[odt] equation labels

[odt] equation labels

[Myles English]

Hello {Jambunathan},

I have found that Equations become labelled as Figures in the version I
am using:

emacs 23.3.1
org-mode from git commit 71f1c1be (Oct 26)

(?I'm not sure if it is the most recent version of contrib/org-odt as
the README.org says "This release is is as good as org-20110613" etc)

The test equations in latex-mathml.org in this message:

http://lists.gnu.org/archive/html/emacs-orgmode/2011-09/msg00198.html

are labelled as "Equation" in the odt files but when I export it fresh I get
"Figure".

Thank you for the recent MathML stuff by the way.

Myles

Re: [odt] equation labels

[Jambunathan K]

Myles English <mylesenglish@gmail.com> writes:

> Hello {Jambunathan},
>
> I have found that Equations become labelled as Figures in the version I
> am using:
>
> emacs 23.3.1
> org-mode from git commit 71f1c1be (Oct 26)
> The test equations in latex-mathml.org in this message:
>
> http://lists.gnu.org/archive/html/emacs-orgmode/2011-09/msg00198.html
>
> are labelled as "Equation" in the odt files but when I export it fresh I get
> "Figure".

This was a regression. I pushed a fix few moments ago. Could you please
pull again?

> (?I'm not sure if it is the most recent version of contrib/org-odt as
> the README.org says "This release is is as good as org-20110613" etc)

I have not updated README.org for a while and please ignore whatever it
claims.  You are using the right version of odt. So no worries.

> Thank you for the recent MathML stuff by the way.
>
> Myles
>
>

-- 

Re: [odt] equation labels

[Myles English]

>> On Mon, 31 Oct 2011 03:41:18 +0530, Jambunathan K said:

  > Myles English <mylesenglish@gmail.com> writes:
  >> I have found that Equations become labelled as Figures in the
  >> version I am using:
  >> 
  >> emacs 23.3.1 org-mode from git commit 71f1c1be (Oct 26) The test
  >> equations in latex-mathml.org in this message:
  >> 
  >> http://lists.gnu.org/archive/html/emacs-orgmode/2011-09/msg00198.html
  >> 
  >> are labelled as "Equation" in the odt files but when I export it
  >> fresh I get "Figure".

  > This was a regression. I pushed a fix few moments ago. Could you
  > please pull again?

Thanks for the push, there are three things I notice now:

1) my document won't open and causes libreoffice to crash! I get:
   "terminate called after throwing an instance of
     what():  vector::_M_default_append" on the command line

2) the first equation in latex-mathml.org is not numbered, I would
   expect this if it was using a begin{equation*} environment but not a
   begin{equation}.

3) the second equation looks a bit like this:

   x=root(b)               (1)
   Radicals

   but I would have expected something like:

   x=root(b)
   Equation 1.: Radicals

Is there a new variable that I need to set to get (e.g.) "Equation 1."?

Just to be explicit, the test file latex-mathml.org I am referring to
contains:

#+TITLE:     latex-mathml.org
#+AUTHOR:    Jambunathan K
#+EMAIL:     address@hidden
#+DATE:      2011-09-09 Fri
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE:  en
#+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc

#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport
#+LINK_UP:   
#+LINK_HOME: 
#+XSLT:

* LaTeX Fragments

** LaTeX Fragment1
#   See org-format-latex-options

    There is a equation down below.

   \begin{equation}
     e = \frac{1}{2}mv^2
   \end{equation}

** LaTeX Fragment2

#+CAPTION: Radicals
#+LABEL: Equation:1
   \begin{equation}
   x=\sqrt{b}
   \end{equation}

   If $a^2=b$ and \( b=2 \), then the solution must be either $$
   a=+\sqrt{2} $$ or \[ a=-\sqrt{2} \].


Myles

Re: [odt] equation labels

[Myles English]

>> On Mon, 31 Oct 2011 11:54:35 +0000, Myles English said:

>> On Mon, 31 Oct 2011 03:41:18 +0530, Jambunathan K said:

  >> Myles English <mylesenglish@gmail.com> writes:
  >>> I have found that Equations become labelled as Figures in the
  >>> version I am using:
  >>> 
  >>> emacs 23.3.1 org-mode from git commit 71f1c1be (Oct 26) The test
  >>> equations in latex-mathml.org in this message:
  >>> 
  >>> http://lists.gnu.org/archive/html/emacs-orgmode/2011-09/msg00198.html
  >>> 
  >>> are labelled as "Equation" in the odt files but when I export it
  >>> fresh I get "Figure".

  >> This was a regression. I pushed a fix few moments ago. Could you
  >> please pull again?

  > Thanks for the push, there are three things I notice now:

  > 1) my document won't open and causes libreoffice to crash! I get:
  > "terminate called after throwing an instance of what():
  > vector::_M_default_append" on the command line

  > 2) the first equation in latex-mathml.org is not numbered, I would
  > expect this if it was using a begin{equation*} environment but not a
  > begin{equation}.

  > 3) the second equation looks a bit like this:

  >    x=root(b) (1) Radicals

  >    but I would have expected something like:

  >    x=root(b) Equation 1.: Radicals

Alright, points 2 and 3 are cleared up by me understanding that the
asterisk in \begin{equation*} has no visible effect, and that instead of
having "Equation 1.:" in the caption below the formula, there is a "(1)"
on the RHS.

Point 1 is entirely my own problem.

Myles

Re: [odt] equation labels

[Jambunathan K]

Myles

(I have read the followup post to this set of questions)

Myles English <mylesenglish@gmail.com> writes:
>>> On Mon, 31 Oct 2011 03:41:18 +0530, Jambunathan K said:
>
>   > Myles English <mylesenglish@gmail.com> writes:
>   >> I have found that Equations become labelled as Figures in the
>   >> version I am using:
>   >> 
>   >> emacs 23.3.1 org-mode from git commit 71f1c1be (Oct 26) The test
>   >> equations in latex-mathml.org in this message:
>   >> 
>   >> http://lists.gnu.org/archive/html/emacs-orgmode/2011-09/msg00198.html
>   >> 
>   >> are labelled as "Equation" in the odt files but when I export it
>   >> fresh I get "Figure".
>
>   > This was a regression. I pushed a fix few moments ago. Could you
>   > please pull again?
>
> Thanks for the push, there are three things I notice now:
>
> 1) my document won't open and causes libreoffice to crash! I get:
>    "terminate called after throwing an instance of
>      what():  vector::_M_default_append" on the command line

1. You are using custom styles for your latex fragment
2. latex-to-mathml converter - as it stands today - assumes the latex
   fragment is completed in and of itself and doesn't honor the style
   settings.

Putting 1 and 2 together, I am assuming that the XML created by the ODT
emitter contains garbage which is causing LibreOffice to be confused. In
my observation, ill-formed XML triggers "file is corrupt and should I
repair the file?" from LibreOffice. A crash seems strange to me.

1. http://article.gmane.org/gmane.emacs.orgmode/48714
   - Above link has my note on -ncf option to mathtoweb

2. http://orgmode.org/worg/org-faq.html
   - Above link has a note on how to debug corrupt odt files.
     (Hint: search for corrupt)

> 2) the first equation in latex-mathml.org is not numbered, I would
>    expect this if it was using a begin{equation*} environment but not a
>    begin{equation}.

Currently the odt exporter doesn't peek in to the latex fragment and
infer what manner of equation it is. This is something that I could take
up ...

,----
| (defvar org-latex-regexps
|   '(("begin" "^[ \t]*\\(\\\\begin{\\([a-zA-Z0-9\\*]+\\)[^\000]+?\\\\end{\\2}\\)" 1 t)
|     ;; ("$" "\\([ 	(]\\|^\\)\\(\\(\\([$]\\)\\([^ 	\r\n,.$].*?\\(\n.*?\\)\\{0,5\\}[^ 	\r\n,.$]\\)\\4\\)\\)\\([ 	.,?;:'\")]\\|$\\)" 2 nil)
|     ;; \000 in the following regex is needed for org-inside-LaTeX-fragment-p
|     ("$1" "\\([^$]\\|^\\)\\(\\$[^ 	\r\n,;.$]\\$\\)\\([- 	.,?;:'\")\000]\\|$\\)" 2 nil)
|     ("$" "\\([^$]\\|^\\)\\(\\(\\$\\([^ 	\r\n,;.$][^$\n\r]*?\\(\n[^$\n\r]*?\\)\\{0,2\\}[^ 	\r\n,.$]\\)\\$\\)\\)\\([- 	.,?;:'\")\000]\\|$\\)" 2 nil)
|     ("\\(" "\\\\([^\000]*?\\\\)" 0 nil)
|     ("\\[" "\\\\\\[[^\000]*?\\\\\\]" 0 nil)
|     ("$$" "\\$\\$[^\000]*?\\$\\$" 0 nil))
|   "Regular expressions for matching embedded LaTeX.")
`----


> 3) the second equation looks a bit like this:
>
>    x=root(b)               (1)
>    Radicals
>
>    but I would have expected something like:
>
>    x=root(b)
>    Equation 1.: Radicals
>
> Is there a new variable that I need to set to get (e.g.) "Equation
> 1."?

Being a non-latex user, I am not familiar with what the usual practice
is. If the latter option is how captioned equations are normally typeset
I can take it up. Can you confirm that the expectations above are *not*
your own but that of *any* user?

> Just to be explicit, the test file latex-mathml.org I am referring to
> contains:
>
> #+TITLE:     latex-mathml.org
> #+AUTHOR:    Jambunathan K
> #+EMAIL:     address@hidden
> #+DATE:      2011-09-09 Fri
> #+DESCRIPTION:
> #+KEYWORDS:
> #+LANGUAGE:  en
> #+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
> #+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
>
> #+EXPORT_SELECT_TAGS: export
> #+EXPORT_EXCLUDE_TAGS: noexport
> #+LINK_UP:   
> #+LINK_HOME: 
> #+XSLT:
>
> * LaTeX Fragments
>
> ** LaTeX Fragment1
> #   See org-format-latex-options
>
>     There is a equation down below.
>
>    \begin{equation}
>      e = \frac{1}{2}mv^2
>    \end{equation}
>
> ** LaTeX Fragment2
>
> #+CAPTION: Radicals
> #+LABEL: Equation:1
>    \begin{equation}
>    x=\sqrt{b}
>    \end{equation}
>
>    If $a^2=b$ and \( b=2 \), then the solution must be either $$
>    a=+\sqrt{2} $$ or \[ a=-\sqrt{2} \].
>
>
> Myles
>
>

-- 

Re: [odt] equation labels

[Jambunathan K]

>> 2) the first equation in latex-mathml.org is not numbered, I would
>>    expect this if it was using a begin{equation*} environment but not a
>>    begin{equation}.
>
> Currently the odt exporter doesn't peek in to the latex fragment and
> infer what manner of equation it is. This is something that I could take
> up ...

As thing stand today, to produce a numbered equation just attach
#+LABEL: to it. This is how odt exporter determines when a formula is
numbered or not.
-- 

Re: [odt] equation labels

[Myles English]

Jambunathan,

>> On Wed, 02 Nov 2011 01:09:41 +0530, Jambunathan K said:

  > Myles

  > (I have read the followup post to this set of questions)

  > Myles English <mylesenglish@gmail.com> writes:
  >>>> On Mon, 31 Oct 2011 03:41:18 +0530, Jambunathan K said:
  >> 
  >> > Myles English <mylesenglish@gmail.com> writes: >> I have found
  >> that Equations become labelled as Figures in the >> version I am
  >> using:
  >> >> 
  >> >> emacs 23.3.1 org-mode from git commit 71f1c1be (Oct 26) The test
  >> >> equations in latex-mathml.org in this message:
  >> >> 
  >> >>
  >> http://lists.gnu.org/archive/html/emacs-orgmode/2011-09/msg00198.html
  >> >> 
  >> >> are labelled as "Equation" in the odt files but when I export it
  >> >> fresh I get "Figure".
  >> 
  >> > This was a regression. I pushed a fix few moments ago. Could you
  >> > please pull again?
  >> 
  >> Thanks for the push, there are three things I notice now:
  >> 
  >> 1) my document won't open and causes libreoffice to crash! I get:
  >> "terminate called after throwing an instance of what():
  >> vector::_M_default_append" on the command line

  > 1. You are using custom styles for your latex fragment
  > 2. latex-to-mathml converter - as it stands today - assumes the
  > latex fragment is completed in and of itself and doesn't honor the
  > style settings.

  > Putting 1 and 2 together, I am assuming that the XML created by the
  > ODT emitter contains garbage which is causing LibreOffice to be
  > confused. In my observation, ill-formed XML triggers "file is
  > corrupt and should I repair the file?" from LibreOffice. A crash
  > seems strange to me.

There is (git from a couple of days ago) a problem with referring to
equations containing an underscore in the label, I am fairly sure it was
allowed before, e.g.:

--8<---------------cut here---------------start------------->8---
#+LABEL: Equation:new_eq
     \begin{equation}
     x=\sqrt{b}
     \end{equation}

Referring to an equation with an underscore: \ref{Equation:new_eq}
--8<---------------cut here---------------end--------------->8---

I get a libreoffice popup:

"Read Error. Format error discovered in the file in sub-document
content.xmlat 2236,92(row,col)."

I think it was many of these errors that caused the crash.

  > 1. http://article.gmane.org/gmane.emacs.orgmode/48714 - Above link
  > has my note on -ncf option to mathtoweb

  > 2. http://orgmode.org/worg/org-faq.html - Above link has a note on
  > how to debug corrupt odt files.  (Hint: search for corrupt)

  >> 2) the first equation in latex-mathml.org is not numbered, I would
  >> expect this if it was using a begin{equation*} environment but not
  >> a begin{equation}.

  > Currently the odt exporter doesn't peek in to the latex fragment and
  > infer what manner of equation it is. This is something that I could
  > take up ...

  > ,---- | (defvar org-latex-regexps | '(("begin" "^[
  > \t]*\\(\\\\begin{\\([a-zA-Z0-9\\*]+\\)[^\000]+?\\\\end{\\2}\\)" 1 t)
  > | ;; ("$" "\\([ (]\\|^\\)\\(\\(\\([$]\\)\\([^
  > \r\n,.$].*?\\(\n.*?\\)\\{0,5\\}[^ \r\n,.$]\\)\\4\\)\\)\\([
  > .,?;:'\")]\\|$\\)" 2 nil) | ;; \000 in the following regex is needed
  > for org-inside-LaTeX-fragment-p | ("$1" "\\([^$]\\|^\\)\\(\\$[^
  > \r\n,;.$]\\$\\)\\([- .,?;:'\")\000]\\|$\\)" 2 nil) | ("$"
  > "\\([^$]\\|^\\)\\(\\(\\$\\([^
  > \r\n,;.$][^$\n\r]*?\\(\n[^$\n\r]*?\\)\\{0,2\\}[^
  > \r\n,.$]\\)\\$\\)\\)\\([- .,?;:'\")\000]\\|$\\)" 2 nil) | ("\\("
  > "\\\\([^\000]*?\\\\)" 0 nil) | ("\\[" "\\\\\\[[^\000]*?\\\\\\]" 0
  > nil) | ("$$" "\\$\\$[^\000]*?\\$\\$" 0 nil)) | "Regular expressions
  > for matching embedded LaTeX.")  `----

Crikey!  That's quite a regexp.  I think the only consideration is
whether you want it to be consistent with pdf export.  Taking
consistency to an extreme could lead to a new #+begin_equation block
(<-- I haven't thought this through at all).  Having said that I am
happy with the way it works at the moment.

  >> 3) the second equation looks a bit like this:
  >> 
  >> x=root(b) (1) Radicals
  >> 
  >> but I would have expected something like:
  >> 
  >> x=root(b) Equation 1.: Radicals
  >> 
  >> Is there a new variable that I need to set to get (e.g.) "Equation
  >> 1."?

  > Being a non-latex user, I am not familiar with what the usual
  > practice is. If the latter option is how captioned equations are
  > normally typeset I can take it up. Can you confirm that the
  > expectations above are *not* your own but that of *any* user?

Actually I have changed my mind, it does look better like that, it is
just that is was different behaviour to what happened before.

Myles

Re: [odt] equation labels

[Nick Dokos]

Myles English <mylesenglish@gmail.com> wrote:

> 
> There is (git from a couple of days ago) a problem with referring to
> equations containing an underscore in the label, I am fairly sure it was
> allowed before, e.g.:
> 
> #+LABEL: Equation:new_eq
>      \begin{equation}
>      x=\sqrt{b}
>      \end{equation}
> 
> Referring to an equation with an underscore: \ref{Equation:new_eq}
> 
> I get a libreoffice popup:
> 
> "Read Error. Format error discovered in the file in sub-document
> content.xmlat 2236,92(row,col)."
> 

I can reproduce that and it may be a consequence of a change that
I introduced at the top level export engine about six months ago.
Let me take a look.

Nick

Re: [odt] equation labels

[Myles English]

Nick,

>> On Wed, 02 Nov 2011 09:38:20 -0400, Nick Dokos said:

  > Myles English <mylesenglish@gmail.com> wrote:
  >> 
  >> There is (git from a couple of days ago) a problem with referring
  >> to equations containing an underscore in the label, I am fairly
  >> sure it was allowed before, e.g.:
  >> 
  >> #+LABEL: Equation:new_eq \begin{equation} x=\sqrt{b} \end{equation}
  >> 
  >> Referring to an equation with an underscore: \ref{Equation:new_eq}
  >> 
  >> I get a libreoffice popup:
  >> 
  >> "Read Error. Format error discovered in the file in sub-document
  >> content.xmlat 2236,92(row,col)."
  >> 

  > I can reproduce that and it may be a consequence of a change that I
  > introduced at the top level export engine about six months ago.  Let
  > me take a look.

  > Nick

I may be mistaken but I think it became broken more recently, circa 7th
Oct.

Myles

Re: [odt] equation labels

[Nick Dokos]

Myles English <mylesenglish@gmail.com> wrote:

> 
> Nick,
> 
> >> On Wed, 02 Nov 2011 09:38:20 -0400, Nick Dokos said:
> 
>   > Myles English <mylesenglish@gmail.com> wrote:
>   >> 
>   >> There is (git from a couple of days ago) a problem with referring
>   >> to equations containing an underscore in the label, I am fairly
>   >> sure it was allowed before, e.g.:
>   >> 
>   >> #+LABEL: Equation:new_eq \begin{equation} x=\sqrt{b} \end{equation}
>   >> 
>   >> Referring to an equation with an underscore: \ref{Equation:new_eq}
>   >> 
>   >> I get a libreoffice popup:
>   >> 
>   >> "Read Error. Format error discovered in the file in sub-document
>   >> content.xmlat 2236,92(row,col)."
>   >> 
> 
>   > I can reproduce that and it may be a consequence of a change that I
>   > introduced at the top level export engine about six months ago.  Let
>   > me take a look.
> 
>   > Nick
> 
> I may be mistaken but I think it became broken more recently, circa 7th
> Oct.
> 

OK - phew (although I may not be out of the woods yet). It seems that the
underscore in the link is interpreted as a subscript:

,----
| ...
| Referring to an equation with an underscore: <text:sequence-ref text:ref-name="Equation:new<text:span text:style-name="OrgSubscript">eq</text:span>"/>
`----

Thanks,
Nick

Re: [odt] equation labels

[Jambunathan K]

>>   >> There is (git from a couple of days ago) a problem with referring
>>   >> to equations containing an underscore in the label, I am fairly
>>   >> sure it was allowed before, e.g.:
>>   >> 
>>   >> #+LABEL: Equation:new_eq \begin{equation} x=\sqrt{b} \end{equation}
>>   >> 
>>   >> Referring to an equation with an underscore: \ref{Equation:new_eq}
>>   >> 
>>   >> I get a libreoffice popup:
>>   >> 
>>   >> "Read Error. Format error discovered in the file in sub-document
>>   >> content.xmlat 2236,92(row,col)."
>>   >> 
> OK - phew (although I may not be out of the woods yet). It seems that the
> underscore in the link is interpreted as a subscript:
>
> ,----
> | ...
> | Referring to an equation with an underscore: <text:sequence-ref
> | text:ref-name="Equation:new<text:span
> | text:style-name="OrgSubscript">eq</text:span>"/>
> `----

Nick, Thanks for debugging this and isolating the root cause.
Myles, I have pushed a fix few minutes ago. Hope things are OK now.

-- 

Re: [odt] equation labels

[Myles English]

>> On Wed, 02 Nov 2011 23:51:31 +0530, Jambunathan K said:

>>   >> There is (git from a couple of days ago) a problem with referring
>>   >> to equations containing an underscore in the label, I am fairly
>>   >> sure it was allowed before, e.g.:
>>   >> 
>>   >> #+LABEL: Equation:new_eq \begin{equation} x=\sqrt{b} \end{equation}
>>   >> 
>>   >> Referring to an equation with an underscore: \ref{Equation:new_eq}
>>   >> 
>>   >> I get a libreoffice popup:
>>   >> 
>>   >> "Read Error. Format error discovered in the file in sub-document
>>   >> content.xmlat 2236,92(row,col)."
>>   >> 
  >> OK - phew (although I may not be out of the woods yet). It seems
  >> that the underscore in the link is interpreted as a subscript:
  >> 
  >> ,---- | ...  | Referring to an equation with an underscore:
  >> <text:sequence-ref | text:ref-name="Equation:new<text:span |
  >> text:style-name="OrgSubscript">eq</text:span>"/> `----

  > Nick, Thanks for debugging this and isolating the root cause.
  > Myles, I have pushed a fix few minutes ago. Hope things are OK now.

References work fine now, Thanks.

Myles

session with python-mode.el complains of void py-toggle-shells

[Myles English]

Hi,

I think it should be possible to execute a python block in a session
using python-mode.el but get this message:

"Symbol's function definition is void: py-toggle-shells"

Using the latest git head and opening this file with:

$ emacs -Q thisfile.org

then executing these src blocks in order, shows the problem:

#+BEGIN_SRC emacs-lisp
  (require 'org)
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((python . t)))
#+END_SRC

#+RESULTS:
| (python . t) |

* A heading

This works okay:

#+begin_src python :results output :session a
import sys
#+end_src

#+RESULTS:

Try with python3:

#+begin_src elisp
(setq org-babel-python-command "python3"
      py-python-command "python3"
)
#+end_src

#+RESULTS:
: python3

works also:

#+begin_src python :results output :session a
import sys
#+end_src

#+RESULTS:

Try using python-mode.el:

#+begin_src elisp
(setq org-babel-python-mode 'python-mode)
(load-file "/usr/share/emacs/site-lisp/python-mode.el")
#+end_src

#+RESULTS:
: t

#+begin_src python :results output :session a
import sys
#+end_src

Gives this *Message*:

org-babel-python-initiate-session-by-key: Symbol's function definition
is void: py-toggle-shells

Do I need to configure something else?

Thanks,

Myles

Re: session with python-mode.el complains of void py-toggle-shells

[Nick Dokos]

Myles English <mylesenglish@gmail.com> wrote:

> Hi,
> 
> I think it should be possible to execute a python block in a session
> using python-mode.el but get this message:
> 
> "Symbol's function definition is void: py-toggle-shells"
> 
> Using the latest git head and opening this file with:
> 
> $ emacs -Q thisfile.org
> 
> then executing these src blocks in order, shows the problem:
> 
> #+BEGIN_SRC emacs-lisp
>   (require 'org)
>   (org-babel-do-load-languages
>    'org-babel-load-languages
>    '((python . t)))
> #+END_SRC
> 
> #+RESULTS:
> | (python . t) |
> 
> * A heading
> 
> This works okay:
> 
> #+begin_src python :results output :session a
> import sys
> #+end_src
> 
> #+RESULTS:
> 
> Try with python3:
> 
> #+begin_src elisp
> (setq org-babel-python-command "python3"
>       py-python-command "python3"
> )
> #+end_src
> 
> #+RESULTS:
> : python3
> 
> works also:
> 
> #+begin_src python :results output :session a
> import sys
> #+end_src
> 
> #+RESULTS:
> 
> Try using python-mode.el:
> 
> #+begin_src elisp
> (setq org-babel-python-mode 'python-mode)
> (load-file "/usr/share/emacs/site-lisp/python-mode.el")
> #+end_src
> 
> #+RESULTS:
> : t
> 
> #+begin_src python :results output :session a
> import sys
> #+end_src
> 
> Gives this *Message*:
> 
> org-babel-python-initiate-session-by-key: Symbol's function definition
> is void: py-toggle-shells
> 
> Do I need to configure something else?
> 

I get in trouble much sooner than you do: when evaluating the first code
block.  The error in my case was that run-python was called with the
wrong number of args (from the same function: it's a couple of lines
before py-toggle-shells is called). I'm running

GNU Emacs 24.3.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.24.4) of 2012-12-29

and run-python does indeed need a required arg in this version:

,----
| run-python is an interactive autoloaded compiled Lisp function in
| `python.el'.
| 
| (run-python CMD &optional DEDICATED SHOW)
| 
| Run an inferior Python process.
| Input and output via buffer named after
| `python-shell-buffer-name'.  If there is a process already
| running in that buffer, just switch to it.
`----

So I changed the call to


 	(run-python py-python-command)

and then all the code blocks could execute with no problem. Has
run-python changed signature recently?

This may or may not be the problem you are running into however.

Nick

Re: [PATCH] session with python-mode.el complains of void py-toggle-shells

[Myles English]

Hi Nick,

Nick Dokos writes:

> Myles English <mylesenglish@gmail.com> wrote:

>> I think it should be possible to execute a python block in a session
>> using python-mode.el but get this message:
>> 
>> "Symbol's function definition is void: py-toggle-shells"

I have made a bit of progress with the patch below.  The breakage may
have been due to changes in python-mode.el .  The patch works for
versions 6.0.10 and 6.1.0.

> I get in trouble much sooner than you do: when evaluating the first code
> block.  The error in my case was that run-python was called with the
> wrong number of args (from the same function: it's a couple of lines
> before py-toggle-shells is called). I'm running
>
> GNU Emacs 24.3.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.24.4) of 2012-12-29
>
> and run-python does indeed need a required arg in this version:
>
> ,----
> | run-python is an interactive autoloaded compiled Lisp function in
> | `python.el'.
> | 
> | (run-python CMD &optional DEDICATED SHOW)
> | 
> | Run an inferior Python process.
> | Input and output via buffer named after
> | `python-shell-buffer-name'.  If there is a process already
> | running in that buffer, just switch to it.
> `----
>
> So I changed the call to
>
>
>  	(run-python py-python-command)
>
> and then all the code blocks could execute with no problem. Has
> run-python changed signature recently?

Doing git blame ob-python.el shows that not much has changed in that
file over the last couple of years.

> This may or may not be the problem you are running into however.

I have made some progress and the patch below passes this test:

#+BEGIN_SRC emacs-lisp
(add-to-list 'load-path
	     "~/.emacs.d/plugins/org-mode/lisp")
  (require 'org)
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((python . t)))
(setq org-babel-python-mode 'python-mode)
#+END_SRC

#+begin_src python :results output :session a
import sys
#+end_src

#+begin_src python :results output :session a
print(sys.path)
#+end_src

Patch:

--- lisp/ob-python.el
+++ lisp/ob-python.el
@@ -32,7 +32,7 @@
 
 (declare-function org-remove-indentation "org" )
 (declare-function py-shell "ext:python-mode" (&optional argprompt))
-(declare-function py-toggle-shells "ext:python-mode" (arg))
+(declare-function py-toggle-shell "ext:python-mode" (arg))
 (declare-function run-python "ext:python" (&optional cmd noshow new))
 
 (defvar org-babel-tangle-lang-exts)
@@ -162,16 +162,17 @@ then create.  Return the initialized session."
        ;; Make sure that py-which-bufname is initialized, as otherwise
        ;; it will be overwritten the first time a Python buffer is
        ;; created.
-       (py-toggle-shells py-default-interpreter)
+       (py-toggle-shell py-default-interpreter)
        ;; `py-shell' creates a buffer whose name is the value of
        ;; `py-which-bufname' with '*'s at the beginning and end
        (let* ((bufname (if (and python-buffer (buffer-live-p python-buffer))
                            (replace-regexp-in-string ;; zap surrounding *
                             "^\\*\\([^*]+\\)\\*$" "\\1" python-buffer)
                          (concat "Python-" (symbol-name session))))
-              (py-which-bufname bufname))
-         (py-shell)
-         (setq python-buffer (concat "*" bufname "*"))))
+              (py-buffer-name bufname))
+         (setq python-buffer (concat "*" bufname "*"))
+         (py-shell nil nil nil nil nil python-buffer)
+         ))
        (t
        (error "No function available for running an inferior Python")))
       (setq org-babel-python-buffers



Myles

Re: session with python-mode.el complains of void py-toggle-shells

[Bastien]

Nick Dokos <nicholas.dokos@hp.com> writes:

>  	(run-python py-python-command)
>
> and then all the code blocks could execute with no problem. Has
> run-python changed signature recently?

Yes, from Emacs 24.1 to Emacs 24.2.

I fixed this, thanks.

-- 
 Bastien

Re: [PATCH] session with python-mode.el complains of void py-toggle-shells

[Bastien]

Hi Myles,

thanks for digging into this.  

I'm copying Andreas as the maintainer of python-mode.el.

Myles English <mylesenglish@gmail.com> writes:

> --- lisp/ob-python.el
> +++ lisp/ob-python.el
> @@ -32,7 +32,7 @@
>  
>  (declare-function org-remove-indentation "org" )
>  (declare-function py-shell "ext:python-mode" (&optional argprompt))
> -(declare-function py-toggle-shells "ext:python-mode" (arg))
> +(declare-function py-toggle-shell "ext:python-mode" (arg))

If this function's name changed, there should be an alias in
python-mode.el.

>  (declare-function run-python "ext:python" (&optional cmd noshow new))
>  
>  (defvar org-babel-tangle-lang-exts)
> @@ -162,16 +162,17 @@ then create.  Return the initialized session."
>         ;; Make sure that py-which-bufname is initialized, as otherwise
>         ;; it will be overwritten the first time a Python buffer is
>         ;; created.
> -       (py-toggle-shells py-default-interpreter)
> +       (py-toggle-shell py-default-interpreter)
>         ;; `py-shell' creates a buffer whose name is the value of
>         ;; `py-which-bufname' with '*'s at the beginning and end
>         (let* ((bufname (if (and python-buffer (buffer-live-p python-buffer))
>                             (replace-regexp-in-string ;; zap surrounding *
>                              "^\\*\\([^*]+\\)\\*$" "\\1" python-buffer)
>                           (concat "Python-" (symbol-name session))))
> -              (py-which-bufname bufname))
> -         (py-shell)
> -         (setq python-buffer (concat "*" bufname "*"))))
> +              (py-buffer-name bufname))
> +         (setq python-buffer (concat "*" bufname "*"))
> +         (py-shell nil nil nil nil nil python-buffer)
> +         ))

The docstring of py-shell doesn't say much about why python-buffer
would be needed as an argument here.  Is it so?

If yes, we need to make this compatible with previous versions of 
python-mode.el.  

(The argument PY-BUFFER-NAME is not documented in latest
python-mode.el)

Andreas, can you help sorting this out?

Thanks,

-- 
 Bastien

Re: [PATCH] session with python-mode.el complains of void py-toggle-shells

[Andreas Röhler]

Am 23.01.2013 14:04, schrieb Bastien:
> Hi Myles,
>
> thanks for digging into this.
>
> I'm copying Andreas as the maintainer of python-mode.el.
>
> Myles English <mylesenglish@gmail.com> writes:
>
>> --- lisp/ob-python.el
>> +++ lisp/ob-python.el
>> @@ -32,7 +32,7 @@
>>
>>   (declare-function org-remove-indentation "org" )
>>   (declare-function py-shell "ext:python-mode" (&optional argprompt))
>> -(declare-function py-toggle-shells "ext:python-mode" (arg))
>> +(declare-function py-toggle-shell "ext:python-mode" (arg))
>

Hi Bastien,

> If this function's name changed, there should be an alias in
> python-mode.el.
>

right

>>   (declare-function run-python "ext:python" (&optional cmd noshow new))
>>
>>   (defvar org-babel-tangle-lang-exts)
>> @@ -162,16 +162,17 @@ then create.  Return the initialized session."
>>          ;; Make sure that py-which-bufname is initialized, as otherwise
>>          ;; it will be overwritten the first time a Python buffer is
>>          ;; created.
>> -       (py-toggle-shells py-default-interpreter)
>> +       (py-toggle-shell py-default-interpreter)
>>          ;; `py-shell' creates a buffer whose name is the value of
>>          ;; `py-which-bufname' with '*'s at the beginning and end
>>          (let* ((bufname (if (and python-buffer (buffer-live-p python-buffer))
>>                              (replace-regexp-in-string ;; zap surrounding *
>>                               "^\\*\\([^*]+\\)\\*$" "\\1" python-buffer)
>>                            (concat "Python-" (symbol-name session))))
>> -              (py-which-bufname bufname))
>> -         (py-shell)
>> -         (setq python-buffer (concat "*" bufname "*"))))
>> +              (py-buffer-name bufname))
>> +         (setq python-buffer (concat "*" bufname "*"))
>> +         (py-shell nil nil nil nil nil python-buffer)
>> +         ))
>
> The docstring of py-shell doesn't say much about why python-buffer
> would be needed as an argument here.  Is it so?
>
> If yes, we need to make this compatible with previous versions of
> python-mode.el.
>
> (The argument PY-BUFFER-NAME is not documented in latest
> python-mode.el)
>
> Andreas, can you help sorting this out?
>
> Thanks,
>

Okay, I'll dig into.

For the moment: assume this code should not be needed, python-mode.el should act that all.
But let me have a closer look,

Cheers,

Andreas

Re: [PATCH] session with python-mode.el complains of void py-toggle-shells

[Bastien]

Hi Andreas,

Andreas Röhler <andreas.roehler@online.de> writes:

> Okay, I'll dig into.
>
> For the moment: assume this code should not be needed,
> python-mode.el should act that all.  But let me have a closer look,

Great, thanks a lot!

-- 
 Bastien

Re: [PATCH] session with python-mode.el complains of void py-toggle-shells

[Andreas Röhler]

[-- Attachment #1: Type: text/plain, Size: 384 bytes --]

Am 24.01.2013 15:10, schrieb Bastien:
> Hi Andreas,
>
> Andreas Röhler <andreas.roehler@online.de> writes:
>
>> Okay, I'll dig into.
>>
>> For the moment: assume this code should not be needed,
>> python-mode.el should act that all.  But let me have a closer look,
>
> Great, thanks a lot!
>

So let's start with this...

BTW, being deeply impressed by org-mode and babel in special.

[-- Attachment #2: ob-python.el.diff --]
[-- Type: text/x-patch, Size: 994 bytes --]

commit e7a5839b5a10d0a27e26b8f1d16296f4c20a1350
Author: Andreas Roehler <andreas.roehler@online.de>
Date:   Thu Feb 21 20:46:49 2013 +0100

    Depend default python-mode from existing feature
    
    The former
    
    (if (featurep 'xemacs) 'python-mode 'python)
    
    makes a wrong assumption, as python-mode.el provides 'python-mode
    which does not depend from use of XEmacs
    
    A next step should enable users to choose environment via defcustom

diff --git a/lisp/ob-python.el b/lisp/ob-python.el
index 02d762c..1b3b892 100644
--- a/lisp/ob-python.el
+++ b/lisp/ob-python.el
@@ -43,7 +43,7 @@
 (defvar org-babel-python-command "python"
   "Name of the command for executing Python code.")
 
-(defvar org-babel-python-mode (if (featurep 'xemacs) 'python-mode 'python)
+(defvar org-babel-python-mode (if (featurep 'python-mode) 'python-mode 'python)
   "Preferred python mode for use in running python interactively.
 This will typically be either 'python or 'python-mode.")
 

Re: [PATCH] session with python-mode.el complains of void py-toggle-shells

[Andreas Röhler]

[-- Attachment #1: Type: text/plain, Size: 353 bytes --]

Am 24.01.2013 15:10, schrieb Bastien:
> Hi Andreas,
>
> Andreas Röhler <andreas.roehler@online.de> writes:
>
>> Okay, I'll dig into.
>>
>> For the moment: assume this code should not be needed,
>> python-mode.el should act that all.  But let me have a closer look,
>
> Great, thanks a lot!
>

ob-python.el patch again

better provision for XEmacs users

[-- Attachment #2: ob-python.el.diff --]
[-- Type: text/x-patch, Size: 1039 bytes --]

commit 0fd2ac7ede3d7c8602a0a71fe1dc1678773baee4
Author: Andreas Roehler <andreas.roehler@online.de>
Date:   Fri Feb 22 09:08:28 2013 +0100

    Depend default python-mode from existing feature
    
    The former
    
    (if (featurep 'xemacs) 'python-mode 'python)
    
    makes a wrong assumption, as python-mode.el provides 'python-mode
    which does not depend from use of XEmacs
    
    python-mode.el should provide a defcustom still to choose environment
    
    TINYCHANGE

diff --git a/lisp/ob-python.el b/lisp/ob-python.el
index 02d762c..c9118e9 100644
--- a/lisp/ob-python.el
+++ b/lisp/ob-python.el
@@ -43,7 +43,7 @@
 (defvar org-babel-python-command "python"
   "Name of the command for executing Python code.")
 
-(defvar org-babel-python-mode (if (featurep 'xemacs) 'python-mode 'python)
+(defvar org-babel-python-mode (if (or (featurep 'python-mode)(featurep 'xemacs)) 'python-mode 'python)
   "Preferred python mode for use in running python interactively.
 This will typically be either 'python or 'python-mode.")
 

Re: [PATCH] session with python-mode.el complains of void py-toggle-shells

[Bastien]

Hi Andreas,

Andreas Röhler <andreas.roehler@easy-emacs.de> writes:

> ob-python.el patch again

I applied a more complete patch, turning `org-babel-python-command'
and `org-babel-python-mode' into defcustoms.

`org-babel-python-mode' will not default to 'python-mode until
'python-mode is featured, so users will typically want to set
this variable, exposing it as a defcustom is useful IMO.

Thanks for the patch!

-- 
 Bastien