we are keeping two things in the contrib directory
1) the library-of-babel.org file, this is with the goal of lowering
the barrier of entry for contribution of functions to the library
of babel
2) we are also keeping a langs directory in the contrib directory
because some language files do not have FSF copyright assignment
-- current org-babel-oz.el is the only such file
* contrib/babel/lisp/org-babel.el (org-babel-where-is-src-block-result):
on result insertion, ensure that code blocks don't overrun
subsequent lines or source blocks
* contrib/babel/lisp/org-babel-exp.el (org-export-blocks-postblock-hook):
adding function to cleanup leftovers after block exportation
(org-exp-res/src-name-cleanup): function to cleanup leftovers from
block exportation
* contrib/babel/lisp/langs/org-babel-latex.el (org-babel-latex-body-to-tex-file):
now calling `org-export-latex-fix-inputenc' to sort out encodings in
latex package list
* contrib/babel/lisp/org-babel.el (org-babel-set-interpreters): less
greedy regexp for inline source blocks ensures that there is no
confusion when two inline blocks are on the same line.
e.g. placing the following at the top of your buffer
will result in all source-code blocks in the buffer having their
:session header argument set to "example"
* contrib/babel/lisp/org-babel-lob.el (org-babel-lob-execute): now
included buffer-wide header arguments in lob header arguments
* contrib/babel/lisp/org-babel.el (org-babel-params-from-buffer): new
function for grabbing header arguments from the top of the buffer
(org-babel-parse-src-block-match): now includes buffer-wide header
arguments
(org-babel-parse-inline-src-block-match): now includes buffer-wide
header arguments
(org-babel-current-buffer-properties): buffer-local variable to hold
buffer-wide header arguments
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-lob-one-liners):
exportation of #+lob and #+call type lines is now correctly handling
the addition of the indentation information to the info list
* contrib/babel/lisp/org-babel-lob.el
(org-babel-lob-one-liner-regexp):
(org-babel-lob-get-info):
(org-babel-lob-execute):
all org-babel elements should now work when indented
* contrib/babel/lisp/org-babel-ref.el
(org-babel-ref-at-ref-p):
all org-babel elements should now work when indented
* contrib/babel/lisp/org-babel.el
(org-babel-set-interpreters):
(org-babel-execute-src-block):
(org-babel-expand-src-block):
(org-babel-get-src-block-info):
(org-babel-hash-at-point):
(org-mode-hook):
(org-babel-parse-src-block-match):
(org-babel-where-is-src-block-result):
(org-babel-read-result):
(org-babel-insert-result):
(org-babel-result-end):
all org-babel elements should now work when indented
Thanks to Sébastien Vauban for pointing this out -- as well as the
previous babel commit :)
* contrib/babel/lisp/org-babel.el (org-babel-insert-result):
results are now indented to the level of any existing #+results
line.
* contrib/babel/lisp/org-babel-ref.el (org-babel-ref-resolve-reference):
now able to recognize #+tblname, #+resname and #+results lines which
do not start on column 0
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-inline-src-blocks):
only evaluate inline source code blocks if they do not appear in a
verbatim or quoted context
(org-babel-in-example-or-verbatim): check if the point is currently
located in a verbatim or quoted context
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-results):
removing forced verbatim '=' tags from around inline source code
results, if users want their results displayed in this way they can
add the '='s easily themselves, but there is no way to remove '='s
inserted automatically by Org-babel.
this is required because in the temporary org-mode file used during
export code blocks may be removed entirely leading to unresolved
references
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-src-blocks):
expanding noweb references during export now takes place in the
pre-export buffer
(org-babel-exp-inline-src-blocks): expanding noweb references during
export now takes place in the pre-export buffer
(org-babel-exp-results): ensure that the expanded body is passed
through to org-babel-execute-src-block
Thanks to Tom Dye for pointing out the need for this fix
* contrib/babel/lisp/org-babel.el (org-babel-expand-noweb-references):
now able to find noweb references even outside of the narrowed
portion of the buffer when the buffer is narrowed
* contrib/babel/lisp/org-babel-ref.el (org-babel-ref-resolve-reference):
now able to resolve references which are located outside of the
narrowed portion of the buffer when the buffer is narrowed
Thanks to Graham Smith for pointing out the need for in-place
results updates
* contrib/babel/lisp/org-babel.el (org-babel-merge-params): adding
append and prepend as exclusive options to the :results header
argument
(org-babel-insert-result): now updating results in place, and
honoring the `prepend' and `append' :results header arguments
* contrib/babel/lisp/org-babel.el (org-babel-header-arg-names): adding
:noeval header argument which can be specified to inhibit the
execution of a source block during export.
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-do-export):
adding :noeval header argument which can be specified to inhibit the
execution of a source block during export.
* contrib/babel/lisp/org-babel-comint.el (org-babel-comint-with-output):
Placing a more general regexp substitution for matching newlines
returned by comint. This new option should definitely cover all
cases.
* contrib/babel/lisp/org-babel-comint.el (org-babel-comint-with-output):
If there is dangling text left after the process mark in a comint
buffer, it will now be safely stored away during babel execution,
and then replaced when babel is finished with the buffer.
This commit also fixes some indentation issues.
* contrib/babel/lisp/langs/org-babel-ruby.el (org-babel-ruby-initiate-session):
Adding a small wait after stating a new ruby session. This avoids
errors with `ansi-color-process-output' not being able to find the
process mark.
* contrib/babel/lisp/org-babel.el (org-babel-insert-result): Replaced
call to `org-cycle' with a call to the simpler and more appropriate
`org-table-align'.
* contrib/babel/library-of-babel.org (Read/Write): adding
library-of-babel functions for file I/O
* contrib/babel/lisp/org-babel-exp.el (org-babel-exp-do-export):
This brings babel more inline with Sweave, by ensuring that any code
block which could change the state in a persistent session is
executed. Prior to this change the following org-mode text like would
not export as expected because the x variable would not be
initialized.
** inline expressions
:PROPERTIES:
:session: *R*
:END:
#+begin_src R :exports code :results silent
x<-5
#+end_src
the sum of 1 and 4 is equal to src_R{x}
* contrib/lisp/org-special-blocks.el (org-special-blocks-make-special-cookies):
Emacs 22 doesn't have string-match-p
* lisp/org-freemind.el (org-freemind-write-mm-buffer):
(org-freemind-get-node-style):
Emacs 22 doesn't have string-match-p
* lisp/org-html.el (org-html-make-link):
Use new org-string-match-p for compatibility
* contrib/babel/lisp/org-babel-tangle.el (org-babel-spec-to-string):
The insertion of automatically generated comments into tangled code
is now customizable through the `org-babel-tangle-w-comments'
variable.
* contrib/babel/lisp/org-babel.el
(org-babel-params-from-properties):
Check for language-specific header arguments
(org-babel-parse-src-block-match):
Pass lang parameter when checking properties for header args
(org-babel-parse-inline-src-block-match):
Pass lang parameter when checking properties for header args
Carsten Dominik <carsten.dominik@gmail.com> writes:
> On May 17, 2010, at 4:39 PM, Michael Sperber wrote:
>
>> In particular, fixing the require won't be enough: org-babel-python.el
>> uses `run-python' and interacts with the inferior Python, whereas
>> python-mode.el defines `py-shell'.
>>
>> Should I try to abstract over the differences?
>
> Yes, this would be much appreciated. (I think, Eric or Dan?)
OK, I've attached a patch that makes `org-babel-python' work on XEmacs.
Most of the issues are pure XEmacs issues. Notes:
- XEmacs doesn't have [[:digit:]] - I hope to rectify this in the
future, but it seems there's no downside in this particular case to
replacing by [0-9].
- XEmacs doesn't have `move-end-of-line', but does have `end-of-line'.
I don't understand the intent of having both of these, but the code
seems fine with `end-of-line'.
- It seems there are way too few `require's throughout org-babel. I
don't know if it's OK to add the ones I needed.
- `org-babel-python-evaluate' looked broken as-is: It doesn't use the
`body' argument properly, the result is (I think) processed in the
wrong order and not properly split into lines. I've fixed all these,
but a review is probably in order.
Currently, this uses the presence of a temporary file to signal that
Matlab Emacs Link evaluation is not yet complete.
Emacs Link support added in collaboration with Christopher Long.
To use EmacsLink, the user will need to set
org-babel-matlab-with-emacs-link to a non-nil value, and also arrange
that (matlab-with-emacs-link) evaluates to a non-nil value.
Added a handler for blockquotes.
Also added :body-newline-paragraph to the org-set-generic-type. This is
intended to help handling output formats (like tikiwiki) where newlines are
treated as paragraph separators, instead of being used to fill (i.e., the
destination is expected to do the word-wrapping). If this is set to T then
org-export-generic will emit a newline character when it sees a blank
line. This should be used in concert with a value like "%s " for
:body-line-format and nil for :body-line-wrap.
org-babel-expand-body:lang function needs to be implemented by every
language, and is used to expand the body of a code block for
execution or tangling
adding a suite of functions to org-babel.el which can be used to
handle hlines, rownames, and columnnames in input tables. These
functions can be called from any org-babel-language.el file.
done in close collaboration with Dan Davison
Prior to this, a terminal hline would leave dangling empty cells:
#+TBLNAME: A
|---+---+---|
| a | b | c |
|---+---+---|
#+begin_src emacs-lisp :var tab=A
tab
#+end_src
#+results:
|---+---+---|
| a | b | c |
|---+---+---|
| | | |
Previously "R" could overshadow "Ruby", and "C" could overshadow
"Clojure", causing blocks of the longer language name to fail to
load. This issue has now been fixed
thanks to Maurizio Vitale for the suggestion. This allows literal
values to be passed to code blocks through `sbe' without forcing the
use of quotes inside the table.
This deals with external process :results value mode for R, ruby,
python, perl and clojure: if the shell process has a non-zero exit
code, a buffer containing stderr is displayed.
Prior to this commit,
OUTPUT-BUFFER nil
REPLACE 'replace
ERROR-BUFFER 'current-buffer
resulted in stdout going with stderr to the current buffer, contra the
docstring. With this change stdout is discarded in this case. The
docstring does stipulate that stdout always should go to *Shell
Command Output*; this change does not make that happen in this case.
At this commit, org-babel-shell-command-on-region is a direct copy of
shell-command-on-region. In addition to switching to use the org-babel
version, we change the argument passed so that they agree with the
docstring of s-c-o-r.
Despite the change in arguments, the same behaviour results because
s-c-o-r does not behave as documented in emacs23. Future commits will
be able to fix these bugs in the org-babel version, as necessary.
This change fixes a bug in the remote execution branch, involving the
way that org-babel-tramp-handle-call-process-region is used
to (conditionally) handle calls to call-process-region. When
org-babel-execute-src-block called itself recursively (e.g. when
resolving a reference to another src block), a circular binding of
symbols and values resulted.
When using ':results value' in certain situations, results are written
to file by the foreign language process and subsequently read from
file by emacs into an elisp table structure. If the foreign language
process is running remotely, then the results are written
remotely. These changes ensure that in that case, an appropriate
remote file name is constructed to read the remote data.
These changes solve two problems: both are discussed in the following thread
http://lists.gnu.org/archive/html/tramp-devel/2010-02/msg00025.html
of which a summary follows.
Firstly, shell-command-on-region does not work with tramp in the same
way that shell-command does. I.e. whereas
(let ((default-directory "/user@remote-host:"))
(shell-command "hostname" t))
gives the remote hostname,
(let ((default-directory "/user@remote-host:"))
(shell-command-on-region (point) (mark) "hostname" t))
does not.
The reason is that shell-command-on-region calls call-process-region,
which does not use a tramp handler for remote files. However, such a
file handler does exist (unused) in the tramp sources:
tramp-handle-call-process-region. There is a slight problem in that
there is a bug in that function definition in current tramp (which has
persisted because the function is not normally used).
Therefore, we define an org-babel version of
tramp-handle-call-process-region which fixes the bug, and we bind
call-process-region to org-babel-tramp-handle-call-process-region for
the duration of org-babel-execute-src-block.
This introduces a new header argument :dir. For the duration of source
block execution, default-directory is set to the value of this header
argument. Consequences include:
- external interpreter processes run in that directory
- new session processes run in that directory (but existing ones are unaffected)
- relative paths for file output are relative to that directory
The name of a directory on a remote machine may be specified with
tramp syntax (/user@host:path), in which case the interpreter
executable will be sought in tramp-remote-path, and if found will
execute on the remote machine in the specified remote directory.
Use shell-command-on-region, bringing R into line with ruby, python,
clojure, shell. In addition to consistency (and perhaps efficiency),
this will also be preferable in the case of a remote R process because
it means that transfer of the input to the remote process is dealt
with automatically by tramp.
Before this change we have
#+begin_src ruby :results value :session
["1", "3"]
#+end_src
#+results:
: 1", "3
After, we have
#+begin_src ruby :results value :session
["1", "3"]
#+end_src
#+results:
| 1 | 3 |
This change provides for better export of named source-code blocks,
with specific support for more attractive html export. The arguments
are included with the source code name, and both the source code name
and code body are wrapped in a div to support styling with css. For
example the following CSS can be used to associate a source-code block
name with it's code body, and to slightly indent the body.
.org-src-container {
border-left: 4px solid gray;
padding: 0.5em 0.5em 0.5em 1em; }
.org-src-container pre {
margin-left: 1em; }
the progress-marker local variable set inside of a let in
org-exp-blocks is used to constrain searches in org-babel-exp to
ensure that a babel block doesn't overwrite non-babel src blocks
When exporting to html the source-code block name will be included
as a <label> immediately preceding the exported code. This <label>
is decorated with the 'org-src-name' css class.
When exporting to LaTeX with the listings package the source-code
block name will be included as a listings \title for the code
block. Currently the name will not be exported when the listings
package is not in use.
So, for example since the following <<example>> noweb reference
appears behind the SQL comment syntax the entire inserted body will
also be SQL commented
-- <<example>>
expands to
-- this is the
-- multi-line body of example
Note that noweb replacement text which does *not* contain any
newlines will not be affected by this change, so it is still
possible to use inline noweb references.
Thanks to Sébastien Vauban for this idea.
Variable names in gnuplot source code preceded by the '$' character
will be expanded to their value before the code is executed. For
example the following will results in the evaluation of 'plot
sin(x)' by gnuplot.
"sin(x)"
plot $fun
Insertion of new results was failing if the block was followed by
end-of-buffer. Also, if the block was followed by non-empty lines, the
\#+resname was being inserted away from column 0.
pressing tab while on the front of a results line will fold the
results in the same manner as tabbing on the front of a block will
fold the block. To automatically hide all blocks when entering a
new file add the `org-babel-result-hide-all' function to your
`org-mode-hook'
"results" is now an acceptable alias for "resname". Org-babel
will begin inserting results using the "results" option however
either option will remain viable moving forward.
The initial `org-babel-hash-show' characters of the hash will
remain visible. Pressing C-c C-c with the point on one of these
initial characters will copy the hash to the kill ring, should you
need to know it for any particular reason.
This can be overridden with the use of the header argument :cache on
the block, or subtree level. To set the global behavior to caching
add the following to your emacs init
(setq org-babel-default-header-args
(delete '(:nocache) org-babel-default-header-args))
This commit expands the #+resname: line to include a sha1 hash of
the contents of the source-code block (including header arguments).
This hash is saved in raw text in the resname line. When a source
block is evaluated it's hash is recalculated and checked against the
hash in it's results line, if they are equal the current results are
returned with no recalculation.
Optional prefix argument when evaluating a source block will force
re-calculation.
caching behavior can be inhibited through the use of the :nocache
header argument. for global inhibition of caching add :nocache to
the `org-babel-default-header-args' variable.
it is now possible to only assign a portion of a value to a variable
in a source block. So for example the following will only assign
the second and third lines of the table 'example-table' to the
variable 'data'
:var data=example-table[1:2]
and the following will only assign the second column of the first row
:var data=example-table[0,1]
note that all indices are 0 based
it is possible to index into the results of source-code blocks as
well as tables. any number of dimensions can be indexed as long as
they are separated by ','s and ranges can be indexed using the ':'
operator. for more information on indexing behavior see
`org-babel-ref-index-list'
Carsten Dominik
Eric Schulte
Bernt Hansen
Nicolas Goaziou
Dan Davison
Michael Sperber
Benjamin Andresen
Robert P. Goldman
Julien Barnier
Christian Egli
Joel Boehland
Joel Boehland
Eric Schulte