* lisp/ob-core.el (org-babel-where-is-src-block-head): Refactor. In
particular, do not return a marker, ever. Also update docstring.
* testing/lisp/test-ob.el (test-ob/org-babel-remove-result--results-org):
Fix tests containing invalid Org syntax.
* lisp/ob-core.el (org-babel-map-src-blocks,
org-babel-map-inline-src-blocks): Make sure to ignore case when
looking for source blocks.
Reported-by: Christopher Genovese <genovese@cmu.edu>
<http://permalink.gmane.org/gmane.emacs.orgmode/93454>
* lisp/ob-exp.el (org-babel-exp-inline-code-template): New
customizable variable to export inline source code (similar to
`org-babel-exp-code-template').
(org-babel-exp-code): New `type' argument to differentiate between
inline and standard code blocks.
* lisp/ob-core.el (org-babel-inline-src-block-regexp): Allow empty set
of switches and header arguments as in "src_sh[]{echo foo;}". Also
permit spaces before them.
* testint/lisp/test-org-element.el
(test-org-element/inline-src-block-parser): Test extended syntax for
inline source code.
* testing/lisp/test-ob-exp.el (ob-exp/exports-inline-code): New
function for testing inline source code handling. Also add three new
failing tests exhibiting unexpected results with ":results code"
switches.
* testing/lisp/test-ob.el
(test-org-babel/org-babel-get-inline-src-block-matches): Test for
inline source blocks with empty header arguments.
* testing/examples/babel.org: New sections for testing (i) exported
inline source code (used by `ob-exp/exports-inline-code'); (ii)
parsing inline source blocks with empty header arguments (used by
`test-org-babel/org-babel-get-inline-src-block-matches').
Until now pieces of inline source code were handled as standard code
blocks during export. These changes enable them to be exported.
* lisp/ob-core.el (org-babel-common-header-args-w-values): Add
:output-dir'.
Otherwise tthis property is not inherited correctly from
subtree-/file-level properties.
* lisp/ob-core.el (org-babel-noweb-error-all-langs): Raise noweb
errors regardless of language.
(org-babel-expand-noweb-references): Make use of the new
`org-babel-noweb-error-all-langs' variable.
* lisp/ob-core.el: Add comment to forward declaration of
'org-src-preserve-indentations'.
* lisp/ob-exp.el: Require org-src to import
'org-src-preserve-indentations'.
* lisp/ob-haskell.el, lisp/ob-python.el: Remove superfluous forward
declaration of 'org-src-preserve-indentations', since it gets
imported by other requires.
* ob-core.el (org-babel-insert-result): Test all list elements against
listp and (eq element 'hline) instead of checking just the first.
org-babel table output uses different formatting for a list of lists,
but detects it incorrectly causing an error. An example of a block
causing an error is an emacs lisp source block containing just 1 line:
'((1) 2)
* ob-core.el (org-babel-demarcate-block): Upcase or downcase
the inserted #+begin_src and #+end_src depending on the
current case of #+begin_src and #+end_src.
Thanks to Alexander Baier for reporting this.
* lisp/ob-core.el (org-babel-generate-file-param): New function.
(org-babel-get-src-block-info): Use it.
(org-babel-merge-params): Handle :file-ext.
(org-babel-graphical-output-file): error if no :file or :file-ext.
* testing/lisp/test-ob.el (test-org-babel/file-ext-and-output-dir):
New test.
* doc/org.texi (Specific header arguments): Add doc for :file-ext and
:output-dir header args.
* lisp/ob-R.el (org-babel-expand-body:R): Don’t calculate
graphics-file.
(org-babel-execute:R): Only look for a graphics-file if needed.
* lisp/ob-core.el (org-babel-graphical-output-file): New generic function.
* lisp/ob-R.el (org-babel-R-graphical-output-file): Delete specific version.
(org-babel-expand-body:R): Use generic version.
* lisp/ob-maxima.el (org-babel-maxima-graphical-output-file): Delete
specific version.
(org-babel-maxima-expand): Use generic version.
* lisp/ob-octave.el (org-babel-octave-graphical-output-file): Delete
specific version
(org-babel-execute:octave): Use generic version.
* org.el (org-trim): Rewrite and make a defsubst.
* org-bibtex.el (org-bibtex-get): Use `org-trim' instead of
`org-babel-trim'.
* ob-core.el (org-babel-trim): Delete and alias to `org-trim'.
(org-babel-chomp): Delete and alias to `org-trim-trailing'.
(org-trim-trailing): New defsubst.
(org-babel-examplize-region): Fix version.
* ob-core.el (org-babel-remove-result-one-or-many): New function.
* ob-keys.el (org-babel-key-bindings): Add a keybinding for the
new function `org-babel-remove-result-one-or-many'.
TINYCHANGE
* lisp/ob-core.el (org-babel-exp-reference-buffer): New variable, as
a replacement for `org-current-export-file'.
(org-babel-check-confirm-evaluate): Use new variable.
* lisp/ob-exp.el (org-babel-exp-in-export-file): Use new variable.
(org-babel-exp-get-export-buffer): Remove function.
(org-babel-exp-process-buffer): Change signature.
* lisp/ob-ref.el (org-babel-ref-resolve): Use new variable during
export in order to properly resolve references.
* lisp/ox.el (org-export-execute-babel-code): Use new variable.
* contrib/lisp/org-wikinodes.el (org-wikinodes-process-links-for-export):
Remove a cond branch as it is always
false (`org-current-export-file' couldn't be a string).
* testing/lisp/test-ob-lob.el (test-ob-lob/export-lob-lines): Update
test.
* testing/lisp/test-ob.el (test-ob/eval-header-argument): Update test.
* testing/lisp/test-ob-exp.el (ob-export/reference-in-post-header):
New test.
During export, Babel executes sequentially all blocks in the buffer
being exported. This can lead to modifications preventing some
references from being resolved. As a workaround, Babel stores
a pristine copy of the buffer in a variable so it can always find
needed references.
Before this patch, the variable storing this copy was
`org-current-export-file' and was dynamically bound in "ox.el". It
was used to resolve noweb references (`org-babel-expand-noweb-references')
but not regular references (`org-babel-ref-resolve').
Now, the variable is `org-babel-exp-reference-buffer' and it is bound
from `org-babel-exp-process-buffer'. It is used to resolve all
references. In particular, this allows to use references in :post
header.
Thanks to Jarmo Hurri for reporting it.
* ob-core.el (org-babel-insert-result): Use `org-babel-examplify-region'.
(org-babel-capitalize-examplize-region-markers): Rename to
`org-babel-capitalize-example-region-markers'.
(org-babel-examplize-region): Mark obsolete and rename to
`org-babel-examplify-region'.
* lisp/ob-core.el (org-babel-current-result-hash): Additional info
argument so that named call line results may be found.
(org-babel-set-current-result-hash): Additional info argument so
that named call line results may be found.
* lisp/ob-lob.el (org-babel-lob-execute): Passing info to hash finding
functions so that named results may be found.
The bulk of the new code in org-babel-sha1-hash is borrowed from
org-babel-expand-src-block.
* lisp/ob-core.el (org-babel-sha1-hash): Expanded noweb references
when calculating hashes.
* org.el (org-babel-do-in-edit-buffer): Declare.
(org-babel-load-file, org-insert-comment)
(org-comment-or-uncomment-region): Don't require 'ob-core.
(org-mode-map): Remap `comment-dwim' to `org-comment-dwim'.
(org-comment-dwim): New command.
* ob-core.el (org-babel-do-in-edit-buffer): Make an autoload.
See http://lists.gnu.org/archive/html/emacs-devel/2013-12/msg00154.html
for a discussion about this bug.
* lisp/ob-C.el (org-remove-indentation): Declare function to appease
compiler.
* lisp/ob-core.el (org-remove-indentation): Declare function to
appease compiler.
* lisp/ob-fortran.el (org-remove-indentation): Declare function to
appease compiler.
* lisp/ob-C.el (org-babel-C-execute): Remove common indentation when
trimming.
* lisp/ob-core.el (org-babel-read-result): Remove common indentation
when trimming.
(org-babel-update-block-body): Remove common indentation when
trimming.
* lisp/ob-fortran.el (org-babel-execute:fortran): Remove common
indentation when trimming.
* lisp/ob-tangle.el (org-babel-process-comment-text): Better default
to process tangled comments.
* lisp/ob-core.el (org-babel-execute-src-block): Set location info
parameter for inline src blocks.
(org-babel-get-src-block-info): Set location info parameter for
inline src blocks.
This fixes a bug noticed by Rick Frankel in which two subsequent
#+call: lines will both update the same results. Before this commit
both of the following call lines would update the same result.
#+name: call-me
#+BEGIN_SRC emacs-lisp :var v="nil"
v
#+END_SRC
#+call: call-me("one")
#+call: call-me(v="two")
#+RESULTS:
: one
Now both lines are given their own result.
#+name: call-me
#+BEGIN_SRC emacs-lisp :var v="nil"
v
#+END_SRC
#+call: call-me("one")
#+RESULTS:
: one
#+call: call-me(v="two")
#+RESULTS:
: two
* lisp/ob-core.el (org-every): Declared function for compiler.
(org-babel-safe-header-args): Moved before first use.
(org-babel-header-args-safe-fn): Moved before first use.
Always call org-confirm-babel-evaluate from the head of the code
block being evaluated so that the info may be found with
e.g., (org-babel-get-src-block-info 'light)
* lisp/ob-core.el (org-babel-check-confirm-evaluate): Call
org-confirm-babel-evaluate from code block head.
* lisp/ob-core.el (org-babel-insert-header-arg): Optional arguments
for usage from Emacs Lisp programs. In addition this function will
now insert header arguments in the correct place instead of at the
current point.
This patch is based off of a request and an initial patch supplied by
Daniele Pizzolli.
* lisp/ob-core.el (org-babel-remove-result): Added an option to keep
the results keyword when removing the content of results.
* lisp/ob-core.el (org-babel-default-header-args): It is likely that
someone meant to set :padlines to "yes", but accidentally set
:padnewlines to "yes". Either way lets just remove this which
shouldn't have any functional effect.
Thanks to Rick Frankel for help debugging this problem.
* lisp/ob-core.el (org-babel-merge-params): When merging parameters, if
a variable is replaced with a new value, then delete colnames/rownames
for the original value of that variable.
* lisp/ob-core.el (org-babel-check-confirm-evaluate): Return result of
evaluating the function pointed to by`org-confirm-babel-evaluate'
when it is a functionp and its value as a variable otherwise.
This fixes a regression introduced in 5fe486807e and restores the fix
applied earlier in 8d272b0d3b (and then replaced by a cond form in
ece347e32c, which later got factored out again).
* lisp/ob-core.el (org-babel-find-named-result): Call lines are not
results.
(org-babel-where-is-src-block-result): Don't implicitly name the
results of call lines.
* lisp/ob-exp.el (org-babel-exp-non-block-elements): There is now
another element on the call line info list.
* lisp/ob-lob.el (org-babel-lob-get-info): Return the name (if any)
at the end of the info list.
(org-babel-lob-execute): Pass the name through to execution.
* lisp/ob-core.el (org-babel-get-rownames),
lisp/org-table.el (org-table-transpose-table-at-point): Replace the
inadvertent use of mapcar* (from cl) by plain mapcar and direct cons
manipulation.
The error was not caught at compilation time since both source files
require cl during compilation for using cl macros. These were the
only uses of mapcar* in Org, but I didn't check for other cl
_functions_ (as opposed to macros, which would need to be checked if
their implementation uses cl functions).
* lisp/ob-core.el (org-babel-execute-src-block): Ensure that the
location is set before anything else is done.
* lisp/ob-ref.el (org-babel-ref-parse): Evaluate Emacs Lisp values in
header arguments at the location of the original code block.
* testing/lisp/test-ob.el (test-ob/location-of-header-arg-eval): Test
defending the new header argument evaluation behavior.
* lisp/ob-core.el (org-babel-params-from-properties): Use
`org-babel-current-src-block-location' for evaluating new-style
header-argument properties. Remove superfluous save-match-data
clauses. Comment which properties get evaluated where.
* lisp/ob-gnuplot.el (org-babel-expand-body:gnuplot): Use new header
arguments.
* lisp/ob-core.el (org-babel-common-header-args-w-values): Mention new
header arguments.
(org-babel-expand-body:generic): Use new header arguments.
* doc/org.texi (Specific header arguments): Document new header
arguments.
* lisp/ob-core.el (org-babel-read-result): More robust matching of
examplized ranges.
(org-babel-result-end): More robust matching of examplized ranges.
The `org-babel-params-from-properties' command was calling
`org-babel-merge-params', the output of which was then being fed back
to another call to `org-babel-merge-params'. The merge params
function is not designed to allow this form of recursive calling, and
as a result many variables were being set to empty values.
The first noticed side effect of this bug was the breakage of the
org-babel-load-file command, which relies on default header
arguments (namely :tangle), which were overwritten by the bug above.
The fix involved having the `org-babel-params-from-properties'
function return a list of alists, which may then all be handed to the
top-level merge-params call.
* lisp/ob-core.el (org-babel-params-from-properties): Now returns a list
of alists and does *not* call `org-babel-merge-params'.
(org-babel-parse-src-block-match): Handle new list of lists output of
`org-babel-params-from-properties'.
(org-babel-parse-inline-src-block-match): Handle new list of lists
output of `org-babel-params-from-properties'.
* lisp/ob-exp.el (org-babel-exp-src-block): Handle new list of lists
output of `org-babel-params-from-properties'.
(org-babel-exp-non-block-elements): Handle new list of lists output of
`org-babel-params-from-properties'.
* lisp/ob-lob.el (org-babel-lob-execute): Handle new list of lists
output of `org-babel-params-from-properties'.
* lisp/ob-core.el (org-babel-insert-header-arg,
org-babel-parse-src-block-match): Replace `if' with empty else part
by `when' for readability. (org-babel-params-from-properties):
Inquire for language specific and default header properties.
Language specific header properties take precedence over default
header properties and old-style header property specifications.
This allows for header arguments to be specified as
properties (including inheritance).
#+PROPERTY: header-args :cache "no"
#+PROPERTY: header-args:R :session "*R-property*"
:PROPERTIES:
:header-args: :cache "yes"
:header-args:R: :session "*R-drawer*"
:END:
* doc/org.texi (Top): Documentation for new tangle-mode header argument.
(Specific header arguments): Documentation for new tangle-mode header
argument.
(rownames): Documentation for new tangle-mode header argument.
(tangle-mode): Documentation for new tangle-mode header argument.
* lisp/ob-core.el (org-babel-common-header-args-w-values): Adding the
new :tangle-mode header argument.
(org-babel-read): Read values starting with a "#" character as emacs
lisp.
* lisp/ob-tangle.el (org-babel-tangle): Use the new :tangle-mode header
argument.
* lisp/org-pcomplete.el (pcomplete/org-mode/block-option/src): Use the
new :tangle-mode header argument.
* lisp/ob-core.el (org-babel-where-is-src-block-head): return
point-marker instead of point.
(org-babel-current-exec-src-block-head): new global variable which is
bound during `org-babel-execute-src-block-maybe'
(org-babel-get-src-block-info): return a list of 7 elements, last
being the header location
Evaluation backends might need to use the exact location of the block in
original org file. For example when inserting the correct source
references for visual debugging. With this patch the information on
current block is available in `org-babel-current-exec-src-block-head'.
* lisp/ob-core.el (org-babel-parse-inline-src-block-match),
lisp/ob-exp.el (org-babel-exp-src-block): Give header arguments from
properties priority over default header arguments.
The previous commit e79e8943de did fix this only in
ob-core.el (org-babel-parse-src-block-match). It was already correct
in ob-lob.el (org-babel-lob-execute).
* lisp/ob-core.el (org-babel-inline-result-wrap): Defcustom controlling
the wrapping of inline results.
(org-babel-examplize-region): Use new defcustom controlling the
wrapping of inline results.
* org-agenda.el (org-agenda-write):
* ob-core.el (org-babel-expand-src-block): Use
`org-called-interactively-p'.
Thanks to Jason L Wright for reporting this.
* lisp/ob-core.el (org-babel-execute-src-block): Return nil in case of
`:results none'. Also run `org-babel-after-execute-hook' in this
circumstance.
Previously, the code returned the string "results silenced" in the case
of =:results none=, as this is the return value of the call to
`message'; additionally, the after-execute hook was not being run.
* ob-core.el (org-babel-insert-result): Fix bug when inserting
results as a list: ensure we split a string containing "\n".
Thanks to Sébastien Vauban for reporting this.
* lisp/ob-core.el (org-babel-when-in-src-block): New macro.
(org-babel-execute-src-block-maybe)
(org-babel-expand-src-block-maybe)
(org-babel-load-in-session-maybe, org-babel-pop-to-session-maybe):
Use it.
org-babel-get-src-block-info is a potentially expensive operation, which
is why its ‘light’ argument exists. But in any case, it is overkill to
query the whole info, if all that is needed is whether point is in a
block or not. Factor the simplified common code out into a macro.
* lisp/ob-core.el (org-babel-execute-src-block): Use `copy-tree'
to prevent setf from modifying users variables withing let-bound
`info' variable.
Otherwise, the setf calls in this function can reach into and change
other configuration variables, such as the library of babel.
* lisp/ob-core.el (org-babel-execute-src-block): Make sure we process
file results before they are passed to the post-processing code block,
and not afterwards. Tangles these two header arguments in the code,
but makes for more intuitive behavior and enables important use cases.
* lisp/ob-core.el (org-babel-common-header-args-w-values): Add :post to
the list of header arguments.
(org-babel-execute-src-block): Post process results when the :post
header argument has been supplied.
* doc/org.texi (var): Remove the "Alternate argument syntax" section
from the documentation.
* lisp/ob-core.el (org-babel-src-name-w-name-regexp): Update the regexp
used to match code block names.
(org-babel-get-src-block-info): Remove the code used to parse this
alternate variable specification syntax.
* lisp/ob-core.el (org-babel-temp-file): For remote hosts, modify the prefix
and leave `temporary-file-directory' unchanged.
The reason setting `temporary-file-directory' doesn't work here is
because `make-temp-file' recursively calls itself (indirectly).
Modifying `temporary-file-directly', affects the recursive calls as well,
which results in a "No such file file or directory" error.
The fix is to leave `temporary-file-directory' unaltered, for remote
hosts, and instead modifying the 'prefix' argument to `make-temp-file'
appropriately.
TINYCHANGE
* lisp/ob-core.el (org-babel-confirm-evaluate-answer-no): Dynamically
scoped variable, if bound non-nil the confirmation dialog will not
be initiated and denial of evaluation is assumed.
The new variable `org-babel-confirm-evaluate-answer-no´ can be bound
to suppress the user interaction as is needed for async export, as
discussed in http://thread.gmane.org/gmane.emacs.orgmode/67719
multiple changes to remove overly long lines.
* lisp/ob-core.el (org-babel-execute-src-block): A cond makes it more
clear that we definitely do not execute without user confirmation.
(org-babel-where-is-src-block-result): Overly long line.
* lisp/ob-core.el (org-babel-check-confirm-evaluate): New macro to
establish bindings based on INFO.
* lisp/ob-core.el (org-babel-check-evaluate): New defsubst that checks
if the evaluation of a code block is disabled. Refactors the first
part of the original function `org-babel-confirm-evaluate´.
* lisp/ob-core.el (org-babel-confirm-evaluate): New defsubst that
checks if the user should be queried and returns the answer. Keeps
the second part of the original function `org-babel-confirm-evaluate´.
* lisp/ob-core.el (org-babel-execute-src-block): Do not ask for
confirmation if the cached result is current.
* lisp/ob-core.el (org-babel-confirm-evaluate): Re-implement using
bindings for common subexpressions.
There was a minor bug in the reporting of an aborted evaluation as
"disabled" when no export was happening and eval-no-export was t since
the state of the export was not checked again.
* lisp/ob-core.el (org-babel-call-process-region-original): Change
declaration into definition with nil initial value at the beginning
of the file and drop the later definition. Add comment that the
dynamic scoping of this variable is done for tramp.
Reverting "Fix a typo I introduced while editing Achim's commit 091bf0"
Reverting "ob-core.el: Do not ask for confirmation if cached value is current"
This reverts commit 091bf02514.
* ob-core.el (org-babel-execute-src-block): Do not run
`org-babel-confirm-evaluate´ if source block has a cache and the
cache value is current (there is no evaluation involved in this
case).
* lisp/org.el (org-reverse-string): Add `org-reverse-string' to
reverse a string.
* lisp/org-id.el(org-id-new, org-id-decode): Replace
`org-id-reverse-string' by `org-reverse-string'.
* lisp/ob-core.el(org-babel-trim): Replace `org-babel-reverse-string'
by `org-reverse-string' and declare it.
TINYCHANGE
* add a header-row delimiter to the tables returned from mysql
* add new sql-specific header args for the database connection, and implements them for mysql
* add support for :colnames (mysql only)
* (minor) add an edebug spec to org-babel-result-cond to allow edebugging through it
* add some doc about what header args are used
The syntax of result hashes with times are now as show below.
#+RESULTS[<TIME> HASH]:
* lisp/ob-core.el (org-babel-result-regexp): Simplified regexp given new
time hash layout.
(org-babel-current-result-hash): New match string.
(org-babel-hide-hash): New match string.
(org-babel-where-is-src-block-result): New match string, and inserting
hashes in the new format.
* ob-core.el (org-babel-next-src-block)
(org-babel-previous-src-block): Rewrite using
`org-next-block'.
* org.el (org-next-block, org-previous-block): New navigation
commands.
(org-mode-map): Bind the new commands to C-c C-F and C-c C-B
respectively.
Thanks to Bill White for suggesting this.
* ob-core.el (org-ts-regexp): Remove duplicate defconst'ing.
(org-babel-result-regexp): Don't use `org-ts-regexp', use a
regexp string directly.
This is not the best solution, we should be able to use
`org-ts-regexp' here, but the dependencies makes it hard.
So let's not define org-ts-regexp twice, just use a raw
regexp instead, and add a FIXME warning about this.
suggested by Thomas Alexander Gerds
* lisp/ob-core.el (org-babel-result-regexp): Now matching time stamp as
well.
(org-babel-hash-show-time): Variable controlling the display of time
stamps.
(org-babel-current-result-hash): With hash time stamps.
(org-babel-hide-all-hashes): With hash time stamps.
(org-babel-where-is-src-block-result): With hash time stamps.
* lisp/ob.el: Only use the :wrap argument up to the first space when creating
the #+END_ directive.
Using an option like ":wrap SRC fundamental" was generating and end marker of
"#+END_SRC fundamental", which caused the new exporter to fail to handle to
block properly.
Patch from Michael Gauland.
Nicolas Goaziou
Nicolas Berthier
Aaron Ecay
Bastien Guerry
Eric Schulte
Achim Gratz
Ian Kelling
Michael Weylandt
Nicolas Goaziou
Michael Albinus
Carsten Dominik
Aditya Siram
Vitalie Spinu
Sebastien Vauban
Suhail Shergill
Grégoire Jadi
Gary Oberbrunner
Eric Schulte