-maybe-remote-file
* ob-dot.el (org-babel-execute:dot):
Use org-babel-process-file-name
* ob-ditaa.el (org-babel-execute:ditaa):
Use org-babel-process-file-name
* ob-clojure.el (org-babel-clojure-evaluate-external-process):
Use org-babel-process-file-name
* ob-asymptote.el (org-babel-execute:asymptote):
Use org-babel-process-file-name
* ob-R.el (org-babel-R-assign-elisp): Don't use
org-babel-maybe-remote-file, use org-babel-process-file-name
(org-babel-R-evaluate-external-process):
Use org-babel-process-file-name
(org-babel-R-evaluate-session):
Use org-babel-process-file-name
* ob-C.el (org-babel-C-execute):
Use org-babel-process-file-name
In addition to passing the file path through `expand-file-name',
tramp-style remote file names are converted to conventional (local)
file paths. The reason is that, if a tramp file name was in use in
emacs, then the shell command will be executing on the remote machine
in question. Further, by default the file name is passed through
`shell-quote-argument'.
Thanks to Richard Riley for the initial idea and implementation
* lisp/ob.el (org-babel-demarcate-block): interactive demarcation of
code blocks
* lisp/ob-keys.el (org-babel-key-bindings): key bindings for block
demarcation
* doc/orgcard.tex: documentation in the ref card
* lisp/ob-keys.el (org-babel-key-bindings): adding key-binding for
`org-babel-goto-src-block-head'
* lisp/ob.el (org-babel-goto-src-block-head): jump to the head of the
current code block
* lisp/ob.el (org-babel-next-src-block): now raising more informative
error when no further code blocks can be found
(org-babel-previous-src-block): now raising more informative error
when no previous code blocks can be found
Thanks to Sébastien Vauban for making the case for this behavior
* lisp/ob.el (org-babel-insert-result): remove existing results when
nil results are returned
* ob.el (org-babel-temp-file): Don't use babel temporary
directory in remote case; use make-temp-file with remote file
name so that temp file is guaranteed not to exist previously
on remote machine.
(org-babel-tramp-localname): New function to return local name
portion of possibly remote file specification
* ob-R.el (org-babel-R-evaluate-external-process): Respond to
changes in `org-babel-temp-file'; pass local file name to
remote R process.
(org-babel-R-evaluate-session) Respond to
changes in `org-babel-temp-file'; pass local file name to
remote R process.
this makes it possible to export while not evaluating some code
blocks
* lisp/ob-exp.el (org-babel-exp-do-export): removing hacky ":noeval",
which is now an alias to ":eval no"
* lisp/ob.el (org-babel-confirm-evaluate): ":noeval" is an alias for
":eval no", also no longer throwing errors
(org-babel-header-arg-names): adding both eval and noeval as general
header arguments
(org-babel-execute-src-block): now using the new non-error
confirmation functionality
ob-org has two non-standard header arguments in that it exports it's
results by default and the result type defaults to raw, this ensures
that the body of a begin_src org block exports transparently.
This is a breaking change in that if you are currently using org
code blocks to export org-fontified code you will have to set the
":exports" header argument for org-mode blocks to "code" on a block,
file, language or system-wide basis.
* Makefile (LISPF): adding ob-org.el to the makefile
* lisp/ob-org.el: defines handling of org code blocks
* lisp/ob.el (org-babel-insert-result): now when "org" is a result
type the results are wrapped in an org code block
Thanks to Noorul Islam for pointing out this issue
* lisp/ob.el (org-babel-remove-temporary-directory): the version of
`delete-directory' found in files.el can not be assumed to be
present on all versions, so this copies the recursive behavior of
that command in such a way that all calls to delete-directory will
also work with the built-in internal C implementation of that
function. This is not overly difficult as all elements of the
directory can be assumed to be files.
Eric Schulte
Nicolas Goaziou
Dan Davison
Bastien Guerry
Achim Gratz
Carsten Dominik
Dan Davison
David Maus
Glenn Morris