[O] bug#25132: 26.0.50; emacs hangs when loading org file with python source blocks

2016-12-07 Thread David Dynerman
Dear Glenn + bug-gnu-emacs,

Did you try the steps to reproduce? Indeed Clément was right! The bug also 
reliably reproduces also with org 8.2.10, if you additionally set 
org-src-fontify-natively to t.

Please let me know if you need any more information for the bug report,
David

Clément Pit--Claudel  writes:

> On 2016-12-07 21:08, Glenn Morris wrote:
>> David Dynerman wrote:
>>> The bug does NOT occur with org 8.2.10.
>> 
>> Since that's the version included with Emacs, I'm confused as to why
>> you've been encouraged to report this to bug-gnu-emacs.
>
> I can reproduce the issue in emacs -Q on master; hence my suggestion to 
> report it here.  Glenn, can you try running the following after downloading 
> the attached file?
>
>emacs -Q --eval '(setq debug-on-signal t org-src-fontify-natively t)' 
> test.org 
>
> It hangs reproducibly for me.  No idea why the OP can't reproduce it (David, 
> are you sure it doesn't occur with org 8.2.10? Could it be that 
> org-src-fontify-natively isn't enabled by default in 8.2.10?)
>
> Clément.





Re: [O] org-depend: dependencies between TODO entries in different files

2016-12-07 Thread Carsten Dominik
Hi,

I can take a look at that.  Unless Nicolas already is working on it, of
course.

One additional point is, of course, that org-depend is not part of the
core, but was written as a proof of concept.  Is anyone besides Karl using
it regularly?  I don't want to break anything by changing it.  Maybe it
would, in fact, be better to first look in the local file and then try
org-id-find.

Carsten

On Thu, Aug 25, 2016 at 5:11 PM, Karl Voit  wrote:

> * Nicolas Goaziou  wrote:
> > Hello,
>
> Hello Nicolas,
>
> > Karl Voit  writes:
> >
> >> Function org-depend-block-todo uses org-find-entry-with-id (from
> >> org.el) which is using org-find-property which starts with
> >> (goto-char (point-min)) not jumping to any other org-mode buffer.
> >>
> >> Is there a reason behind this design choice?
> >
> > What design choice?
>
> ... that org-depend is using the current document only.
>
> > 1. That `org-find-property' only searches in the current document?
> >
> > 2. That `org-depend-block-todo' uses `org-find-entry-with-id' instead of
> >e.g., `org-id-find'?
> >
> > Property API assumes properties are local to the document. When you
> > search for property "FOO", it means "FOO" in the current buffer, not
> > "FOO" is some other random Org file somewhere in your hard-disk.
>
> Ah, good to know.
>
> Is there a document, where someone is able to learn those
> "meta-patterns" like "Property API assumes properties are local to
> the document"?
>
> > ID property is special for that matter.
>
> Clearly, when you take a look at "id:example-id".
>
> > Whenever Org sets such a property, it updates a location database
> > (which means ID properties shouldn't be changed "manually").
>
> Being curious: since I only set IDs manually (by typing them into
> the PROPERTIES drawer by myself), do I have to take care of
> "updating some database"?
>
> > So, ID property can efficiently be used to refer to remote
> > documents.
>
> ... which I find ultimately useful to get a "personal wiki".
>
> > As a consequence, it may be useful to use `org-id-find' and
> > fall-back to `org-find-property' in `org-depend-block-todo'.
> >
> >> Who is the current maintainer of org-depend.el? Carsten ist
> >> listed as author in the header.
> >
> > I guess nobody. Do you want to take care of it?
>
> Trust me: with my very limited knowledge of Elisp and Org-mode
> internals, you do not want to see a commit from my side that is
> something other than a typo fix or documentation. ;-)
>
> Can you do us the favour?
>
> Thanks for your insight!
>
> --
> mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML to Org-mode:
>> get Memacs from https://github.com/novoid/Memacs <
>
> https://github.com/novoid/extract_pdf_annotations_to_orgmode + more on
> github
>
>
>


[O] [PATCH] ox-confluence.el: Add support for ordered list

2016-12-07 Thread Lungang Fang
Hi there,

This is a patch for contrib/lisp/ox-confluence.el generated following
instructions on http://orgmode.org/worg/org-contribute.html#patches . It
adds support for ordered list.

-- 
Lungang Fang


* contrib/lisp/ox-confluence.el (org-confluence-item): Support ordered
list

When converting a bullet item, examine the type of it and convert
accordingly.

TINYCHANGE
---
 contrib/lisp/ox-confluence.el | 9 ++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/contrib/lisp/ox-confluence.el b/contrib/lisp/ox-confluence.el
index 5de9e0f..de8b00e 100644
--- a/contrib/lisp/ox-confluence.el
+++ b/contrib/lisp/ox-confluence.el
@@ -81,9 +81,12 @@
   (format "_%s_" contents))

 (defun org-confluence-item (item contents info)
-  (concat (make-string (1+ (org-confluence--li-depth item)) ?\-)
-  " "
-  (org-trim contents)))
+  (let* ((plain-list (org-export-get-parent item))
+ (type (org-element-property :type plain-list))
+ (bullet (if (eq type `ordered) ?\# ?\-)))
+(concat (make-string (1+ (org-confluence--li-depth item)) bullet)
+" "
+(org-trim contents

 (defun org-confluence-fixed-width (fixed-width contents info)
   (format "\{\{%s\}\}" contents))
-- 
2.9.3 (Apple Git-75)


[O] Fwd: [PATCH] Add support for ordered list to ox-confluence.el

2016-12-07 Thread Lungang Fang
Resend since the previous one seems lost.


Hi there,

Attached is a patch for contrib/lisp/ox-confluence.el generated following
instructions on http://orgmode.org/worg/org-contribute.html#patches . It
adds support for ordered list.

I didn't find where I should send this patch. Hopefully, this is the
correct email list for patch request. If it is not, could anyone please
tell me the correct way to submit a patch request to org-mode?

Regards,
-- 
Lungang Fang




-- 
Lungang Fang
Sydney, NSW 2153, Australia
M: +61 431 208 979 | E: lungang.f...@gmail.com


0001-ox-confluence.el-Add-support-for-ordered-list.patch
Description: Binary data


Re: [O] Include sections of org document in tangled files

2016-12-07 Thread Charles C. Berry

On Wed, 7 Dec 2016, David Dynerman wrote:


Dear Chuck,

Your suggestion worked fantastically - I got it working and am very excited.

Now, the next step is figuring out how to handle typesetting math in single way 
between org and python docstrings. Math in Python docstrings is usually done by 
RestructuredText markdown, e.g.:

:math:`f(x) = x^2`

while the org code should just be, for example,

\[
f(x) = x^2
\]



So the goal would be have noweb not only include a documentation block 
in the python code, but also call a translation function that identifies 
LaTeX fragments in the org source and converts them to ReST markdown.




This is do-able.

First, look at

(info "(org) Noweb reference syntax")

and note that the noweb reference

<>

will call `my-src-block' with the `x' var set to "value_for_x" and insert 
the output into the current src block.


Second, https://github.com/masayuko/ox-rst has a reStructuredText backend. 
So, you can install ox-rst.el, then write an emacs-lisp src block:



#+NAME: export-body
#+BEGIN_SRC emacs-lisp :var src-block-name="my-code" :results raw
  (save-excursion
(org-babel-goto-named-src-block
 src-block-name)
(org-export-string-as
 (org-babel-expand-src-block)
 'rst t))
#+END_SRC

and then a src-block like this

#+BEGIN_SRC emacs-lisp :noweb yes :tangle yes
<>
#+END_SRC

will insert the rst formatted text from the `my-code' src block when the 
latter src block is tangled.


p.s. Untested with 'rst.

HTH,

Chuck





[O] bug#25132: 26.0.50; emacs hangs when loading org file with python source blocks

2016-12-07 Thread Clément Pit--Claudel
On 2016-12-07 21:08, Glenn Morris wrote:
> David Dynerman wrote:
>> The bug does NOT occur with org 8.2.10.
> 
> Since that's the version included with Emacs, I'm confused as to why
> you've been encouraged to report this to bug-gnu-emacs.

I can reproduce the issue in emacs -Q on master; hence my suggestion to report 
it here.  Glenn, can you try running the following after downloading the 
attached file?

   emacs -Q --eval '(setq debug-on-signal t org-src-fontify-natively t)' 
test.org 

It hangs reproducibly for me.  No idea why the OP can't reproduce it (David, 
are you sure it doesn't occur with org 8.2.10? Could it be that 
org-src-fontify-natively isn't enabled by default in 8.2.10?)

Clément.


test.org
Description: Lotus Organizer


signature.asc
Description: OpenPGP digital signature


[O] bug#25132: 26.0.50; emacs hangs when loading org file with python source blocks

2016-12-07 Thread Glenn Morris
David Dynerman wrote:

> The bug does NOT occur with org 8.2.10.

Since that's the version included with Emacs, I'm confused as to why
you've been encouraged to report this to bug-gnu-emacs.





[O] writing letters using the latex letters class?

2016-12-07 Thread Stig Brautaset


I've tried to get a simple letter to export to PDF using the latex 
letters
class, but I can't get it to work in any satisfactory way. I want 
to get

something like the following generated:

,
| \documentclass{letter}
| \signature{Sender McSenderface}
| 
| \address{My address \\ My town \\ My country}
| 
| \begin{document}
| \begin{letter}{Recipient name \\ Recipient address \\ Recipient 
 country}
| 
| \opening{Dear Sir or Madam:}
| 
| Aliquam erat volutpat. Nunc eleifend leo vitae magna. In id erat 
 non orci
| commodo lobortis. Proin neque massa, cursus ut, gravida ut, 
 lobortis eget,

| lacus. Sed diam.
| 
| \closing{Yours Sincerely,}
| 
| \end{letter}

| \end{document}
`

I was hoping I could generate that from (something like) the 
following org

document:

,
| #+latex_class: letter
| #+signature: Sender McSenderface
| #+address: My address \\ My town \\ My country
| #+recipient: Recipient name \\ Recipient address \\ Recipient 
  country

| #+opening: Dear Sir or Madam
| #+closing: Yours Sincerely,
| 
| Aliquam erat volutpat. Nunc eleifend leo vitae magna. In id erat 
 non orci
| commodo lobortis. Proin neque massa, cursus ut, gravida ut, 
 lobortis eget,

| lacus. Sed diam.
`

Is this a pipe dream? I tried mucking about with 
org-latex-classes, and got as

far as this:

,
| (add-to-list 'org-latex-classes
|  '("letter"
|"\\documentclass{letter}
| \\usepackage{hyperref}
|[NO-DEFAULT-PACKAGES]
|[NO-PACKAGES]"
|("\\section{%s}" . "\\section*{%s}")
|("\\subsection{%s}" . "\\subsection*{%s}")
|("\\subsubsection{%s}" . "\\subsubsection*{%s}")
|("\\paragraph{%s}" . "\\paragraph*{%s}")
|("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
`

That at least got me past the "Unknow LaTeX class 'letter'" error, 
but it
doesn't produce a nice letter. I only get my lorem ipsum text. I 
can't figure
out how to get the \begin{letter}{...} stuff inside the 
\begin{document} part
automatically, nor how to inject text from #+recipient: into the 
second block

of the \begin{letter}{...} macro.

Any help appreciated.

Stig



Re: [O] buffer local org-src-preserve-indentation not respected

2016-12-07 Thread David Dynerman
Dear Nicolas,

Nicolas Goaziou  writes:

> Fixed. Thank you.

Thank you very much.

I just tried, and I still encounter this buf on the current git code. 
Reproduction is the same as before:

#+BEGIN_SRC python :tangle preserve-indent.py
class Foo:
bar = 5
#+END_SRC

Here is some interstitial text!

#+BEGIN_SRC python :tangle preserve-indent.py
def __init__(self):
self.bar = 7
#+END_SRC

If I globally set org-src-preserve-indentation to t, then tangle, the output 
file has the correct specified indentation with the second block. If I make 
org-src-preserve-indentation buffer local and set it to t, then the second 
block is tanlged without any leading indentation.

Perhaps the tangling code doesn't see the buffer local setting of 
org-src-preserve-indentation from the buffer being tangled?

Thank you very much for all your hard work,
David




Re: [O] Include sections of org document in tangled files

2016-12-07 Thread David Dynerman
Dear Chuck,

Your suggestion worked fantastically - I got it working and am very excited.

Now, the next step is figuring out how to handle typesetting math in single way 
between org and python docstrings. Math in Python docstrings is usually done by 
RestructuredText markdown, e.g.:

:math:`f(x) = x^2`

while the org code should just be, for example,

\[
f(x) = x^2
\]

So the goal would be have noweb not only include a documentation block in the 
python code, but also call a translation function that identifies LaTeX 
fragments in the org source and converts them to ReST markdown.

That's a separate project though, for now your suggestion is really cool!

Thanks a lot,
David

"Charles C. Berry"  writes:

> #+NAME: doc
> #+BEGIN_SRC org :exports results :results replace
>This is an introduction. We're going to write some code that
>implements (a finite version of) the formula
>
>\[
>f(x) = 1 + x + \frac{x^2}{2} + \frac{x^3}{6} + \ldots +
>\frac{x^n}{n!} + \ldots
>\]
>
>Here's some background about the exponential function.
>
> #+END_SRC
>
> #+header: :noweb (unless org-export-current-backend "yes")
> #+BEGIN_SRC python :tangle myfunction.py
>from math import factorial
>
>def f(x,n):
>"""
><>
>"""
>
>y = 0
>for i in range(n+1):
>y = y + x**i/factorial(i)
>
>return y
> #+END_SRC
>
>
>> The idea would be that when I export this to HTML, I get a nice literate
>> programming math jax'd section introduction that explains what the
>> function is doing.
>
> Right. The above does that.
>
> You need `org' as a babel language. Eval'ing `(require 'ob-org)' is good 
> enough for just trying to export this, but customizing 
> `org-babel-load-languages' to include `org' is better if you use this 
> regularly.
>
>
>> Then, when I tangle to generate the python file, the
>> org section introduction would be included as the python docstring of
>> the function.
>>
>
> And it does that.
>
> ---
>
> There is an issue you might want to address if you use this approach. 
> First, the first triple quotes must not be on the same line as the 
> included src block reference. That is because """>""" will 
> prepend the quotes to every line in `src-blk-ref'.
>
> If you do not want the newlines between the quotes and the docstring, I 
> think there is a post-tangle hook you can use to clean the tangled version 
> by removing those newlines.
>
> Also, you can use an export filter to remove the quotes and the noweb 
> reference for a cleaner looking exported doc.
>
> Note that you need to use a unique name for each src-block.
>
> HTH,
>



Re: [O] question about org-coderef-label-format and HTML export

2016-12-07 Thread Nicolas Goaziou
Hello,

D M German  writes:

> I think I found a bug. It works in some cases but not in others:
>
> the following code properly defines the references abc and bfc. But it
> does not define the one for (ref:jump). Here is a link to the exported
> HTML file:
>
> http://turingmachine.org/~dmg/temp/ref-test.html
> http://turingmachine.org/~dmg/temp/ref-test.org
>
> #+BEGIN_SRC C++ -r -l "//(ref:%s)" +n :main no :results output :exports both 
> #include 
> int main()
> { //(ref:abc)
>std::cout << "Hello world" << std::endl;
>std::cout << "Hello world 2" << std::endl;
>//(ref:jump)
>return 0; //(ref:bcf)
> }
> #+END_SRC

Fixed. Thank you.

Regards,

-- 
Nicolas Goaziou



Re: [O] [PATCH] org-bibtex.el: Make headline format costomizable

2016-12-07 Thread Eric Danan
Here it is, hope I did everything correctly.


* lisp/org-bibtex.el (org-bibtex-write): Make this function read the
  headline format from the newly created variable
  `org-bibtex-headline-format-function' instead of systematically using
  the entry title.  (org-bibtex-headline-foramt-function): Create this
  variable to hold a function of one argument, the entry alist, and
  return the string to be inserted as headline.  The default value
  replicates the current behavior of returning the entry title.

TINYCHANGE
---
 etc/ORG-NEWS   |  2 ++
 lisp/org-bibtex.el | 14 +-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/etc/ORG-NEWS b/etc/ORG-NEWS
index 78f28cbe..056443ac 100644
--- a/etc/ORG-NEWS
+++ b/etc/ORG-NEWS
@@ -84,6 +84,8 @@ Where clue > 0

 *** Horizontal rules are no longer ignored in LaTeX table math mode

+*** Org-Bibtex
+ New variable : ~org-bibtex-headline-format-function~
 ** Removed options

 *** ~org-agenda-repeating-timestamp-show-all~ is removed.
diff --git a/lisp/org-bibtex.el b/lisp/org-bibtex.el
index db5d97b3..3dabc68f 100644
--- a/lisp/org-bibtex.el
+++ b/lisp/org-bibtex.el
@@ -237,6 +237,18 @@ (defcustom org-bibtex-treat-headline-as-title t
   :version "24.1"
   :type 'boolean)

+(defcustom org-bibtex-headline-format-function
+  (lambda (entry)
+(cdr (assq :title entry)))
+  "Function returning the headline text for `org-bibtex-write'.
+It should take a single argument, the bibtex entry (an alist as
+returned by `org-bibtex-read').  The default value simply returns
+the entry title."
+  :group 'org-bibtex
+  :version "25.1"
+  :package-version '(Org . "9.1")
+  :type 'function)
+
 (defcustom org-bibtex-export-arbitrary-fields nil
   "When converting to bibtex allow fields not defined in `org-bibtex-fields'.
 This only has effect if `org-bibtex-prefix' is defined, so as to
@@ -678,7 +690,7 @@ (defun org-bibtex-write ()
  (val (lambda (field) (cdr (assoc field entry
  (togtag (lambda (tag) (org-toggle-tag tag 'on
 (org-insert-heading)
-(insert (funcall val :title))
+(insert (funcall org-bibtex-headline-format-function entry))
 (org-bibtex-put "TITLE" (funcall val :title))
 (org-bibtex-put org-bibtex-type-property-name
 (downcase (funcall val :type)))
-- 
2.8.3

On Sat, Dec 3, 2016 at 8:59 AM, Nicolas Goaziou  wrote:
> Hello,
>
> Eric Danan  writes:
>
>> When adding an org-bibtex entry with `org-bibtex-write' (or any
>> command relying on it), the headline is the title. The patch below
>> simply makes the headline customizable through a new variable.
>
> Thank you.
>
>> If you find it worth to incorporate this into org-bibtex I should
>> probably add a dosctring for the new variable
>
> Yes, please. Also, an entry in ORG-NEWS is welcome.
>
>> `org-bibtex-headline-format' and I would also have a few questions:
>> 1. Should I name this variable differently?
>
> Indeed. It should indicate it represents a function:
> `org-bibltex-headline-format-function' is better, IMO, since a "format"
> could be a format string.
>
>> 2. Should I use `defcustom' instead of `defvar'?
>
> Correct. Mind the :version and :package-version keywords.
>
>> 3. Should I move the `defvar' / `defcustom' at the beginning of the file?
>
> Yes.
>
>> 4. In the default value of the variable should I make use of the `val'
>> function that is let-bound inside `org-bibtex-write'?
>
> I think the default value is fine. Another option is to create a new
> `org-bibtex-headline-default' function and bound the variable to that.
>
>> +(defvar org-bibtex-headline-format
>> +  (lambda (entry)
>> +(cdr (assoc :title entry
>
> Nitpick
>
>   `assoc' -> `assq'
>
> Regards,
>
> --
> Nicolas Goaziou



[O] bug#19606: 24.4; Emacs hangs when editing a 5-line Org file

2016-12-07 Thread Glenn Morris
Eli Zaretskii wrote:

> Yes, thanks.  Unfortunately, it doesn't say more than the previous
> backtrace: Emacs is displaying some display string with invisible
> property.  Why that would lead to an infloop, I don't see.
>
> My suggestion at this point would be to ask on the Org list whether
> your Org-related setup that triggers this (somehow related to flyspell
> mode) might be the problem.  It could be that the infloop is actually
> on the Lisp level in some code that is part of Org or your
> customizations.
>
> Failing that, I suggest to try to present a minimal reproduction
> recipe and post it here.

Closing after 2 years with no further progress.





Re: [O] Emacs hangs while loading org file with python blocks

2016-12-07 Thread David Dynerman
Dear Alan & Clément,

Thanks for trying to reproduce - it's good to know it's not only happening to 
me.

I've just sent the bug report upstream to bug-gnu-emacs.

David

Alan Schmitt  writes:

> Hello David,
>
> On 2016-12-06 17:41, David Dynerman  writes:
>
>> I've now managed to extract a minimal org file that reproduces the hang:
>
> I can confirm it hangs emacs: it even hanged gnus as it was trying to
> display your email.
>
> Best,
>
> Alan
>
> -- 
> OpenPGP Key ID : 040D0A3B4ED2E5C7
> Monthly Athmospheric CO₂, Mauna Loa Obs. 2016-10: 401.57, 2015-10: 398.29



Re: [O] Time-Event-Diagrams

2016-12-07 Thread Eric S Fraga
On Tuesday,  6 Dec 2016 at 17:54, Karl Voit wrote:

[...]

> Since you just mentioned invoking org-plot/gnuplot, I guess there
> should be any result somewhere somehow which did not work at my
> side.
>
> I could not locate any file or directory /tmp/org-plot11956t0A.

By default, the table plotting shows the plot in a window.  If you want
to save the plot to a file, add something along the lines of

  file:"myplot.png"

to the #+PLOT line.

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 26.0.50.1, Org release_9.0.1-99-gd65aa3


signature.asc
Description: PGP signature


Re: [O] org-ref file path to pdf

2016-12-07 Thread Georg W. Otto
John Kitchin  writes:

> This doesn't sound like something that should be happening I think. How
> current is your org-ref?
>
> I do not use the notes feature so it does not get tested too often. You
> may be able to control the format of the notes created with the variable
> org-ref-note-title-format if you are using the default notes function
> that adds a headline. 
>
>

my org ref version was 20160503 from elpa. I updated it to 20161129 and
here the part of org-ref-open-bibtex-notes that inserts a link to the
pdf is commented out. However I like this functionality, so I keep the
older version of org-ref-open-bibtex-notes in my init file.

Sorry about asking about a functionality that has been removed, but I
still do not understand why it it does expand my ~/dir to
/home/user/dir.

My org-ref-open-bibtex-notes is set to adaptive.

It might happen here, but I do not understand elisp enough to tell:

(setq pdf (-first 'f-file?
  (--map (f-join it (concat key ".pdf"))
 (-flatten (list org-ref-pdf-directory)

(if (file-exists-p pdf)
(insert (format
 " [[file:%s][pdf]]\n\n"
 pdf)))


Cheers,

Georg

-- 
Georg Otto
The UCL Institute of Child Health




Re: [O] org-ref file path to pdf

2016-12-07 Thread John Kitchin
This doesn't sound like something that should be happening I think. How
current is your org-ref?

I do not use the notes feature so it does not get tested too often. You
may be able to control the format of the notes created with the variable
org-ref-note-title-format if you are using the default notes function
that adds a headline. 


Georg W. Otto writes:

> Dear all,
>
>
> This is probably something that has come up before, but so far I haven't
> found a solution:
>
> My problem concerns automatic file path expansion in my org-ref
> setting. According to the instructions in
>
> https://github.com/jkitchin/org-ref
> and
> https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_my_orgmode_workflow_for_notetaking/
>
> I set up the paths to my bibliography, my notes and my pdfs like this:
>
> (setq org-ref-bibliography-notes "~/Dropbox/bibliography/notes.org"
>   org-ref-default-bibliography '("~/Dropbox/bibliography/references.bib")
>   org-ref-pdf-directory "~/Dropbox/bibliography/bibtex-pdfs/")
>
>
> Navigation to a bibtex entry and running org-ref-open-bibtex-notes
> creates an orgmode heading in notes.org that contains a link to the pdf
> file of the publication. Unfortunately, that link uses an expanded file
> path, i.e:
> /home//Dropbox/bibliography/bibtex-pdfs/BibtexKey.pdf
>
> so it is useless when generated by a different user. Would it be
> possible to create a link that does not expand the file path, like this
>
> ~/Dropbox/bibliography/bibtex-pdfs/BibtexKey.pdf
>
> I appreciate your help.
>
> Georg


-- 
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu



Re: [O] Emacs hangs while loading org file with python blocks

2016-12-07 Thread Alan Schmitt
Hello David,

On 2016-12-06 17:41, David Dynerman  writes:

> I've now managed to extract a minimal org file that reproduces the hang:

I can confirm it hangs emacs: it even hanged gnus as it was trying to
display your email.

Best,

Alan

-- 
OpenPGP Key ID : 040D0A3B4ED2E5C7
Monthly Athmospheric CO₂, Mauna Loa Obs. 2016-10: 401.57, 2015-10: 398.29


signature.asc
Description: PGP signature


Re: [O] tangling and COMMENT entries

2016-12-07 Thread Alan Schmitt
On 2016-12-07 00:27, Nicolas Goaziou  writes:

> Hello,
>
> Alan Schmitt  writes:
>
>> When using org-babel-load-file, are entries with a COMMENT keyword
>> supposed to be tangled?
>
> I don't think so. Could you provide an ECM?

As I could not get an ECM, I tried deleting the generated .el files and
restarted emacs. They were then correctly generated, without the
COMMENTed sections. I'm going to try to understand how this could have
happened in the first place, but I cannot reproduce it right now. So
everything is working as expected.

Thanks,

Alan

-- 
OpenPGP Key ID : 040D0A3B4ED2E5C7
Monthly Athmospheric CO₂, Mauna Loa Obs. 2016-10: 401.57, 2015-10: 398.29


signature.asc
Description: PGP signature


Re: [O] Latex export fails for plain lists deeper than four, works for html

2016-12-07 Thread Nicolas Goaziou
Hello,

Scott Otterson  writes:

> Hi Nicolas, thanks for trying to replicate this on Linux.  What happens for
> you if it doesn't crash?  Does the latex export just work and produce a pdf
> with a set of properly nested lists?

It produces a pdf with improperly nested lists (deeper levers are just
treated as level 4).

> Would you be willing to sent me .tex your latex export produces?  It seems
> unlikely, but maybe org use a different/additional latex library on Linux
> than it does in Windows.  Or alternatively, TexLive installs different/more
> libraries on Windows.  Anyway, it would be nice to figure it out.

Here it is.

Regards,

-- 
Nicolas Goaziou
% Created 2016-12-07 Wed 12:24
% Intended LaTeX compiler: pdflatex
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\author{Nicolas Goaziou}
\date{\today}
\title{}
\hypersetup{
 pdfauthor={Nicolas Goaziou},
 pdftitle={},
 pdfkeywords={},
 pdfsubject={},
 pdfcreator={Emacs 25.1.1 (Org mode 9.0.1)}, 
 pdflang={English}}
\begin{document}

\tableofcontents

\begin{enumerate}
\item level 1.1
\begin{enumerate}
\item level 2.1
\begin{enumerate}
\item level 3.1
\begin{enumerate}
\item level 4.1
\begin{enumerate}
\item level 5.1 (works if this level is deleted)
\item level 5.2 (works if this level is deleted)
\end{enumerate}
\item level 4.2
\end{enumerate}
\item level 3.2
\end{enumerate}
\item level 2.2
\end{enumerate}
\item level 1.2
\end{enumerate}
\end{document}


Re: [O] Multiple underscores crash org latex export; other exporters survive

2016-12-07 Thread Nicolas Goaziou
Hello,

Scott Randby  writes:

> On 12/06/2016 06:50 PM, Nicolas Goaziou wrote:
>> I fixed it in maint. Basically, a_b_c is translated as a\(_b\)\(_c\).
>
> With this solution, "a" will be exported as text while "b" and "c" will
> be exported as a single subsrcipt using the math font.

Not at all. I simplified the output for clarity but the real generated
code is

  a\(_{\text{b}}\)\(_{\text{c}}\)

> I would prefer that a_b_c be translated as \(a_{b_{c}}\).

As you pointed out, the string is ambiguous anyway. The point of the fix
is to generate valid LaTeX code. You can obtain the above unambiguously
with

  a_{b_c}

Regards,

-- 
Nicolas Goaziou



Re: [O] tangling and COMMENT entries

2016-12-07 Thread Rainer M Krug
Alan Schmitt  writes:

> Hello,
>
> When using org-babel-load-file, are entries with a COMMENT keyword
> supposed to be tangled? I thought they were not, but I'm seeing them in
> the generated .el file.

I am using COMMETNS all the time to exclude blocks from tangling in my
emacs.org - and it works.


,
| Org mode version 9.0 (release_9.0-60-g047451 @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
`

Cheers,

Rainer

>
> Thanks,
>
> Alan

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


signature.asc
Description: PGP signature


Re: [O] question about org-coderef-label-format and HTML export

2016-12-07 Thread D M German
 Nicolas Goaziou twisted the bytes to say:


 Nicolas> Hello,
 Nicolas> dmg  writes:

 >> I was playing with org-coderef-label-format to reference lines of code
 >> in blocks.
 >> 
 >> I created a small example that overrides the default value:
 >> 
 >> #+BEGIN_SRC C++ :main no :flags -std=c++14 -Wall --pedantic -Werror
 >> :results output :exports both -r -l "//(ref:%s)" +n

 Nicolas> Switches are to be located before Babel parameters:

  #+begin_src C++ -r -l "//(ref:%s)" +n :main no ..

Thank you, Nicolas, I appreciate your response. It almost works now.

I think I found a bug. It works in some cases but not in others:

the following code properly defines the references abc and bfc. But it
does not define the one for (ref:jump). Here is a link to the exported
HTML file:

http://turingmachine.org/~dmg/temp/ref-test.html
http://turingmachine.org/~dmg/temp/ref-test.org

#+BEGIN_SRC C++ -r -l "//(ref:%s)" +n :main no :results output :exports both 
#include 
int main()
{ //(ref:abc)
   std::cout << "Hello world" << std::endl;
   std::cout << "Hello world 2" << std::endl;
   //(ref:jump)
   return 0; //(ref:bcf)
}
#+END_SRC


 Nicolas> Regards,

thank you again,

--daniel


 Nicolas> -- 
 Nicolas> Nicolas Goaziou

--
Daniel M. German  "Computer Science is no more
   about computers than astronomy
   Edsger Dijkstra  -> is about telescopes"
http://turingmachine.org/
http://silvernegative.com/
dmg (at) uvic (dot) ca
replace (at) with @ and (dot) with .