2010-08-03 Dan Davison <davison@stats.ox.ac.uk>
* ob-R.el (org-babel-R-evaluate): Specify that tabular data is
tab-delimited
Prior to this we had
#+begin_src R
c("some words", "with spaces")
#+end_src
#+results:
| some | words |
| with | spaces |
2010-08-03 Dan Davison <davison@stats.ox.ac.uk>
* ob-python.el (org-babel-python-table-or-string): Fix
recognition of lists and tuples
Prior to this we had
#+begin_src python
return [1, 2]
#+end_src
#+results:
: [1, 2]
Hi,
I'm starting to work with ob-octave and found several problems:
The first, for which I have a fix (see patch below) is that octave's
output was passed on as a string instead of being interpreted as a table:
[diff removed]
Now this works:
8<------------------------------------------------------------
#+source: test_output
#+begin_src octave :results value vector
[[1 2 3];[4 5 6]]
#+end_src
#+results: test_output
| 1.00000000e+00 | 2.00000000e+00 | 3.00000000e+00 |
| 4.00000000e+00 | 5.00000000e+00 | 6.00000000e+00 |
8<------------------------------------------------------------
(before the patch you'd get a single table element with something like
"1 2 3\n 4 5 6\n" inside).
The second problem is that if I use octave table output as input to
another block, it gets interpreted as a string instead of a vector:
8<------------------------------------------------------------
#+results: test_output
| 1.25000000e+00 |
#+source: check_input
#+begin_src octave :var input=test_output() :results output
ischar( input )
size( input )
#+end_src
#+results: check_input
: input = 1.25000000e+00
: ans = 1
: ans =
: 1 14
8<------------------------------------------------------------
This has to do with the EXP notation. The 'e+00' suffix makes the
whole table into a string. The problem is with "%S" in the formatting
inside org-babel-octave-var-to-octave.
The following patch seems to fix it (and makes it possible to work with
complex numbers inside the tables)::
[diff removed]
A third problem is with org-babel-octave-var-to-octave.
For example:
: (org-babel-octave-var-to-octave '( ( 1 2 3 ) ( 4 5 6 ) ))
: -> "[[1, 2, 3], [4, 5, 6]]"
This is not a 2x3 matrix, but a 1x6 vector:
: octave-3.2.3:1> [[1,2,3],[4,5,6]]
: ans =
: 1 2 3 4 5 6
a semicolon ';' or '\n' is needed between rows instead of a comma.
To sum up:
- 2 patches for prepare-session and importing the results back as
org-tables (I don't know if these patches break anything).
- 1 problem with matrix notation in org-babel-octave-var-to-octave.
I'll try to provide a patch for this today.
2010-08-01 Juan Pechiar <Pechiar@computer.org>
* ob-octave.el (org-babel-octave-evaluate-external-process):
use `org-babel-octave-import-elisp-from-file' instead of
`org-babel-eval-read-file'.
(org-babel-octave-var-to-octave): separate matrix rows with
';', and use '%s' as format specifier instead of '%S'
From: Alexandre Passos <alexandre.tp@gmail.com>
> I was editing an org document on a server earlier today, remotely
> using tramp, and continuously exporting it to html. When I added
> LaTeX, it exported once and then not anymore, failing because it
> couldn't create a directory anymore. So I found out that patching
> org-export-latex to pass a "t" parameter to org-make-directory fixes
> this, and it continues to work perfectly. This is the modified version
> of that function, if anyone else is interested in this constrained
> case. The only change I made was right under the "make sure directory
> exists" comment.
Hello,
>>>>> Neil Hepburn writes:
> The latest version (7.01g) seems to have a bug when exporting to PDF
> (and LaTeX) with tables with labels. The export does not label the
> table in the LaTeX file although it is labeled in the .org file.
Curiously, it looks like \label code was removed at some time.
This quick fix should put labels back.
Regards,
-- Nicolas
>From 64855c52b20766db9898ce82316fac11d51de72d Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <n.goaziou@gmail.com>
Date: Wed, 28 Jul 2010 20:54:40 +0200
Subject: [PATCH] Add labels to tables.
* org-latex.el (org-export-latex-tables): add label if any
* org-latex.el (org-export-latex-convert-table.el-table): fix little
mistake when inserting label
Hello,
Like what is already done with drawers, point should not move when
cycling visibility of headings and list items.
The call to `org-back-to-heading' this patch removes seems redundant
anyways.
Regards,
-- Nicolas
>From 17cd55557d747366c90fad47b44edeac2daf920b Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <n.goaziou@gmail.com>
Date: Sun, 25 Jul 2010 23:14:08 +0200
Subject: [PATCH] Cursor stays at same column when cycling visibility.
* org.el (org-cycle-internal-local): Removed an unnecessary call to
`org-back-to-heading' that was preventing point to stay at its
column when cycling visibility.
The attached patch suppresses a compiler warning in org-gnus.el
* lisp/org-gnus.el:
Suppress compiler warning by declaring outside function
nnimap-retrieve-headers-from-file.
On Sat, Jul 31, 2010 at 12:54 PM, Simon Guest <simon.guest@tesujimath.org>wrote:
> Hi,
>
> I'm making my first real Org mode Beamer presentation, using org-mode
> 7.01g, and trying to set the ignore_heading for a multi-column slide.
>
> In column mode, when I hit 'e' in the Env column, Emacs says:
> Wrong type argument: commandp, org-beamer-set-environment-tag
> (and org-beamer-set-environment-tag does not appear to be defined
> anywhere).
>
> It's triggered from this code in org-colview.el
> ((equal key "BEAMER_env")
> (setq eval '(org-with-point-at pom
> (call-interactively 'org-beamer-set-environment-tag))))
>
> Any idea what's wrong?
>
>
This function was renamed to org-beamer-select-environment and I think it
was not changed here.
The attached patch should solve the problem.
* lisp/org-colview.el
Use org-beamer-select-environment instead
of org-beamer-set-environment-tag
Thanks and Regards
Noorul
Nick Dokos <nicholas.dokos@hp.com> wrote:
> John Hendy <jw.hendy@gmail.com> wrote:
>
> > Just to be sure I created an blank org file with only this:
> >
> > * test
> >
> > #+CAPTION: test table
> > #+ATTR_LaTeX: placement=[H]
> > | 1 | 2 | 3 | 4 |
> > |------+------+------+------|
> > | test | test | test | test |
> > | test | test | test | test |
> >
> > It gets exported to this:
> >
> > \begin{table}[htb]
> > \caption{test table}
> > \begin{center}
> > \begin{tabular}{llll}
> >
> > Did something change between 6.35 and 7.01 or in the LaTeX table options?
> >
>
> I think that placement works fine for figures, but not for tables. In
> fact, I cannot find the code that's supposed to do this for tables: I
> suspect that it never existed. So unless I'm mistaken, it seems that
> tables never got the placement treatment that figures did.
>
Try the following patch (might be wrong in detail, and its scope might
be too limited, but I hope it's not too far off: at least it seems to
work on your simple table.) It may also be white-space damaged, so some
reformatting may be needed after applying it.
Nick
>From 4c8cdde9f3d80edc882efe83562a934fd9a6a8c8 Mon Sep 17 00:00:00 2001
From: Nick Dokos <nicholas.dokos@hp.com>
Date: Fri, 23 Jul 2010 17:54:06 -0400
Subject: [PATCH] Process latex placement attribute for tables.
Figures got placement attributes previously, but tables never did.
David Maus <dmaus@ictsoc.de> writes:
Hi David,
>>I'm trying to add a workaround to org-gnus.el which should save the
>>slowness of querying the IMAP server by looking up the article number
>>in the group's .overview file. But since I don't have nnimap groups,
>>we have to play some question & answer game. ;-)
>
>>Please apply this patch and set
>>`org-gnus-nnimap-query-article-no-from-file' to t.
>
> The patch does not work: It calls `nnimap-retrieve-headers-from-file'
> without the required arguments (group server)
Argh, stupid me! Here's a corrected patch.
--8<---------------cut here---------------start------------->8---
--8<---------------cut here---------------end--------------->8---
> and the headers are not fetched because
> `nnimap-retrieve-headers-from-file' looks for a NOV cache file, not
> .overview.
Aren't overview file and NOV file synonyms?
Hm, anyway. In the Gnus docs I've found this paragraph:
,----[ (info "(gnus)IMAP") ]
| `nnimap-nov-is-evil'
| Never generate or use a local NOV database. Defaults to the value
| of `gnus-agent'.
|
| Using a NOV database usually makes header fetching much faster,
| but it uses the `UID SEARCH UID' command, which is very slow on
| some servers (notably some versions of Courier). Since the Gnus
| Agent caches the information in the NOV database without using the
| slow command, this variable defaults to true if the Agent is in
| use, and false otherwise.
`----
So maybe we're trying to replace one slow command with another slow
command. Especially, the fact that Courier is explicitly mentioned is a
bit frustrating. Well, let's try it out and see if it helps a bit.
> Alas: I couldn't figure out how to enable NOV cache for my nnimap
> group. Setting `nnimap-nov-is-evil' to nil didn't help.
This variable defaults to the value of `gnus-agent', so I assume the
agent has to be enabled (which is default), and most probably the IMAP
server has to be agentized as well. That can be done in the server
buffer (`^' in *Group*), and then:
,----[ (info "(gnus)Server Agent Commands") ]
| `J a'
| Add the current server to the list of servers covered by the Gnus
| Agent (`gnus-agent-add-server').
`----
Bye,
Tassilo
* lisp/org.el (org-insert-time-stamp): Fix org-insert-time-stamp so
that the value of org-last-inserted-timestamp includes time range.
Previously, org-last-inserted-timestamp included only the
beginning of a time range (e.g., 10:00 instead of 10:00-12:00).
This caused parsing problems elsewhere, such as when rescheduling
items with repeating timestamps and a time range (the repeater
was removed during rescheduling).
* org-wl.el (org-wl-store-link-message): Provide link property
for message-id without angle brackets.
The message-id header field can be used to maintain the connection
between an Org entry and an internet message. The angle brackets have
a special meaning when performing a TAGS/PROPS/TODO query (Cf. Org
mode manual 10.3.3). To be able to use the message-id as an entry
property we have to remove the angle brackets to be able to perform a
search for the entry associated with a particular message.
* lisp/ob-tangle.el (org-babel-find-file-noselect-refresh): finds a
file ensuing that the latest changes on disk are represented
(org-babel-with-temp-filebuffer): now only kills the buffer of the
tangled file, and doesn't kill said buffer if the file is already
being visited
* lisp/org-capture.el (org-capture-finalize): Fix clock in of interrupted
task during capture finalize
Calling org-capture-get inside the org-with-point-at macro does not
work when the current clocking task and the capture target buffer are
the same. In this case the captured task would continue clocking
instead of switching back to the previously clocking task.
* lisp/org-agenda.el (org-agenda-filter-preset): Document the limitation
for the filter preset - it can only be used for an entire agenda view,
not in an individual block in a block agenda.
* doc/org.texi (Agenda commands): Document the limitation
for the filter preset - it can only be used for an entire agenda view,
not in an individual block in a block agenda.
* lisp/org-exp.el (org-export-format-source-code-or-example): escape
underscores in code block names on latex listings export
* lisp/org-latex.el (org-export-latex-listings-w-names): make export
of code block names to latex optional
* lisp/org-capture.el (org-capture-target-buffer): Throw an error
if we have no target file.
(org-capture-select-template): Use a default template if the user has
not specified any.
* lisp/ob-lob.el (org-babel-lob-execute): changing indentation to
improve line length
(org-babel-lob-get-info): now catching indexes passed through lob
calls
(org-babel-lob-one-liner-regexp): now matches optional indexes into
variable results
* lisp/org-table.el (org-table-convert-region): don't continue csv
importation which the point catches the end, this fixes an infinite
loop which was caused by the (point) never catching up with the
"end" marker
Hi,
I've just noticed that I get an infinite loop when importing csv tables
into Org-mode tables. For example calling
(org-table-convert-region (point-min) (point-max) '(4))
from inside of a simple text file containing the following
--8<---------------cut here---------------start------------->8---
1,2,3
1
2
3
5
--8<---------------cut here---------------end--------------->8---
results in an infinite loop. The attached patch fixes this issue [1],
however it seems weird that this would just surface now, given that the
code in question has been in the repo since last fall
,----
| commit 59c9c4cdd4
| Author: Carsten Dominik <carsten.dominik@gmail.com>
| Date: Mon Oct 26 12:31:16 2009 +0100
|
| Correctly interpret CVS tables with quoted fields
|
| The csv parser was very primitive, ignoring quoted fields. This is
| now fixed.
`----
Has anyone else noticed this problem? Should I go ahead and apply this
patch?
Best -- Eric
Footnotes:
[1]
>From 3c3f4ca9a34dca23051ca2f4e4518b416338d4f4 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Mon, 19 Jul 2010 13:45:25 -0700
Subject: [PATCH] org-table: fix infinite loop in table importation
* lisp/org-table.el (org-table-convert-region): don't continue csv
importation which the point catches the end, this fixes an infinite
loop which was caused by the (point) never catching up with the
"end" marker
* lisp/org-macs.el (org-string-nw-p): New function.
* lisp/org-capture.el (org-capture-import-remember-templates): Interpret
an empty string as request to use `org-default-notes-file'.
(org-capture-target-buffer): If the FILE is not a (non-empty) string,
use `org-default-notes-file'.
* lisp/org-colview-xemacs.el (org-columns-compile-map):
(org-columns-number-to-string):
(org-columns-string-to-number): Handle estimate ranges.
(org-estimate-mean-and-var): New function.
(org-estimate-combine): New function.
(org-estimate-print): New function.
(org-string-to-estimate): New function.
Carsten,
Here is a patch for a new 'est+' summary type, including corresponding changes for xemacs and the manual. I've done basic testing on the GNU emacs version, but not the xemacs code.
I'm not sure the change to the manual provides the right amount of information
in the right place; I'd be happy to re-write to make it find in
better. Similarly, the name of the summary type is entirely up to you.
I didn't know whether to send this directly to you, or to the list; if it should go to the list I'd be happy to send it there directly.
Thanks for the chance to contribute,
Mike
This is the eighth patch in a series that makes some straightforward
corrections to a number of docstrings. Each change is normally to:
- correct a typo, or
- fix up hyperlinks to function or variable names, or
- ensure slightly better conformance with the documentation guidelines
and tips given in the Elisp manual
* lisp/org-capture.el (org-capture-fill-template): Do inserting file
contents and expanding sexp escapes first, so that further escape
processing can happen in the inserted text.
This was a request by Sebastian Rose.
This is the fifth patch in a series that makes some straightforward
corrections to a number of docstrings. Each change is normally to:
- correct a typo, or
- fix up hyperlinks to function or variable names, or
- ensure slightly better conformance with the documentation guidelines
and tips given in the Elisp manual
No attempt is made to provide missing docstrings or document arguments.
Cheers,
Phil
* lisp/ob-tangle.el (org-babel-with-temp-filebuffer): a macro for
quickly visiting files with cleanup
(org-babel-tangle): now using the locally defined
with-temp-filebuffer macro
Thanks for Nicolas Goaziou for pointing this out
* lisp/ob-exp.el (org-babel-exp-src-blocks): don't attempt to export
blocks when there is no info match -- this fixes a bug in the latex
export of code blocks located before the first headline
* lisp/ob-ocaml.el (org-babel-expand-body:ocaml): now able to
initialize complex ocaml values without error
(org-babel-execute:ocaml): more sophisticated parsing of results,
only grabbing the line immediately preceding the eoe indicator
(org-babel-ocaml-elisp-to-ocaml): a new function for converting
complex elisp values like lists to ocaml syntax
(org-babel-ocaml-read-array): quoting arrays so that they aren't
interpreted as function calls
This is the third patch in a series that makes some straightforward
corrections to a number of docstrings. Each change is normally to:
- correct a typo, or
- fix up hyperlinks to function or variable names, or
- ensure slightly better conformance with the documentation guidelines
and tips given in the Elisp manual
No attempt is made to provide missing docstrings or document arguments.
Cheers,
Phil
This is a second patch in a series that makes some straightforward
corrections to a number of docstrings. Each change is normally to:
- correct a typo, or
- fix up hyperlinks to function or variable names, or
- ensure slightly better conformance with the documentation guidelines
and tips given in the Elisp manual
No attempt is made to provide missing docstrings or document arguments.
Cheers,
Phil
This patch makes some straightforward corrections to a number of
docstrings. Each change is normally to:
- correct a typo, or
- fix up hyperlinks to function or variable names, or
- ensure slightly better conformance with the documentation guidelines
and tips given in the Elisp manual
No attempt is made to provide missing docstrings or document arguments.
Cheers,
Phil
* org-agenda.el (org-search-view): Fixed inclusion of agenda-archives
in org-agenda-text-search-extra-files.
org-search-view lacked a local binding for
org-agenda-text-search-extra-files. Thus when pop was called on the
variable, the agenda-archives symbol was removed and subsequent
searches failed to include the archives.
* lisp/ob-ref.el (org-babel-ref-resolve-reference): removed an error
introduced while fixing compiler warnings -- required mirroring of
the count cl-seqs function under the org-mode namespace.
* lisp/org.el (org-count): adding an org-mode version of the cl-seqs
count function
* lisp/ob-dot.el (org-babel-expand-body:dot): now inserts variable
arguments rather than ignoring them
(org-babel-execute:dot): making use of org-babel-expand-body:dot
Dan Davison
Eric Schulte
Juan Pechiar
Bastien Guerry
Nicolas Goaziou
Noorul Islam
Nick Dokos
Tassilo Horn
Matt Lundin
David Maus
John Wiegley
Bernt Hansen
Jambunathan K
Carsten Dominik
Eric S Fraga
Michael Gauland
Philip Rooke
Gregory J. Grubbs
Julien Barnier