From mantegazza at ill.fr  Tue Dec  1 02:29:45 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Tue, 1 Dec 2015 08:29:45 +0100
Subject: [IPython-dev] Embedded shell setup
Message-ID: <20151201082945.505d84b7@ill.fr>

Hi!

In 2003, we started to develop an application to drive a big instrument
(a neutron spectrometer), in a french research institute. Since 2004, this
application runs 24h a day, almost all days.

It is entirely written in python, and is heavily based on Pyro for
clients/servers communication, and, of course IPython, for user
interaction.

With these 2 great pieces of code, we have build a very strong tool.
Fernando helped us a lot to customize IPython, and integrate it in our
code. Thanks again for all your help, Fernando!

Even if our app. evolved during all these years, it is still based on
softwares versions of the early 2k (debian lenny, IPython 0.7.2, Pyro
3.7) :o/

It is time to do a major upgrade! That's why we need some help...

Here is what we are doing when we instanciate what we call the
'console' (client part of our app.); we already adapted it to IPython 2.3,
but there are still things which does not work (loading 'pymad' profile),
and surely thing which could be better (hooks, custom completer...).

We would really appreciate feedback!

Thanks,

----------------------------------------------------------------

config = IPython.config.loader.Config()
promptManager = config.PromptManager
promptManager.in_template = "{color.LightRed}PyMAD>>> "
promptManager.out_template = ' '
# profile is not loaded does not work!
config.profile = "pymad"
startMsg = "\nWelcome to PyMAD"
startMsg += "\n\nAvailable objects: %s " % sortedProxies
startMsg += "\n\nAvailable helpers: %s\n" % helpers.keys()
exitMsg = "\nBye!\n"

# Instanciate embedded ipython instance
ipshell = InteractiveShellEmbed(config,
                                banner1=startMsg,
                                exit_msg=exitMsg)

ipshell.set_custom_exc((Exception, ), pymadHandler)
ipshell.set_custom_completer(proxy_matches)
ipshell.set_custom_completer(python_function_parameters)

# Is there a better way to customize Completer?
ipshell.Completer._default_arguments = \
    new.instancemethod(_default_arguments,
                       ipshell.Completer,
                       ipshell.Completer.__class__)
ipshell.Completer.merge_completions = False

# Is there a better way to customize prefilter?
ipshell.prefilter = new.instancemethod(_prefilter_del,
                                       ipshell,
                                       ipshell.__class__)

ipshell.set_hook("pre_run_code_hook", _pre_run_code_hook)
ipshell.set_hook("pre_prompt_hook", _pre_prompt_hook)
#ipshell.set_hook("shutdown_hook", _shutdown_hook) # use atexit module

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From bussonniermatthias at gmail.com  Tue Dec  1 06:28:40 2015
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Tue, 1 Dec 2015 12:28:40 +0100
Subject: [IPython-dev] Embedded shell setup
In-Reply-To: <20151201082945.505d84b7@ill.fr>
References: <20151201082945.505d84b7@ill.fr>
Message-ID: <211A6B1B-EB78-4197-B8B1-0CC1BC67C169@gmail.com>

Hi Frederic.

I haven?t used IPython 0.7.2 but I can try to give you some feedback. 


> On Dec 1, 2015, at 08:29, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:
> 
> Hi!
> 
> In 2003, we started to develop an application to drive a big instrument
> (a neutron spectrometer), in a french research institute. Since 2004, this
> application runs 24h a day, almost all days.
> 
> It is entirely written in python, and is heavily based on Pyro for
> clients/servers communication, and, of course IPython, for user
> interaction.
> 
> With these 2 great pieces of code, we have build a very strong tool.
> Fernando helped us a lot to customize IPython, and integrate it in our
> code. Thanks again for all your help, Fernando!
> 
> Even if our app. evolved during all these years, it is still based on
> softwares versions of the early 2k (debian lenny, IPython 0.7.2, Pyro
> 3.7) :o/
> 
> It is time to do a major upgrade! That's why we need some help...
> 
> Here is what we are doing when we instanciate what we call the
> 'console' (client part of our app.); we already adapted it to IPython 2.3,
> but there are still things which does not work (loading 'pymad' profile),
> and surely thing which could be better (hooks, custom completer...).
> 
> We would really appreciate feedback!
> 
> Thanks,
> 
> ----------------------------------------------------------------
> 
> config = IPython.config.loader.Config()
> promptManager = config.PromptManager

I?m not sure this assignment will work, because of what the config object works.
In doubt I would explicitly use config.PromptManager.in/out_template if you have issues. 
I would have to try and check that. 

> promptManager.in_template = "{color.LightRed}PyMAD>>> "
> promptManager.out_template = ? '

> # profile is not loaded does not work!
> config.profile = ?pymad"

I?m not sure  what yo are trying to do. 
I guess you might want to load a subconfia from another profile ?

https://ipython.org/ipython-doc/2/development/config.html?highlight=load_subconfig#configuration-files-inheritance <https://ipython.org/ipython-doc/2/development/config.html?highlight=load_subconfig#configuration-files-inheritance>


InteractiveShellEmbed is not a subclass of BaseIPythonApplication, so it does not seem have a `profile` configuration. 
The way it works in IPython is TerminalIPythonApp in init_shell call the following:

  def init_shell(self):
        ...
        self.shell = TerminalInteractiveShell.instance(parent=self,
                        ..., profile_dir=self.profile_dir,
                        ipython_dir=self.ipython_dir, ...)



> startMsg = "\nWelcome to PyMAD"
> startMsg += "\n\nAvailable objects: %s " % sortedProxies
> startMsg += "\n\nAvailable helpers: %s\n" % helpers.keys()
> exitMsg = "\nBye!\n"
> 
> # Instanciate embedded ipython instance
> ipshell = InteractiveShellEmbed(config,
>                                banner1=startMsg,
>                                exit_msg=exitMsg)
> 
> ipshell.set_custom_exc((Exception, ), pymadHandler)
> ipshell.set_custom_completer(proxy_matches)
> ipshell.set_custom_completer(python_function_parameters)
> 

I?m not familiar enough with completion, I know that holoview register its own completer:

https://github.com/ioam/holoviews/blob/master/holoviews/ipython/magics.py#L697-L717 <https://github.com/ioam/holoviews/blob/master/holoviews/ipython/magics.py#L697-L717>

it might be of help. 

> # Is there a better way to customize Completer?
> ipshell.Completer._default_arguments = \
>    new.instancemethod(_default_arguments,
>                       ipshell.Completer,
>                       ipshell.Completer.__class__)
> ipshell.Completer.merge_completions = False
> 

I?ll leave this one up to someone else also, 
likely Thomas maybe ?

> # Is there a better way to customize prefilter?
> ipshell.prefilter = new.instancemethod(_prefilter_del,
>                                       ipshell,
>                                       ipshell.__class__)
> 
> ipshell.set_hook("pre_run_code_hook", _pre_run_code_hook)
> ipshell.set_hook("pre_prompt_hook", _pre_prompt_hook)
> #ipshell.set_hook("shutdown_hook", _shutdown_hook) # use atexit module
> 

Thanks, 
-- 
M
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151201/4c75b07a/attachment.html>

From mantegazza at ill.fr  Tue Dec  1 07:12:20 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Tue, 1 Dec 2015 13:12:20 +0100
Subject: [IPython-dev] Embedded shell setup
In-Reply-To: <211A6B1B-EB78-4197-B8B1-0CC1BC67C169@gmail.com>
References: <20151201082945.505d84b7@ill.fr>
 <211A6B1B-EB78-4197-B8B1-0CC1BC67C169@gmail.com>
Message-ID: <20151201131220.5ad9de90@ill.fr>

Le 01/12/2015, Matthias a ?crit :

Hi!

> > config = IPython.config.loader.Config()
> > promptManager = config.PromptManager  
> 
> I?m not sure this assignment will work, because of what the config
> object works. In doubt I would explicitly use
> config.PromptManager.in/out_template if you have issues. I would have to
> try and check that. 

Well, this part works fine (I found this syntax in the examples).

> > # profile is not loaded does not work!
> > config.profile = ?pymad"  
> 
> I?m not sure  what yo are trying to do. 
> I guess you might want to load a subconfia from another profile ?

Yes, exactly.

> https://ipython.org/ipython-doc/2/development/config.html?highlight=load_subconfig#configuration-files-inheritance
> 
> InteractiveShellEmbed is not a subclass of BaseIPythonApplication, so it
> does not seem have a `profile` configuration. The way it works in
> IPython is TerminalIPythonApp in init_shell call the following:
> 
>   def init_shell(self):
>         ...
>         self.shell = TerminalInteractiveShell.instance(parent=self,
>                         ..., profile_dir=self.profile_dir,
>                         ipython_dir=self.ipython_dir, ...)

Thanks for the link.

The files in the 'pymad' profile dir mainly contains magic commands we add
in the shell (these magic commands, combined with TPG - Toy Parser
Generator - gives us a set of dedicated commands to drive our
spectrometer).

But I just found that these magic commands are now registered using
decorators, and can even be defined from classes, which is nice. So, I
rewrote this part, and finally drop the profile dir.

> I?m not familiar enough with completion, I know that holoview register
> its own completer:
> 
> https://github.com/ioam/holoviews/blob/master/holoviews/ipython/magics.py#L697-L717
> 
> it might be of help. 

Yes, it does!

BTW, where can one find the complete list of availables hooks names?

Thanks for your help, Matthias!

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From dsdale24 at gmail.com  Tue Dec  1 15:56:11 2015
From: dsdale24 at gmail.com (Darren Dale)
Date: Tue, 01 Dec 2015 20:56:11 +0000
Subject: [IPython-dev] custom completers, changes since ipython-4?
Message-ID: <CAK6O52n0xyLCEQsBLcdTqYk5u5S0VHkqc9ss0=6nOF48PdQ3rA@mail.gmail.com>

I wrote a custom completer for h5py some years ago, and discovered a
problem after updating ipython to the latest version:

[TerminalIPythonApp] WARNING | Error in loading extension:
h5py.ipy_completer Check your config files in
/home/darren/.ipython/profile_default Traceback (most recent call last):
File "/opt/conda/lib/python2.7/site-packages/IPython/core/shellapp.py",
line 267, in init_extensions
self.shell.extension_manager.load_extension(ext) File
"/opt/conda/lib/python2.7/site-packages/IPython/core/extensions.py", line
89, in load_extension __import__(module_str) File
"/opt/conda/lib/python2.7/site-packages/h5py/ipy_completer.py", line 59, in
<module> from IPython import generics ImportError: cannot import name
generics

I'm sorry if this has an obvious solution that has been announced
somewhere, maybe I don't know where to look anymore. Is there a list of
changes that has been made to the API? What happened to generics?

Thanks,
Darren
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151201/df6908dd/attachment.html>

From rosborn at anl.gov  Tue Dec  1 16:06:03 2015
From: rosborn at anl.gov (Osborn, Raymond)
Date: Tue, 1 Dec 2015 21:06:03 +0000
Subject: [IPython-dev] custom completers, changes since ipython-4?
In-Reply-To: <CAK6O52n0xyLCEQsBLcdTqYk5u5S0VHkqc9ss0=6nOF48PdQ3rA@mail.gmail.com>
References: <CAK6O52n0xyLCEQsBLcdTqYk5u5S0VHkqc9ss0=6nOF48PdQ3rA@mail.gmail.com>
Message-ID: <73824316-E5A4-4E4E-8570-51082C9C8E98@anl.gov>

Hi Darren,

>>> from IPython.utils import generics

seems to work. There may be other changes you need to be aware of, but I?ll leave that to the real experts.

Ray

> On Dec 1, 2015, at 2:56 PM, Darren Dale <dsdale24 at gmail.com> wrote:
> 
> I wrote a custom completer for h5py some years ago, and discovered a problem after updating ipython to the latest version:
> 
> [TerminalIPythonApp] WARNING | Error in loading extension: h5py.ipy_completer Check your config files in /home/darren/.ipython/profile_default Traceback (most recent call last): File "/opt/conda/lib/python2.7/site-packages/IPython/core/shellapp.py", line 267, in init_extensions self.shell.extension_manager.load_extension(ext) File "/opt/conda/lib/python2.7/site-packages/IPython/core/extensions.py", line 89, in load_extension __import__(module_str) File "/opt/conda/lib/python2.7/site-packages/h5py/ipy_completer.py", line 59, in <module> from IPython import generics ImportError: cannot import name generics
> 
> I'm sorry if this has an obvious solution that has been announced somewhere, maybe I don't know where to look anymore. Is there a list of changes that has been made to the API? What happened to generics?
> 
> Thanks,
> Darren
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev

-- 
Ray Osborn, Senior Scientist
Materials Science Division
Argonne National Laboratory
Argonne, IL 60439, USA
Phone: +1 (630) 252-9011
Email: ROsborn at anl.gov



From nick.bollweg at gmail.com  Tue Dec  1 17:59:15 2015
From: nick.bollweg at gmail.com (Nicholas Bollweg)
Date: Tue, 01 Dec 2015 22:59:15 +0000
Subject: [IPython-dev] [proposal] Jupyter Extension Generator
Message-ID: <CACejjWyEMAR3ZzizvbXBichTLCc5QNgKm1NiJadwSx0RvKnYTg@mail.gmail.com>

Hi folks!

I mentioned this in the dev meeting today: let's build (or at least discuss
why we shouldn't build!) a jupyter extension scaffolding/generator system:

https://github.com/jupyter/enhancement-proposals/pull/7

Thanks!

Nick
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151201/140a595a/attachment.html>

From mantegazza at ill.fr  Wed Dec  2 02:11:43 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 08:11:43 +0100
Subject: [IPython-dev] IPython, debian, anaconda - LTS strategy
Message-ID: <20151202081143.1a20ab8d@ill.fr>

Hi!

I was wondering why some of the IPython documentations didn' match what I
had on my disk: it is because I'm running IPython 2.3, and not IPython
3.2; I read too fast the result of apt-cache show :o/

The question is: why, even in my debian sid (unstable), I only have IPython
2.x? Is there a reason for the maintainer not to use the latest stable
release? It seams that IPython 3.x branch is out for some months, now...

One solution is to install IPython 3.x from pip. But is it a good idea?
What about IPython dependencies? I may have to install numpy,
matplotlib, notebook etc from pip too, and this may lead me too far for an
application which has to be very stable (don't want to redo all the work
debian maitainers do!).

Another solution is to use Anaconda. But I don't know how stable this
'distro', and how it will evolve in the future. For example, they package
IPython 4, which does not seem to be stable yet... Don't know if it is
easy to install third-party python packages in this environment.

Any advice welcome.

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From mantegazza at ill.fr  Wed Dec  2 02:42:40 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 08:42:40 +0100
Subject: [IPython-dev] From Pyro to IPython/Jupyter
Message-ID: <20151202084240.341947e5@ill.fr>

Hi!

Our spectrometer driving application is based on Pyro3? to achieve that:
the server registers some objects in the Pyro name server, and clients use
them as if they where local objects.

Our client is build using IPython, for its interactive feature.

But it seams that IPython/Jupyter (4.x branch) provide similar mecanisms:
it is possible to have a central application (kernel ?), and several
clients (frontends) to communicate with it, at the same time.

Am I right? I'm not sure to clearly understand how things interact. But it
would be great if we could build our app. all on top of IPython/Jupyter, as
we already planned to use notebooks to provide a web-based client
console...

Thanks for your help.

? http://pythonhosted.org/Pyro

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From benjaminrk at gmail.com  Wed Dec  2 03:57:57 2015
From: benjaminrk at gmail.com (MinRK)
Date: Wed, 2 Dec 2015 09:57:57 +0100
Subject: [IPython-dev] IPython, debian, anaconda - LTS strategy
In-Reply-To: <20151202081143.1a20ab8d@ill.fr>
References: <20151202081143.1a20ab8d@ill.fr>
Message-ID: <CAHNn8BVnSUNWaCVH25MJhsVZnPoBcu3oH-r7tCZjrK2NnMYFkQ@mail.gmail.com>

On Wed, Dec 2, 2015 at 8:11 AM, Fr?d?ric Mantegazza <mantegazza at ill.fr>
wrote:

Hi!
>
> I was wondering why some of the IPython documentations didn' match what I
> had on my disk: it is because I'm running IPython 2.3, and not IPython
> 3.2; I read too fast the result of apt-cache show :o/
>
> The question is: why, even in my debian sid (unstable), I only have IPython
> 2.x? Is there a reason for the maintainer not to use the latest stable
> release? It seams that IPython 3.x branch is out for some months, now...
>
The people who build packages for the various Linux distros are generally
not the same as the people who develop the software. This can lead to
discrepancies and lag-time before a new release gets packages. IPython 3
shipped in February, and IPython 4 in August. Hopefully things will catch
up soon.


> One solution is to install IPython 3.x from pip. But is it a good idea?
> What about IPython dependencies? I may have to install numpy,
> matplotlib, notebook etc from pip too, and this may lead me too far for an
> application which has to be very stable (don't want to redo all the work
> debian maitainers do!).
>
This is a difficult tradeoff. Because apt-packaging of Python packages
tends to be very slow/conservative, I rarely, if ever, use apt to install
anything for Python, and I wouldn?t really recommend using apt to install
Python-only packages to most users. Dependencies are obviously the tricky
part, and if you mix apt/pip installation, you can get yourself in a bit of
a tangle. Typically, I only use apt for things that may be ?hard? to
install (i.e. compiled with non-Python dependencies), such as numpy, scipy,
matplotlib. But I?m also not a representative user in terms of
understanding dependencies and installation issues.

But there?s obviously a benefit to being conservative - apt-packaged
versions are more likely to be tested/compatible. But to stick with that,
you have to be okay not having the latest and greatest versions of
packages. And sometimes the lag is not due to conservatism or caution, it?s
due to the volunteer package-maintainer community being busy with other
things.

One *big* caveat: If you do use pip, make sure it?s up-to-date. The
debian-bundled pip is also woefully outdated, so you shouldn?t even install
pip with apt, you should probably use get-pip
<https://packaging.python.org/en/latest/installing/#install-pip-setuptools-and-wheel>
to bootstrap it.


> Another solution is to use Anaconda. But I don't know how stable this
> 'distro', and how it will evolve in the future. For example, they package
> IPython 4, which does not seem to be stable yet... Don't know if it is
> easy to install third-party python packages in this environment.
>
Anaconda is pretty quick to ship updates upon release of packages (often
within hours of release). One *major* advantage of using conda over apt is
you can have it both ways. You can have one conda env running ?stable?,
pinning major versions of relevant packages until you have verified that a
release works for your own applications, and another ?unstable? which stays
up-to-date with the latest conda packages. The same technically goes for
virtualenv, but conda?s use of bdists and hardlinks makes multiple envs
more pleasant in my experience.

-MinRK


> Any advice welcome.
>
> --
>     Fr?d?ric MANTEGAZZA             CEA-Grenoble
>     Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
>     Fax      : 33 (0) 476 483 906   17, rue des Martyrs
>     Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/9d247066/attachment.html>

From benjaminrk at gmail.com  Wed Dec  2 04:05:20 2015
From: benjaminrk at gmail.com (MinRK)
Date: Wed, 2 Dec 2015 10:05:20 +0100
Subject: [IPython-dev] custom completers, changes since ipython-4?
In-Reply-To: <73824316-E5A4-4E4E-8570-51082C9C8E98@anl.gov>
References: <CAK6O52n0xyLCEQsBLcdTqYk5u5S0VHkqc9ss0=6nOF48PdQ3rA@mail.gmail.com>
 <73824316-E5A4-4E4E-8570-51082C9C8E98@anl.gov>
Message-ID: <CAHNn8BWxE7+WOhrBOB6e4nixi1xJTcPUdR7gk8LNpFCKhxhJwg@mail.gmail.com>

What version of h5py? It looks like this was fixed a while ago
<https://github.com/h5py/h5py/issues/410>, but this old version
<https://github.com/gem/h5py/blob/master/h5py/ipy_completer.py> would
incorrectly trigger a pre-0.11 branch due to the removal of a deprecated
API (IPython.core.ipapi).

-MinRK
?

On Tue, Dec 1, 2015 at 10:06 PM, Osborn, Raymond <rosborn at anl.gov> wrote:

> Hi Darren,
>
> >>> from IPython.utils import generics
>
> seems to work. There may be other changes you need to be aware of, but
> I?ll leave that to the real experts.
>
> Ray
>
> > On Dec 1, 2015, at 2:56 PM, Darren Dale <dsdale24 at gmail.com> wrote:
> >
> > I wrote a custom completer for h5py some years ago, and discovered a
> problem after updating ipython to the latest version:
> >
> > [TerminalIPythonApp] WARNING | Error in loading extension:
> h5py.ipy_completer Check your config files in
> /home/darren/.ipython/profile_default Traceback (most recent call last):
> File "/opt/conda/lib/python2.7/site-packages/IPython/core/shellapp.py",
> line 267, in init_extensions
> self.shell.extension_manager.load_extension(ext) File
> "/opt/conda/lib/python2.7/site-packages/IPython/core/extensions.py", line
> 89, in load_extension __import__(module_str) File
> "/opt/conda/lib/python2.7/site-packages/h5py/ipy_completer.py", line 59, in
> <module> from IPython import generics ImportError: cannot import name
> generics
> >
> > I'm sorry if this has an obvious solution that has been announced
> somewhere, maybe I don't know where to look anymore. Is there a list of
> changes that has been made to the API? What happened to generics?
> >
> > Thanks,
> > Darren
> > _______________________________________________
> > IPython-dev mailing list
> > IPython-dev at scipy.org
> > https://mail.scipy.org/mailman/listinfo/ipython-dev
>
> --
> Ray Osborn, Senior Scientist
> Materials Science Division
> Argonne National Laboratory
> Argonne, IL 60439, USA
> Phone: +1 (630) 252-9011
> Email: ROsborn at anl.gov
>
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/1a066066/attachment.html>

From matthew.brett at gmail.com  Wed Dec  2 04:20:41 2015
From: matthew.brett at gmail.com (Matthew Brett)
Date: Wed, 2 Dec 2015 01:20:41 -0800
Subject: [IPython-dev] IPython, debian, anaconda - LTS strategy
In-Reply-To: <20151202081143.1a20ab8d@ill.fr>
References: <20151202081143.1a20ab8d@ill.fr>
Message-ID: <CAH6Pt5oCAwSA=0NmagSJisrR=wkjWjnGhwt9z6CaT2uJfLAorA@mail.gmail.com>

Hi,

On Tue, Dec 1, 2015 at 11:11 PM, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:
> Hi!
>
> I was wondering why some of the IPython documentations didn' match what I
> had on my disk: it is because I'm running IPython 2.3, and not IPython
> 3.2; I read too fast the result of apt-cache show :o/
>
> The question is: why, even in my debian sid (unstable), I only have IPython
> 2.x? Is there a reason for the maintainer not to use the latest stable
> release? It seams that IPython 3.x branch is out for some months, now...
>
> One solution is to install IPython 3.x from pip. But is it a good idea?
> What about IPython dependencies? I may have to install numpy,
> matplotlib, notebook etc from pip too, and this may lead me too far for an
> application which has to be very stable (don't want to redo all the work
> debian maitainers do!).
>
> Another solution is to use Anaconda. But I don't know how stable this
> 'distro', and how it will evolve in the future. For example, they package
> IPython 4, which does not seem to be stable yet... Don't know if it is
> easy to install third-party python packages in this environment.

I recently wrote up the procedure I use on Linux (although I more
often use OSX):

https://matthew-brett.github.io/pydagogue/installing_on_debian.html

Cheers,

Matthew


From mantegazza at ill.fr  Wed Dec  2 05:26:09 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 11:26:09 +0100
Subject: [IPython-dev] IPython, debian, anaconda - LTS strategy
In-Reply-To: <CAH6Pt5oCAwSA=0NmagSJisrR=wkjWjnGhwt9z6CaT2uJfLAorA@mail.gmail.com>
References: <20151202081143.1a20ab8d@ill.fr>
 <CAH6Pt5oCAwSA=0NmagSJisrR=wkjWjnGhwt9z6CaT2uJfLAorA@mail.gmail.com>
Message-ID: <20151202112609.49099be4@ill.fr>

Le 02/12/2015, Matthew a ?crit :

> I recently wrote up the procedure I use on Linux (although I more
> often use OSX):
> 
> https://matthew-brett.github.io/pydagogue/installing_on_debian.html

Very usefull, thanks!

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From mantegazza at ill.fr  Wed Dec  2 05:26:34 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 11:26:34 +0100
Subject: [IPython-dev] IPython, debian, anaconda - LTS strategy
In-Reply-To: <CAHNn8BVnSUNWaCVH25MJhsVZnPoBcu3oH-r7tCZjrK2NnMYFkQ@mail.gmail.com>
References: <20151202081143.1a20ab8d@ill.fr>
 <CAHNn8BVnSUNWaCVH25MJhsVZnPoBcu3oH-r7tCZjrK2NnMYFkQ@mail.gmail.com>
Message-ID: <20151202112634.6c2be1dc@ill.fr>

Le 02/12/2015, MinRK a ?crit :

Thanks for your answers!

> Anaconda is pretty quick to ship updates upon release of packages (often
> within hours of release). One *major* advantage of using conda over apt
> is you can have it both ways. You can have one conda env running
> ?stable?, pinning major versions of relevant packages until you have
> verified that a release works for your own applications, and another
> ?unstable? which stays up-to-date with the latest conda packages. The
> same technically goes for virtualenv, but conda?s use of bdists and
> hardlinks makes multiple envs more pleasant in my experience.

Another point in favor of anaconda is it exists on the 3 major systems;
so, anyone will be able to build the same environment to run our
applications... This looks interesting to me.

We will give it a try.

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From takowl at gmail.com  Wed Dec  2 06:59:22 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Wed, 2 Dec 2015 11:59:22 +0000
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <20151202084240.341947e5@ill.fr>
References: <20151202084240.341947e5@ill.fr>
Message-ID: <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>

Hi Fr?d?ric,

On 2 December 2015 at 07:42, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:

> Our spectrometer driving application is based on Pyro3? to achieve that:
> the server registers some objects in the Pyro name server, and clients use
> them as if they where local objects.
>
> Our client is build using IPython, for its interactive feature.
>
> But it seams that IPython/Jupyter (4.x branch) provide similar mecanisms:
> it is possible to have a central application (kernel ?), and several
> clients (frontends) to communicate with it, at the same time.
>

It is possible to have several clients connected with a single kernel, but
it's not really designed for the same use case as Pyro.

With Pyro, the server registers specific objects and methods to be exposed
remotely. With a Jupyter kernel, the client sends code to be executed in
the kernel. It's more like having users SSH in to the server to control the
machine; they have full access to run arbitrary code on the server.

Best wishes,
Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/ed0fb164/attachment.html>

From mantegazza at ill.fr  Wed Dec  2 07:12:38 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 13:12:38 +0100
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
Message-ID: <20151202131238.20f2e3b0@ill.fr>

Le 02/12/2015, Thomas a ?crit :

> It is possible to have several clients connected with a single kernel,
> but it's not really designed for the same use case as Pyro.
> 
> With Pyro, the server registers specific objects and methods to be
> exposed remotely. With a Jupyter kernel, the client sends code to be
> executed in the kernel. It's more like having users SSH in to the server
> to control the machine; they have full access to run arbitrary code on
> the server.

So, the kernel can't be a specific application, but just an
(python or other) execution environment ?

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From takowl at gmail.com  Wed Dec  2 07:16:35 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Wed, 2 Dec 2015 12:16:35 +0000
Subject: [IPython-dev] IPython, debian, anaconda - LTS strategy
In-Reply-To: <20151202081143.1a20ab8d@ill.fr>
References: <20151202081143.1a20ab8d@ill.fr>
Message-ID: <CAOvn4qiq-K3VA+kX+95FF-JCELWMLXrHpDU4DNWQLorvS0WH+Q@mail.gmail.com>

On 2 December 2015 at 07:11, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:

> The question is: why, even in my debian sid (unstable), I only have IPython
> 2.x? Is there a reason for the maintainer not to use the latest stable
> release? It seams that IPython 3.x branch is out for some months, now...
>

As Min mentioned, it's not the core team that do Debian packaging. But
there's another issue: adding new dependencies that aren't already packaged
in Debian slows things down, because all those dependencies have to be
packaged and approved (new packages have an extra approval step on top of
the normal checks). As Python packaging has improved, we've been
increasingly happy to depend on many more external packages, and to split
our own code into smaller units which we release separately. Debian's
systems aren't keeping up with all this very well.

Also, since we always tell people to install using Anaconda or pip, I
suspect there's little impetus for people to work on the Debian packaging -
people who want an up to date version can easily bypass Debian.

Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/62d02f32/attachment.html>

From takowl at gmail.com  Wed Dec  2 07:22:21 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Wed, 2 Dec 2015 12:22:21 +0000
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <20151202131238.20f2e3b0@ill.fr>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
Message-ID: <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>

On 2 December 2015 at 12:12, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:

> So, the kernel can't be a specific application, but just an
> (python or other) execution environment ?
>

You could make a custom execution environment which only exposes a
particular set of commands relevant to e.g. controlling a mass
spectrometer. But broadly, a kernel is there to be the execution backend
for a user typing in code, not an RPC framework. If you're happy with the
way you use Pyro, you'd probably have to do quite a bit of work to
reimplement a similar interface on top of our kernel/client model.

Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/29396c36/attachment.html>

From mantegazza at ill.fr  Wed Dec  2 07:24:32 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 13:24:32 +0100
Subject: [IPython-dev] IPython, debian, anaconda - LTS strategy
In-Reply-To: <CAOvn4qiq-K3VA+kX+95FF-JCELWMLXrHpDU4DNWQLorvS0WH+Q@mail.gmail.com>
References: <20151202081143.1a20ab8d@ill.fr>
 <CAOvn4qiq-K3VA+kX+95FF-JCELWMLXrHpDU4DNWQLorvS0WH+Q@mail.gmail.com>
Message-ID: <20151202132432.3c106abb@ill.fr>

Le 02/12/2015, Thomas a ?crit :

> As Min mentioned, it's not the core team that do Debian packaging.

Yes, I'm aware of that. I just wanted to know if IPython devs/users had
some informations about

> But there's another issue: adding new dependencies that aren't already
> packaged in Debian slows things down, because all those dependencies
> have to be packaged and approved (new packages have an extra approval
> step on top of the normal checks). As Python packaging has improved,
> we've been increasingly happy to depend on many more external packages,
> and to split our own code into smaller units which we release
> separately. Debian's systems aren't keeping up with all this very well.

Yes, I think it's a lot of work for maintainers :o/

> Also, since we always tell people to install using Anaconda or pip, I
> suspect there's little impetus for people to work on the Debian
> packaging - people who want an up to date version can easily bypass
> Debian.

It makes sens...

I just tried anaconda (miniconda, in fact), and I've been able to setup a
working env for our application in a few minutes :o) Looks like a very
good way to go.

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From mantegazza at ill.fr  Wed Dec  2 08:27:38 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 14:27:38 +0100
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
Message-ID: <20151202142738.58bc01ab@ill.fr>

Le 02/12/2015, Thomas a ?crit :

> You could make a custom execution environment which only exposes a
> particular set of commands relevant to e.g. controlling a mass
> spectrometer. But broadly, a kernel is there to be the execution backend
> for a user typing in code, not an RPC framework. If you're happy with the
> way you use Pyro, you'd probably have to do quite a bit of work to
> reimplement a similar interface on top of our kernel/client model.

When we started to develop our application (aka PyMAD), we had in mind to
push the instrument responsible to dig into python, and offer him
something closer to a framework, rather than a end-user application.

This, because this guy is someone with 1000 ideas per hour, and often asks
for new stuffs. So, giving to him such (very) high level tools to control
his instrument could have been nice.

But He never dig enough into python to be able to do so. I don't blame him
at all, as it is not easy to change habits. Python was new to him...

But he is about to retire, at the end of this year, and the new
responsible is younger, and uses python to treat his scientific datas. So,
I think it could be nice, this time, to implement what we always wanted to
do.

Saying this, it appears to me that we don't really need a RPC-like
framework, and exposing all the internals of the application could be
great. We will have to find a mecanism to hide some parts for simple users
using the instrument, to avoid them to brake things during their
experiment (:o/), but I think it can be done without too much work.

On the other hand, having the jupyter mecanism, and being able to start a
session from one place, in a pure console, or in a qtconsole, them
go back home and switch to a web-based console to continue to work from
the same point is really great.

Last, it appears that Pyro4 dropped some features mandatory for our
application, like the event service! So, we are stuck to the 3.x version...

That's why I want to explore this idea.

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From takowl at gmail.com  Wed Dec  2 08:51:36 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Wed, 2 Dec 2015 13:51:36 +0000
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <20151202142738.58bc01ab@ill.fr>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
Message-ID: <CAOvn4qiBmbR_FGak53K=B1ibOvPGJdH18xnUumaiDcoz4GizCQ@mail.gmail.com>

On 2 December 2015 at 13:27, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:

> On the other hand, having the jupyter mecanism, and being able to start a
> session from one place, in a pure console, or in a qtconsole, them
> go back home and switch to a web-based console to continue to work from
> the same point is really great.
>

Note that our machinery doesn't make this very easy at present - e.g. the
notebook server only talks to kernels it started, so you can't create a
notebook and attach it to an existing kernel. And running a console or a qt
console with a kernel on another machine involves setting up SSH tunnels.

One simple thing you could do would be to run the notebook server itself on
the machine controlling the instrument - possibly under Jupyterhub, so
users have separate logins. But that's obviously quite a large service to
have running on a computer directly connected to important hardware.

Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/8128b78f/attachment.html>

From rosborn at anl.gov  Wed Dec  2 08:58:24 2015
From: rosborn at anl.gov (Osborn, Raymond)
Date: Wed, 2 Dec 2015 13:58:24 +0000
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <20151202142738.58bc01ab@ill.fr>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
Message-ID: <A80751CE-F81D-4FA0-8003-06ED92104CDD@anl.gov>

Frederic,
We have been testing the use of Pyro4 as a method of loading remote NeXus files within NeXpy, which also uses a Jupyter shell (http://nexpy.github.io/nexpy/). It?s not part of the official distribution yet, but I would be happy to discuss it with you outside this list. As a fellow neutron scatterer, it might be relevant.

Ray

On Dec 2, 2015, at 7:27 AM, Fr?d?ric Mantegazza <mantegazza at ill.fr<mailto:mantegazza at ill.fr>> wrote:

Le 02/12/2015, Thomas a ?crit :

You could make a custom execution environment which only exposes a
particular set of commands relevant to e.g. controlling a mass
spectrometer. But broadly, a kernel is there to be the execution backend
for a user typing in code, not an RPC framework. If you're happy with the
way you use Pyro, you'd probably have to do quite a bit of work to
reimplement a similar interface on top of our kernel/client model.

When we started to develop our application (aka PyMAD), we had in mind to
push the instrument responsible to dig into python, and offer him
something closer to a framework, rather than a end-user application.

This, because this guy is someone with 1000 ideas per hour, and often asks
for new stuffs. So, giving to him such (very) high level tools to control
his instrument could have been nice.

But He never dig enough into python to be able to do so. I don't blame him
at all, as it is not easy to change habits. Python was new to him...

But he is about to retire, at the end of this year, and the new
responsible is younger, and uses python to treat his scientific datas. So,
I think it could be nice, this time, to implement what we always wanted to
do.

Saying this, it appears to me that we don't really need a RPC-like
framework, and exposing all the internals of the application could be
great. We will have to find a mecanism to hide some parts for simple users
using the instrument, to avoid them to brake things during their
experiment (:o/), but I think it can be done without too much work.

On the other hand, having the jupyter mecanism, and being able to start a
session from one place, in a pure console, or in a qtconsole, them
go back home and switch to a web-based console to continue to work from
the same point is really great.

Last, it appears that Pyro4 dropped some features mandatory for our
application, like the event service! So, we are stuck to the 3.x version...

That's why I want to explore this idea.

--
   Fr?d?ric MANTEGAZZA             CEA-Grenoble
   Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
   Fax      : 33 (0) 476 483 906   17, rue des Martyrs
   Courriel : mantegazza at ill.fr<mailto:mantegazza at ill.fr>    F-38054 Grenoble Cedex 09

_______________________________________________
IPython-dev mailing list
IPython-dev at scipy.org<mailto:IPython-dev at scipy.org>
https://mail.scipy.org/mailman/listinfo/ipython-dev

--
Ray Osborn, Senior Scientist
Materials Science Division
Argonne National Laboratory
Argonne, IL 60439, USA
Phone: +1 (630) 252-9011
Email: ROsborn at anl.gov<mailto:ROsborn at anl.gov>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/18e39399/attachment.html>

From mantegazza at ill.fr  Wed Dec  2 09:15:40 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 15:15:40 +0100
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <CAOvn4qiBmbR_FGak53K=B1ibOvPGJdH18xnUumaiDcoz4GizCQ@mail.gmail.com>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
 <CAOvn4qiBmbR_FGak53K=B1ibOvPGJdH18xnUumaiDcoz4GizCQ@mail.gmail.com>
Message-ID: <20151202151540.30f17736@ill.fr>

Le 02/12/2015, Thomas a ?crit :

> Note that our machinery doesn't make this very easy at present - e.g. the
> notebook server only talks to kernels it started, so you can't create a
> notebook and attach it to an existing kernel. And running a console or a
> qt console with a kernel on another machine involves setting up SSH
> tunnels.

Ok. SSH is fine for consoles.

> One simple thing you could do would be to run the notebook server itself
> on the machine controlling the instrument - possibly under Jupyterhub, so
> users have separate logins. But that's obviously quite a large service to
> have running on a computer directly connected to important hardware.

Fortunately, people here don't have bad intentions :o) For example,
login/password strategy on instruments machines is very simple, and almost
anyone can log in any machine. As far as I know, nobody has ever messed up
somebody else experiment ;o)

And all stuff is protected from the outside by strong firewall.

Jupyterhub can be interesting to give a larger access to the instrument
responsible, and simple access to standard users (I understand that this
is something we will have to implement, and not provided by Jupyter).

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From mantegazza at ill.fr  Wed Dec  2 09:28:01 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 2 Dec 2015 15:28:01 +0100
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <A80751CE-F81D-4FA0-8003-06ED92104CDD@anl.gov>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
 <A80751CE-F81D-4FA0-8003-06ED92104CDD@anl.gov>
Message-ID: <20151202152801.5298d6d2@ill.fr>

Le 02/12/2015, Raymond a ?crit :

> We have been testing the use of Pyro4 as a method of loading remote
> NeXus files within NeXpy, which also uses a Jupyter shell
> (http://nexpy.github.io/nexpy/). It?s not part of the official
> distribution yet, but I would be happy to discuss it with you outside
> this list. As a fellow neutron scatterer, it might be relevant.

Great!

I will surely come back to you, but I first need to understand all
concepts behind IPython 4 and Jupyter...

BTW, NeXus is also on our TODO list of things to learn ;o)

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From sebastian.kremiec at gmail.com  Wed Dec  2 15:50:51 2015
From: sebastian.kremiec at gmail.com (Sebastian Kremiec)
Date: Wed, 02 Dec 2015 20:50:51 +0000
Subject: [IPython-dev] New project - K3D
In-Reply-To: <CAAoBLw3t8JkfWXP5MQWn=t90-gEDQb-873a-4A2gdhmrYiLOtQ@mail.gmail.com>
References: <CA+Mf6c+KaP0SyVR44nTSwYJMEMgh3dxHCBqwJwQd-N3=gk5bhw@mail.gmail.com>
 <CAAoBLw3t8JkfWXP5MQWn=t90-gEDQb-873a-4A2gdhmrYiLOtQ@mail.gmail.com>
Message-ID: <CA+Mf6cJC5FBc9zQXqiMk_dOHV1QCkGtqbRnrERdtJfVgVRRGKA@mail.gmail.com>

Hello again,

It's been a while since my previous post. We have been quite busy working
hard to make our project better with every release.

We've made many fixes and improvements, just to name a few (visit
https://github.com/K3D-tools/K3D-jupyter/releases for full list):
- support for new object types (vectors, vector fields 2D and 3D, textures,
voxels)
- voxels edit mode
- full screen mode
- full Python3 support
- ability to group and remove objects
- objects properties can be modified (with live update)
- improved performance
- various bug-fixes

Make sure to checkout examples to see all the new stuff in action.
As previously, any feedback is very welcome and highly appreciated.

Greetings,
K3D Team
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/78877b0a/attachment.html>

From kikocorreoso at gmail.com  Wed Dec  2 16:36:41 2015
From: kikocorreoso at gmail.com (Kiko)
Date: Wed, 2 Dec 2015 22:36:41 +0100
Subject: [IPython-dev] New project - K3D
In-Reply-To: <CA+Mf6cJC5FBc9zQXqiMk_dOHV1QCkGtqbRnrERdtJfVgVRRGKA@mail.gmail.com>
References: <CA+Mf6c+KaP0SyVR44nTSwYJMEMgh3dxHCBqwJwQd-N3=gk5bhw@mail.gmail.com>
 <CAAoBLw3t8JkfWXP5MQWn=t90-gEDQb-873a-4A2gdhmrYiLOtQ@mail.gmail.com>
 <CA+Mf6cJC5FBc9zQXqiMk_dOHV1QCkGtqbRnrERdtJfVgVRRGKA@mail.gmail.com>
Message-ID: <CAB-sx62rBYW5mXcuJ-Ys-hqwR1AmiSyx0hMrYPPcA00C4KpGnw@mail.gmail.com>

It seems pretty interesting but I had to surf a little bit and dive
into the code to figure out what it is k3d.

It would be nice to add some info in the readme to understand what you
can do with the extension, what problems could be solved, why you
should install it,...

:-)

2015-12-02 21:50 GMT+01:00, Sebastian Kremiec <sebastian.kremiec at gmail.com>:
> Hello again,
>
> It's been a while since my previous post. We have been quite busy working
> hard to make our project better with every release.
>
> We've made many fixes and improvements, just to name a few (visit
> https://github.com/K3D-tools/K3D-jupyter/releases for full list):
> - support for new object types (vectors, vector fields 2D and 3D, textures,
> voxels)
> - voxels edit mode
> - full screen mode
> - full Python3 support
> - ability to group and remove objects
> - objects properties can be modified (with live update)
> - improved performance
> - various bug-fixes
>
> Make sure to checkout examples to see all the new stuff in action.
> As previously, any feedback is very welcome and highly appreciated.
>
> Greetings,
> K3D Team
>


From ian.h.bell at gmail.com  Wed Dec  2 16:44:06 2015
From: ian.h.bell at gmail.com (Ian Bell)
Date: Wed, 2 Dec 2015 14:44:06 -0700
Subject: [IPython-dev] New project - K3D
In-Reply-To: <CAB-sx62rBYW5mXcuJ-Ys-hqwR1AmiSyx0hMrYPPcA00C4KpGnw@mail.gmail.com>
References: <CA+Mf6c+KaP0SyVR44nTSwYJMEMgh3dxHCBqwJwQd-N3=gk5bhw@mail.gmail.com>
 <CAAoBLw3t8JkfWXP5MQWn=t90-gEDQb-873a-4A2gdhmrYiLOtQ@mail.gmail.com>
 <CA+Mf6cJC5FBc9zQXqiMk_dOHV1QCkGtqbRnrERdtJfVgVRRGKA@mail.gmail.com>
 <CAB-sx62rBYW5mXcuJ-Ys-hqwR1AmiSyx0hMrYPPcA00C4KpGnw@mail.gmail.com>
Message-ID: <CAJQnXJdoE=tVefb0OW4VZvA+e+G_j4a7Z7muVvLtf1g2nBfOPg@mail.gmail.com>

And a screenshot might be nice on the front page as motivation

Also, windows support would be nice :)

On Wed, Dec 2, 2015 at 2:36 PM, Kiko <kikocorreoso at gmail.com> wrote:

> It seems pretty interesting but I had to surf a little bit and dive
> into the code to figure out what it is k3d.
>
> It would be nice to add some info in the readme to understand what you
> can do with the extension, what problems could be solved, why you
> should install it,...
>
> :-)
>
> 2015-12-02 21:50 GMT+01:00, Sebastian Kremiec <sebastian.kremiec at gmail.com
> >:
> > Hello again,
> >
> > It's been a while since my previous post. We have been quite busy working
> > hard to make our project better with every release.
> >
> > We've made many fixes and improvements, just to name a few (visit
> > https://github.com/K3D-tools/K3D-jupyter/releases for full list):
> > - support for new object types (vectors, vector fields 2D and 3D,
> textures,
> > voxels)
> > - voxels edit mode
> > - full screen mode
> > - full Python3 support
> > - ability to group and remove objects
> > - objects properties can be modified (with live update)
> > - improved performance
> > - various bug-fixes
> >
> > Make sure to checkout examples to see all the new stuff in action.
> > As previously, any feedback is very welcome and highly appreciated.
> >
> > Greetings,
> > K3D Team
> >
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/92116385/attachment.html>

From dsdale24 at gmail.com  Wed Dec  2 17:14:32 2015
From: dsdale24 at gmail.com (Darren Dale)
Date: Wed, 02 Dec 2015 22:14:32 +0000
Subject: [IPython-dev] custom completers, changes since ipython-4?
In-Reply-To: <CAHNn8BWxE7+WOhrBOB6e4nixi1xJTcPUdR7gk8LNpFCKhxhJwg@mail.gmail.com>
References: <CAK6O52n0xyLCEQsBLcdTqYk5u5S0VHkqc9ss0=6nOF48PdQ3rA@mail.gmail.com>
 <73824316-E5A4-4E4E-8570-51082C9C8E98@anl.gov>
 <CAHNn8BWxE7+WOhrBOB6e4nixi1xJTcPUdR7gk8LNpFCKhxhJwg@mail.gmail.com>
Message-ID: <CAK6O52nzkEVw3s3_fSAH16vS3x=KHpXZd4+7NA=RT7huJJNwsQ@mail.gmail.com>

The problem exists in h5py-2.5.0, and is related to the removal of TryNext
from the IPython namespace. The problem has been addressed in the h5py
master branch.

Thanks,
Darren

On Wed, Dec 2, 2015 at 4:05 AM MinRK <benjaminrk at gmail.com> wrote:

> What version of h5py? It looks like this was fixed a while ago
> <https://github.com/h5py/h5py/issues/410>, but this old version
> <https://github.com/gem/h5py/blob/master/h5py/ipy_completer.py> would
> incorrectly trigger a pre-0.11 branch due to the removal of a deprecated
> API (IPython.core.ipapi).
>
> -MinRK
> ?
>
> On Tue, Dec 1, 2015 at 10:06 PM, Osborn, Raymond <rosborn at anl.gov> wrote:
>
>> Hi Darren,
>>
>> >>> from IPython.utils import generics
>>
>> seems to work. There may be other changes you need to be aware of, but
>> I?ll leave that to the real experts.
>>
>> Ray
>>
>> > On Dec 1, 2015, at 2:56 PM, Darren Dale <dsdale24 at gmail.com> wrote:
>> >
>> > I wrote a custom completer for h5py some years ago, and discovered a
>> problem after updating ipython to the latest version:
>> >
>> > [TerminalIPythonApp] WARNING | Error in loading extension:
>> h5py.ipy_completer Check your config files in
>> /home/darren/.ipython/profile_default Traceback (most recent call last):
>> File "/opt/conda/lib/python2.7/site-packages/IPython/core/shellapp.py",
>> line 267, in init_extensions
>> self.shell.extension_manager.load_extension(ext) File
>> "/opt/conda/lib/python2.7/site-packages/IPython/core/extensions.py", line
>> 89, in load_extension __import__(module_str) File
>> "/opt/conda/lib/python2.7/site-packages/h5py/ipy_completer.py", line 59, in
>> <module> from IPython import generics ImportError: cannot import name
>> generics
>> >
>> > I'm sorry if this has an obvious solution that has been announced
>> somewhere, maybe I don't know where to look anymore. Is there a list of
>> changes that has been made to the API? What happened to generics?
>> >
>> > Thanks,
>> > Darren
>> > _______________________________________________
>> > IPython-dev mailing list
>> > IPython-dev at scipy.org
>> > https://mail.scipy.org/mailman/listinfo/ipython-dev
>>
>> --
>> Ray Osborn, Senior Scientist
>> Materials Science Division
>> Argonne National Laboratory
>> Argonne, IL 60439, USA
>> Phone: +1 (630) 252-9011
>> Email: ROsborn at anl.gov
>>
>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at scipy.org
>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151202/c2947a76/attachment.html>

From mantegazza at ill.fr  Thu Dec  3 02:26:12 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Thu, 3 Dec 2015 08:26:12 +0100
Subject: [IPython-dev] Using jupyter_console as embedded shell
Message-ID: <20151203082612.06295e86@ill.fr>

Hi!

Is there a direct matching of the InteractiveShellEmbed in
jupyter_console ? I tried to replace:

  from IPython.terminal.embed import InteractiveShellEmbed
  ipshell = InteractiveShellEmbed(...)
  ipshell.mainloop()

with:

  from jupyter_console.interactiveshell import ZMQTerminalInteractiveShell
  ipshell = ZMQTerminalInteractiveShell(...)
  ipshell.mainloop()

but I get an exception:

"/opt/miniconda2/lib/python2.7/site-packages/jupyter_console/interactiveshell.py",
 line 460, in wait_for_kernel
    self.client.hb_channel.unpause()
AttributeError: 'NoneType' object has no attribute 'hb_channel'

I do have a kernel running (launched with ipython notebook), but I may
need to give the client additional informations?

Thanks for your help,

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From takowl at gmail.com  Thu Dec  3 05:02:34 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Thu, 3 Dec 2015 10:02:34 +0000
Subject: [IPython-dev] Using jupyter_console as embedded shell
In-Reply-To: <20151203082612.06295e86@ill.fr>
References: <20151203082612.06295e86@ill.fr>
Message-ID: <CAOvn4qgB_6SY5QG8k0THM+G2kpKPxfHufgqu2ER-fu4+ro74zQ@mail.gmail.com>

On 3 December 2015 at 07:26, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:

> Is there a direct matching of the InteractiveShellEmbed in
> jupyter_console ?
>

There isn't, because it doesn't really make sense. Embedding an IPython
shell gives you interactive access to the namespace in which you invoke it
- it's like launching a debugger with pdb.set_trace(). jupyter_console is
for communicating with a kernel in a separate process, so you can't embed
it in the namespace where you created it.

You can embed the IPython kernel by calling IPython.embed_kernel(), and
then connect a console to it from another terminal, if that's what you want.

Or if you just want to start jupyter_console programmatically, without
worrying about the namespace, I think that's jupyter_console.app.main().
Passing existing=True should be equivalent to --existing on the command
line.

Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151203/139e6ba7/attachment.html>

From mantegazza at ill.fr  Thu Dec  3 05:10:25 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Thu, 3 Dec 2015 11:10:25 +0100
Subject: [IPython-dev] Using jupyter_console as embedded shell
In-Reply-To: <CAOvn4qgB_6SY5QG8k0THM+G2kpKPxfHufgqu2ER-fu4+ro74zQ@mail.gmail.com>
References: <20151203082612.06295e86@ill.fr>
 <CAOvn4qgB_6SY5QG8k0THM+G2kpKPxfHufgqu2ER-fu4+ro74zQ@mail.gmail.com>
Message-ID: <20151203111025.7c802485@ill.fr>

Le 03/12/2015, Thomas a ?crit :

> There isn't, because it doesn't really make sense. Embedding an IPython
> shell gives you interactive access to the namespace in which you invoke
> it
> - it's like launching a debugger with pdb.set_trace(). jupyter_console is
> for communicating with a kernel in a separate process, so you can't embed
> it in the namespace where you created it.
> 
> You can embed the IPython kernel by calling IPython.embed_kernel(), and
> then connect a console to it from another terminal, if that's what you
> want.
> 
> Or if you just want to start jupyter_console programmatically, without
> worrying about the namespace, I think that's jupyter_console.app.main().
> Passing existing=True should be equivalent to --existing on the command
> line.

I see.

So, I have to move my customization of IPython (completer, custom
exceptions and so), to the kernel, right? The kernel acts as the core of
IPython?

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From takowl at gmail.com  Thu Dec  3 05:28:32 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Thu, 3 Dec 2015 10:28:32 +0000
Subject: [IPython-dev] Using jupyter_console as embedded shell
In-Reply-To: <20151203111025.7c802485@ill.fr>
References: <20151203082612.06295e86@ill.fr>
 <CAOvn4qgB_6SY5QG8k0THM+G2kpKPxfHufgqu2ER-fu4+ro74zQ@mail.gmail.com>
 <20151203111025.7c802485@ill.fr>
Message-ID: <CAOvn4qiHS9KQ=Y1XDzkwPmLwCX+pdAO6unMR2PTLfFmefMK76g@mail.gmail.com>

On 3 December 2015 at 10:10, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:

> So, I have to move my customization of IPython (completer, custom
> exceptions and so), to the kernel, right? The kernel acts as the core of
> IPython?
>

The kernel is the process that loads IPython and handles execution, tab
completion, and so on. Almost everything that's specific to dealing with
Python code happens in the kernel (syntax higlighting in the notebook and
the Qt console are exceptions). All of the Jupyter frontends (notebook,
qtconsole, console) communicate with kernels by sending messages back and
forth over a zmq socket. As far as possible, anything under the 'Jupyter'
name is language agnostic, so it should work as well for Julia, or R, or
any other language as it does for Python (so long as there's a kernel for
the language installed).

Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151203/5047d9a2/attachment.html>

From mantegazza at ill.fr  Thu Dec  3 07:01:59 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Thu, 3 Dec 2015 13:01:59 +0100
Subject: [IPython-dev] Using jupyter_console as embedded shell
In-Reply-To: <CAOvn4qiHS9KQ=Y1XDzkwPmLwCX+pdAO6unMR2PTLfFmefMK76g@mail.gmail.com>
References: <20151203082612.06295e86@ill.fr>
 <CAOvn4qgB_6SY5QG8k0THM+G2kpKPxfHufgqu2ER-fu4+ro74zQ@mail.gmail.com>
 <20151203111025.7c802485@ill.fr>
 <CAOvn4qiHS9KQ=Y1XDzkwPmLwCX+pdAO6unMR2PTLfFmefMK76g@mail.gmail.com>
Message-ID: <20151203130159.52818ef9@ill.fr>

Le 03/12/2015, Thomas a ?crit :

> The kernel is the process that loads IPython and handles execution, tab
> completion, and so on. Almost everything that's specific to dealing with
> Python code happens in the kernel

Ok. Based on this code:

https://github.com/ipython/ipykernel/blob/master/ipykernel/embed.py

I successfully started the kernel, and connected several console to it.

But my config (prompt, completion, exceptions behaviour...) is not taken
into account. What did I miss?

Here is my code:

  from ipykernel.kernelapp import IPKernelApp
  from traitlets.config.loader import Config

  config = Config()
  promptManager = config.PromptManager
  promptManager.in_template = "{color.LightGreen}Simul>>> "
  startMsg = "\nWelcome to PyMAD"
  startMsg += "\n\nAvailable objects: %s " % sortedProxies
  startMsg += "\n\nAvailable helpers: %s\n" % helpers.keys()
  exitMsg = "\nBye!\n"

  app = IPKernelApp.instance(config=config,
                             banner1=startMsg,
                             exit_msg=exitMsg)
  app.initialize([])

  app.shell.set_custom_exc((Exception, ), pymadHandler)
  app.shell.set_custom_completer(proxy_matches)
  app.shell.Completer.merge_completions = False
  app.shell.set_hook("pre_prompt_hook", pre_prompt_hook)
  app.shell.events.register('pre_execute', pre_execute)
  app.shell.register_magics(ServerMagics)

  app.kernel.user_ns = context
  app.start()

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From takowl at gmail.com  Thu Dec  3 07:34:10 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Thu, 3 Dec 2015 12:34:10 +0000
Subject: [IPython-dev] Using jupyter_console as embedded shell
In-Reply-To: <20151203130159.52818ef9@ill.fr>
References: <20151203082612.06295e86@ill.fr>
 <CAOvn4qgB_6SY5QG8k0THM+G2kpKPxfHufgqu2ER-fu4+ro74zQ@mail.gmail.com>
 <20151203111025.7c802485@ill.fr>
 <CAOvn4qiHS9KQ=Y1XDzkwPmLwCX+pdAO6unMR2PTLfFmefMK76g@mail.gmail.com>
 <20151203130159.52818ef9@ill.fr>
Message-ID: <CAOvn4qigJVX71hd48i2xa-3Rzd9RVen8v8DyXJYmdW2=DXqVMg@mail.gmail.com>

On 3 December 2015 at 12:01, Fr?d?ric Mantegazza <mantegazza at ill.fr> wrote:

> But my config (prompt, completion, exceptions behaviour...) is not taken
> into account. What did I miss?
>

The prompts config won't affect the frontends you connect to the kernel -
prompts are produced by the frontend, and are mostly not configurable
(we've thought about making them more configurable, but there aren't many
people asking for that, and it would add quite a bit of complexity, so it
hasn't happened yet).

As far as I know, the completions and custom exception handlers you're
setting up should work; I'm not sure why they don't.

Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151203/81269cc6/attachment.html>

From ian.h.bell at gmail.com  Thu Dec  3 11:39:14 2015
From: ian.h.bell at gmail.com (Ian Bell)
Date: Thu, 3 Dec 2015 09:39:14 -0700
Subject: [IPython-dev] notebook hanging
Message-ID: <CAJQnXJe-3Vuav=Y=UVmF_4ee=_u=E629X=64eGuD6BdXS5hDfg@mail.gmail.com>

Hi!

I'm running into troubles with the Jupyter notebook hanging with the python
kernel.  I'm doing some sympy calculations, and when I say run all cells, I
can evaluate the first cell in the notebook, and then it just hangs - no
error message in console, no error message in window, etc.  The screenshot
below shows the issue.  I've tried to flush out the security directory in
HOME\.ipython\profile_default\security, which worked yesterday, but is no
longer working today.

Has anyone had a similar problem before?

Ian

[image: Inline image 1]
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151203/3352055b/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 45622 bytes
Desc: not available
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151203/3352055b/attachment.png>

From mantegazza at ill.fr  Fri Dec  4 01:34:35 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Fri, 4 Dec 2015 07:34:35 +0100
Subject: [IPython-dev] Python tutorials based on notebook
Message-ID: <20151204073435.59787326@ill.fr>

Hi!

I was wondering is there are some Python tutorials based on notebook?
Something I could re-use to make an nice intriduction to Python...

Thanks,

-- 
    Fr?d?ric
    76 17


From zvoros at gmail.com  Fri Dec  4 02:34:52 2015
From: zvoros at gmail.com (=?UTF-8?B?Wm9sdMOhbiBWw7Zyw7Zz?=)
Date: Fri, 4 Dec 2015 08:34:52 +0100
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <20151204073435.59787326@ill.fr>
References: <20151204073435.59787326@ill.fr>
Message-ID: <5661421C.8040907@gmail.com>

Fr?d?ric,

Have you looked at 
https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks 
? I believe you should be able to find something there that fits the bill.

Cheers,

Zolt?n

On 12/04/2015 07:34 AM, Fr?d?ric Mantegazza wrote:
> Hi!
>
> I was wondering is there are some Python tutorials based on notebook?
> Something I could re-use to make an nice intriduction to Python...
>
> Thanks,
>



From mantegazza at ill.fr  Fri Dec  4 02:48:33 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Fri, 4 Dec 2015 08:48:33 +0100
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <5661421C.8040907@gmail.com>
References: <20151204073435.59787326@ill.fr>
	<5661421C.8040907@gmail.com>
Message-ID: <20151204084833.709ecc07@ill.fr>

Le 04/12/2015, Zolt?n a ?crit :

> Have you looked at 
> https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks 
> ? I believe you should be able to find something there that fits the
> bill.

I missed that! That's exactly what I was looking for :o)

Thanks,

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From efiring at hawaii.edu  Fri Dec  4 11:50:02 2015
From: efiring at hawaii.edu (Eric Firing)
Date: Fri, 4 Dec 2015 06:50:02 -1000
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <20151204073435.59787326@ill.fr>
References: <20151204073435.59787326@ill.fr>
Message-ID: <5661C43A.70604@hawaii.edu>

On 2015/12/03 8:34 PM, Fr?d?ric Mantegazza wrote:
> Hi!
>
> I was wondering is there are some Python tutorials based on notebook?
> Something I could re-use to make an nice intriduction to Python...
>
> Thanks,
>

I have included some notebook-based tutorials in:

http://currents.soest.hawaii.edu/ocn_data_analysis/

Eric


From mantegazza at ill.fr  Mon Dec  7 01:37:03 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Mon, 7 Dec 2015 07:37:03 +0100
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <5661C43A.70604@hawaii.edu>
References: <20151204073435.59787326@ill.fr>
	<5661C43A.70604@hawaii.edu>
Message-ID: <20151207073703.688b6b98@ill.fr>

Le 04/12/2015, Eric a ?crit :

> I have included some notebook-based tutorials in:
> 
> http://currents.soest.hawaii.edu/ocn_data_analysis/

Thanks!

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From eric at cfa.harvard.edu  Mon Dec  7 08:49:18 2015
From: eric at cfa.harvard.edu (ericmandel)
Date: Mon, 7 Dec 2015 05:49:18 -0800 (PST)
Subject: [IPython-dev] embedding js9 into a notebook
In-Reply-To: <CACejjWzfk_+Wq8=v75GS+sQv-z3TxAN2Ypk8HQ-Jpzgkbk0LMQ@mail.gmail.com>
References: <CAFA9sd2Xrah0rzGXR=mZLNdo5BxpKZaPy9i2NAV=ABTssQTtYA@mail.gmail.com>
 <CAB-sx63CPtnvk-QYBVmxgwspFG5+BrHkbvskZN7_8AdoTSpqwA@mail.gmail.com>
 <CAFA9sd3tDvnNneT5j10=UWhEjYhZzrjrvOGYdZoSKYp15-0OPA@mail.gmail.com>
 <CAB-sx60ydPcgx0AKK=TQbagN0J0yCVyf-4DnK8iGuzpOF+LKRg@mail.gmail.com>
 <CAFA9sd2RktiCwAX39ekYLPvrVmVgZ5wgN=YbSnUmQmeiV6xfWg@mail.gmail.com>
 <CACejjWz_+SCPnenm8Y5nARydBsN8vTZGBMb4AKdbaZCrNwsUHw@mail.gmail.com>
 <CAFA9sd1urU1O223AKPE-OPr0KZ=5PGZ=dn4Z1DpSO5AYL3pu3Q@mail.gmail.com>
 <CACejjWzfk_+Wq8=v75GS+sQv-z3TxAN2Ypk8HQ-Jpzgkbk0LMQ@mail.gmail.com>
Message-ID: <1449496158258-5178693.post@n6.nabble.com>

We?ve made some progress integrating JS9 image display into Jupyter. Try
executing this in a cell:

%%html
<div class="JS9Menubar"></div>
<div class="JS9"></div>
<link type="text/css" rel="stylesheet"
href="//js9.si.edu/jupyter/js9-allinone.css">


If you do not have astronomical data, you should be able to drag and drop a
png file onto the display. Create a region from the Regions menu, select an
analysis tool like 3dPlot from the Analysis menu, click the region and move
it around, etc ?

The one thing that really does not work is keyboard input into dialog boxes.
For example, in the Zoom menu, click the ?numeric zoom value? box and try to
enter a zoom factor. The whole display disappears, presumably because the
keypress event is being interpreted as a Jupyter command/edit keypress.

Is there a simple way to focus keyboard events away from Jupyter itself? My
colleague Gijs Molenaar, who actually understands Jupyter (I?m the author of
JS9 and know next to nothing) will get back to this, but for now, it would
be great to be able to tell early adopters how to run JS9 in Jupyter without
crashing it. 

If the answer is that one cannot wrestle the keyboard focus away from
Jupyter, I can disable the dialog boxes. But in that case, it would be
really useful to know that JS9 is in the Jupyter environment. Does Jupyter
load any unique JavaScript or set a variable that I can check for in order
to sense the environment?




--
View this message in context: http://python.6.x6.nabble.com/embedding-js9-into-a-notebook-tp5173096p5178693.html
Sent from the IPython - Development mailing list archive at Nabble.com.


From nick.bollweg at gmail.com  Mon Dec  7 09:25:09 2015
From: nick.bollweg at gmail.com (Nicholas Bollweg)
Date: Mon, 07 Dec 2015 14:25:09 +0000
Subject: [IPython-dev] embedding js9 into a notebook
In-Reply-To: <1449496158258-5178693.post@n6.nabble.com>
References: <CAFA9sd2Xrah0rzGXR=mZLNdo5BxpKZaPy9i2NAV=ABTssQTtYA@mail.gmail.com>
 <CAB-sx63CPtnvk-QYBVmxgwspFG5+BrHkbvskZN7_8AdoTSpqwA@mail.gmail.com>
 <CAFA9sd3tDvnNneT5j10=UWhEjYhZzrjrvOGYdZoSKYp15-0OPA@mail.gmail.com>
 <CAB-sx60ydPcgx0AKK=TQbagN0J0yCVyf-4DnK8iGuzpOF+LKRg@mail.gmail.com>
 <CAFA9sd2RktiCwAX39ekYLPvrVmVgZ5wgN=YbSnUmQmeiV6xfWg@mail.gmail.com>
 <CACejjWz_+SCPnenm8Y5nARydBsN8vTZGBMb4AKdbaZCrNwsUHw@mail.gmail.com>
 <CAFA9sd1urU1O223AKPE-OPr0KZ=5PGZ=dn4Z1DpSO5AYL3pu3Q@mail.gmail.com>
 <CACejjWzfk_+Wq8=v75GS+sQv-z3TxAN2Ypk8HQ-Jpzgkbk0LMQ@mail.gmail.com>
 <1449496158258-5178693.post@n6.nabble.com>
Message-ID: <CACejjWxvveVrJDzDDJkknmimQpzT8Zn_dQzxLK4aVKMErxdNVQ@mail.gmail.com>

Great, I'm glad you've made progress!

The key method is:

Jupyter.keyboard_manager.register_events($("<selector for the node>"))

The nuclear option may also be worth considering: rendering the whole js9
inside an iframe.

Let me know when you are thinking you've advanced to the point where you
want to try to package the whole thing in a repo. It would be easier to
start collaborating on code, and then be able to get a binder (mybinder.org)
going, then consider how to proceed: pure js nbextension, python backend
(widgets), etc.

On Mon, Dec 7, 2015 at 8:58 AM ericmandel <eric at cfa.harvard.edu> wrote:

> We?ve made some progress integrating JS9 image display into Jupyter. Try
> executing this in a cell:
>
> %%html
> <div class="JS9Menubar"></div>
> <div class="JS9"></div>
> <link type="text/css" rel="stylesheet"
> href="//js9.si.edu/jupyter/js9-allinone.css">
>
>
> If you do not have astronomical data, you should be able to drag and drop a
> png file onto the display. Create a region from the Regions menu, select an
> analysis tool like 3dPlot from the Analysis menu, click the region and move
> it around, etc ?
>
> The one thing that really does not work is keyboard input into dialog
> boxes.
> For example, in the Zoom menu, click the ?numeric zoom value? box and try
> to
> enter a zoom factor. The whole display disappears, presumably because the
> keypress event is being interpreted as a Jupyter command/edit keypress.
>
> Is there a simple way to focus keyboard events away from Jupyter itself? My
> colleague Gijs Molenaar, who actually understands Jupyter (I?m the author
> of
> JS9 and know next to nothing) will get back to this, but for now, it would
> be great to be able to tell early adopters how to run JS9 in Jupyter
> without
> crashing it.
>
> If the answer is that one cannot wrestle the keyboard focus away from
> Jupyter, I can disable the dialog boxes. But in that case, it would be
> really useful to know that JS9 is in the Jupyter environment. Does Jupyter
> load any unique JavaScript or set a variable that I can check for in order
> to sense the environment?
>
>
>
>
> --
> View this message in context:
> http://python.6.x6.nabble.com/embedding-js9-into-a-notebook-tp5173096p5178693.html
> Sent from the IPython - Development mailing list archive at Nabble.com.
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151207/938b05d1/attachment.html>

From mmckerns at caltech.edu  Mon Dec  7 10:16:33 2015
From: mmckerns at caltech.edu (Michael McKerns)
Date: Mon, 7 Dec 2015 10:16:33 -0500
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <20151202152801.5298d6d2@ill.fr>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
 <A80751CE-F81D-4FA0-8003-06ED92104CDD@anl.gov>
 <20151202152801.5298d6d2@ill.fr>
Message-ID: <2f18f25bead169c7d841dacf1b24c775.squirrel@webmail.caltech.edu>

Fr?d?ric,

Pyro is good for python to non-python connections, however, if you are
going python to python, a good alternative is to use ParallelPython `pp`,
which has remote python servers. There's an easy-to-install version of it
that's available as `ppft`, which provides better serialization capabilities
than `pp`.  'ppft' uses a lighter weight communication requirement than
anything mentioned already (essentially, it creates a pipe to a connection
across a port and sends by RPC).  This allows you to set up a "remote python
instance", and then ship objects to it across a pipe to be executed
(potentially
in parallel).

There's also `rpyc`, which essentially does the same thing.
(see: http://www.ibm.com/developerworks/linux/library/l-rpyc)
Classic mode in `rpyc` is especially powerful, if you unequivocally
trust your users -- if not, don't use 'Classic', and register all your
functions that you want to make available on the remote machine.

I have used both `rpyc` and `ppft` inside of ssh-tunneled connections,
which can be established automatically via `paramiko` or `pathos`.
For flexible single connections where I want to do something complex,
I often use `rpyc` inside a combination of `paramiko` and `pathos`
(depending on what needs to be done).  For parallel computing on a remote
machine, I use `pathos` plus `ppft`.  Both mechanism have been used
successfully to tunnel into remote machines at the DOE labs for over
10 years, including making remote connections to the ARCS spectrometer
at ORNL, and for creating more complex ad-hoc graphs of distributed
workers (that don't require a master-controller relationship) across
several DOE leadership class machines.  Any of the above is very simple
solution, as it doesn't try to do too much? which is why it works.

In this particular case, the Jupyter/Ipython environment for distributed
computing doesn't seem to me to be quite what you are looking for, at least
not just yet.  However, it would be pretty sweet if Jupyter/Ipython went
that way
eventually, as it can handle much more complexity across the pipe and in what
it can directly hook into than what I'm suggesting.



> Le 02/12/2015, Raymond a ?crit :
>
>> We have been testing the use of Pyro4 as a method of loading remote
>> NeXus files within NeXpy, which also uses a Jupyter shell
>> (http://nexpy.github.io/nexpy/). It?s not part of the official
>> distribution yet, but I would be happy to discuss it with you outside
>> this list. As a fellow neutron scatterer, it might be relevant.
>
> Great!
>
> I will surely come back to you, but I first need to understand all
> concepts behind IPython 4 and Jupyter...
>
> BTW, NeXus is also on our TODO list of things to learn ;o)
>
> --
>     Fr?d?ric MANTEGAZZA             CEA-Grenoble
>     Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
>     Fax      : 33 (0) 476 483 906   17, rue des Martyrs
>     Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>


---

Mike McKerns
California Institute of Technology
http://www.its.caltech.edu/~mmckerns



From eric at cfa.harvard.edu  Mon Dec  7 19:55:40 2015
From: eric at cfa.harvard.edu (ericmandel)
Date: Mon, 7 Dec 2015 16:55:40 -0800 (PST)
Subject: [IPython-dev] embedding js9 into a notebook
In-Reply-To: <CACejjWxvveVrJDzDDJkknmimQpzT8Zn_dQzxLK4aVKMErxdNVQ@mail.gmail.com>
References: <CAFA9sd2Xrah0rzGXR=mZLNdo5BxpKZaPy9i2NAV=ABTssQTtYA@mail.gmail.com>
 <CAB-sx63CPtnvk-QYBVmxgwspFG5+BrHkbvskZN7_8AdoTSpqwA@mail.gmail.com>
 <CAFA9sd3tDvnNneT5j10=UWhEjYhZzrjrvOGYdZoSKYp15-0OPA@mail.gmail.com>
 <CAB-sx60ydPcgx0AKK=TQbagN0J0yCVyf-4DnK8iGuzpOF+LKRg@mail.gmail.com>
 <CAFA9sd2RktiCwAX39ekYLPvrVmVgZ5wgN=YbSnUmQmeiV6xfWg@mail.gmail.com>
 <CACejjWz_+SCPnenm8Y5nARydBsN8vTZGBMb4AKdbaZCrNwsUHw@mail.gmail.com>
 <CAFA9sd1urU1O223AKPE-OPr0KZ=5PGZ=dn4Z1DpSO5AYL3pu3Q@mail.gmail.com>
 <CACejjWzfk_+Wq8=v75GS+sQv-z3TxAN2Ypk8HQ-Jpzgkbk0LMQ@mail.gmail.com>
 <1449496158258-5178693.post@n6.nabble.com>
 <CACejjWxvveVrJDzDDJkknmimQpzT8Zn_dQzxLK4aVKMErxdNVQ@mail.gmail.com>
Message-ID: <1449536140426-5178757.post@n6.nabble.com>

> The key method is:
> Jupyter.keyboard_manager.register_events($("<selector for the node>"))

Perfect! All of the JS9 dialog boxes now work as expected inside Jupyter.
Thanks very much for your timely suggestion.

The only functions that do not work are those requiring $.ajax() calls.
These are not critical, but I would work at fixing them if they ought to
work and if you can give me a hint.

Otherwise, my colleague Gijs and I will be back in touch when he is ready to
deal with final form and packaging issues.




--
View this message in context: http://python.6.x6.nabble.com/embedding-js9-into-a-notebook-tp5173096p5178757.html
Sent from the IPython - Development mailing list archive at Nabble.com.


From mantegazza at ill.fr  Tue Dec  8 01:28:08 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Tue, 8 Dec 2015 07:28:08 +0100
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <2f18f25bead169c7d841dacf1b24c775.squirrel@webmail.caltech.edu>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
 <A80751CE-F81D-4FA0-8003-06ED92104CDD@anl.gov>
 <20151202152801.5298d6d2@ill.fr>
 <2f18f25bead169c7d841dacf1b24c775.squirrel@webmail.caltech.edu>
Message-ID: <20151208072808.7d65bcf8@ill.fr>

Le 07/12/2015, Michael a ?crit :

> Pyro is good for python to non-python connections

Really ? AFAK, Pyro can only be used from Pythons scripts...

> however, if you are going python to python, a good alternative is to use
> ParallelPython `pp`, which has remote python servers. There's an
> easy-to-install version of it that's available as `ppft`, which provides
> better serialization capabilities than `pp`.  'ppft' uses a lighter
> weight communication requirement than anything mentioned already
> (essentially, it creates a pipe to a connection across a port and sends
> by RPC).  This allows you to set up a "remote python instance", and then
> ship objects to it across a pipe to be executed (potentially
> in parallel).
> 
> There's also `rpyc`, which essentially does the same thing.
> (see: http://www.ibm.com/developerworks/linux/library/l-rpyc)
> Classic mode in `rpyc` is especially powerful, if you unequivocally
> trust your users -- if not, don't use 'Classic', and register all your
> functions that you want to make available on the remote machine.

I will have a look at these framworks...

> I have used both `rpyc` and `ppft` inside of ssh-tunneled connections,
> which can be established automatically via `paramiko` or `pathos`.
> For flexible single connections where I want to do something complex,
> I often use `rpyc` inside a combination of `paramiko` and `pathos`
> (depending on what needs to be done).  For parallel computing on a remote
> machine, I use `pathos` plus `ppft`.  Both mechanism have been used
> successfully to tunnel into remote machines at the DOE labs for over
> 10 years, including making remote connections to the ARCS spectrometer
> at ORNL, and for creating more complex ad-hoc graphs of distributed
> workers (that don't require a master-controller relationship) across
> several DOE leadership class machines.  Any of the above is very simple
> solution, as it doesn't try to do too much? which is why it works.

Thanks for your feedback. It's important to know how reliable solutions
are.

> In this particular case, the Jupyter/Ipython environment for distributed
> computing doesn't seem to me to be quite what you are looking for, at
> least not just yet.

Yes, I agree. For now, we will keep our architecture, and use IPython as
embedded shell, as we did before.

Maybe replace Pyro with one of the suggested framework.

-- 
    Fr?d?ric MANTEGAZZA             CEA-Grenoble
    Tel.     : 33 (0) 476 207 617   INAC/SPSMS/MDN
    Fax      : 33 (0) 476 483 906   17, rue des Martyrs
    Courriel : mantegazza at ill.fr    F-38054 Grenoble Cedex 09



From nick.bollweg at gmail.com  Tue Dec  8 06:59:46 2015
From: nick.bollweg at gmail.com (Nicholas Bollweg)
Date: Tue, 08 Dec 2015 11:59:46 +0000
Subject: [IPython-dev] embedding js9 into a notebook
In-Reply-To: <1449536140426-5178757.post@n6.nabble.com>
References: <CAFA9sd2Xrah0rzGXR=mZLNdo5BxpKZaPy9i2NAV=ABTssQTtYA@mail.gmail.com>
 <CAB-sx63CPtnvk-QYBVmxgwspFG5+BrHkbvskZN7_8AdoTSpqwA@mail.gmail.com>
 <CAFA9sd3tDvnNneT5j10=UWhEjYhZzrjrvOGYdZoSKYp15-0OPA@mail.gmail.com>
 <CAB-sx60ydPcgx0AKK=TQbagN0J0yCVyf-4DnK8iGuzpOF+LKRg@mail.gmail.com>
 <CAFA9sd2RktiCwAX39ekYLPvrVmVgZ5wgN=YbSnUmQmeiV6xfWg@mail.gmail.com>
 <CACejjWz_+SCPnenm8Y5nARydBsN8vTZGBMb4AKdbaZCrNwsUHw@mail.gmail.com>
 <CAFA9sd1urU1O223AKPE-OPr0KZ=5PGZ=dn4Z1DpSO5AYL3pu3Q@mail.gmail.com>
 <CACejjWzfk_+Wq8=v75GS+sQv-z3TxAN2Ypk8HQ-Jpzgkbk0LMQ@mail.gmail.com>
 <1449496158258-5178693.post@n6.nabble.com>
 <CACejjWxvveVrJDzDDJkknmimQpzT8Zn_dQzxLK4aVKMErxdNVQ@mail.gmail.com>
 <1449536140426-5178757.post@n6.nabble.com>
Message-ID: <CACejjWzCwr8vuzpgsenWCUMrTQ+as4Bw2tLE5fmgoo8Y+NK9DQ@mail.gmail.com>

What are the symptoms on the ajax calls? This is another area where the
iframe may have the advantage, as the link base would be the static html
page you served up, presumably from where the the js9 stuff would be
saved/packaged, so it would work more like the "normal" usage on the js9
site.

On Mon, Dec 7, 2015 at 8:05 PM ericmandel <eric at cfa.harvard.edu> wrote:

> > The key method is:
> > Jupyter.keyboard_manager.register_events($("<selector for the node>"))
>
> Perfect! All of the JS9 dialog boxes now work as expected inside Jupyter.
> Thanks very much for your timely suggestion.
>
> The only functions that do not work are those requiring $.ajax() calls.
> These are not critical, but I would work at fixing them if they ought to
> work and if you can give me a hint.
>
> Otherwise, my colleague Gijs and I will be back in touch when he is ready
> to
> deal with final form and packaging issues.
>
>
>
>
> --
> View this message in context:
> http://python.6.x6.nabble.com/embedding-js9-into-a-notebook-tp5173096p5178757.html
> Sent from the IPython - Development mailing list archive at Nabble.com.
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151208/bf1caf20/attachment.html>

From mmckerns at caltech.edu  Tue Dec  8 07:28:50 2015
From: mmckerns at caltech.edu (Michael McKerns)
Date: Tue, 8 Dec 2015 07:28:50 -0500
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <20151208072808.7d65bcf8@ill.fr>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
 <A80751CE-F81D-4FA0-8003-06ED92104CDD@anl.gov>
 <20151202152801.5298d6d2@ill.fr>
 <2f18f25bead169c7d841dacf1b24c775.squirrel@webmail.caltech.edu>
 <20151208072808.7d65bcf8@ill.fr>
Message-ID: <e124e163f89e0c1bde9b35f2ce1628b7.squirrel@webmail.caltech.edu>

>> Pyro is good for python to non-python connections
>
> Really ? AFAK, Pyro can only be used from Pythons scripts...

Ah... I was thinking of:
https://github.com/irmen/Pyrolite/
which comes from the same author,
and uses Pyro4.

---

Mike McKerns
California Institute of Technology
http://www.its.caltech.edu/~mmckerns



From mantegazza at ill.fr  Tue Dec  8 07:54:57 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Tue, 8 Dec 2015 13:54:57 +0100
Subject: [IPython-dev] From Pyro to IPython/Jupyter
In-Reply-To: <e124e163f89e0c1bde9b35f2ce1628b7.squirrel@webmail.caltech.edu>
References: <20151202084240.341947e5@ill.fr>
 <CAOvn4qgEDQeH2W6O3kwYobQGy8KXf8bFM-AvV-Abd6Na3DD59A@mail.gmail.com>
 <20151202131238.20f2e3b0@ill.fr>
 <CAOvn4qj22HQ+_d-VN7mcgEyQ0Vbzj10kCD+DOyk6SWANd8nB5A@mail.gmail.com>
 <20151202142738.58bc01ab@ill.fr>
 <A80751CE-F81D-4FA0-8003-06ED92104CDD@anl.gov>
 <20151202152801.5298d6d2@ill.fr>
 <2f18f25bead169c7d841dacf1b24c775.squirrel@webmail.caltech.edu>
 <20151208072808.7d65bcf8@ill.fr>
 <e124e163f89e0c1bde9b35f2ce1628b7.squirrel@webmail.caltech.edu>
Message-ID: <20151208135457.4d54c5b7@ill.fr>

Le 08/12/2015, Michael a ?crit :

> Ah... I was thinking of:
> https://github.com/irmen/Pyrolite/
> which comes from the same author,
> and uses Pyro4.

I see!

-- 
    Fr?d?ric
    76 17


From eric at cfa.harvard.edu  Tue Dec  8 11:05:55 2015
From: eric at cfa.harvard.edu (ericmandel)
Date: Tue, 8 Dec 2015 08:05:55 -0800 (PST)
Subject: [IPython-dev] embedding js9 into a notebook
In-Reply-To: <CACejjWzCwr8vuzpgsenWCUMrTQ+as4Bw2tLE5fmgoo8Y+NK9DQ@mail.gmail.com>
References: <CAFA9sd3tDvnNneT5j10=UWhEjYhZzrjrvOGYdZoSKYp15-0OPA@mail.gmail.com>
 <CAB-sx60ydPcgx0AKK=TQbagN0J0yCVyf-4DnK8iGuzpOF+LKRg@mail.gmail.com>
 <CAFA9sd2RktiCwAX39ekYLPvrVmVgZ5wgN=YbSnUmQmeiV6xfWg@mail.gmail.com>
 <CACejjWz_+SCPnenm8Y5nARydBsN8vTZGBMb4AKdbaZCrNwsUHw@mail.gmail.com>
 <CAFA9sd1urU1O223AKPE-OPr0KZ=5PGZ=dn4Z1DpSO5AYL3pu3Q@mail.gmail.com>
 <CACejjWzfk_+Wq8=v75GS+sQv-z3TxAN2Ypk8HQ-Jpzgkbk0LMQ@mail.gmail.com>
 <1449496158258-5178693.post@n6.nabble.com>
 <CACejjWxvveVrJDzDDJkknmimQpzT8Zn_dQzxLK4aVKMErxdNVQ@mail.gmail.com>
 <1449536140426-5178757.post@n6.nabble.com>
 <CACejjWzCwr8vuzpgsenWCUMrTQ+as4Bw2tLE5fmgoo8Y+NK9DQ@mail.gmail.com>
Message-ID: <1449590755569-5178827.post@n6.nabble.com>

Ah right, the ajax problem is caused by using the wrong link base. I'll have
to think about how to deal with that. Unfortunately, cross-origin framing of
our web sites is tangled in admin policy issues and it's less obvious how to
deal with that.

But also, it's unclear how Jupyter users will want to access JS9. From an
iframe, we could offer the JS9 Web site: drag/drop data into the display. We
also could offer "canned" JS9 pages with different combinations of JS9
plugin options (e.g. show the image panner and magnifier instead of bringing
them up as light windows).  But JS9 is a plugin library allowing Web
designers to roll their own just by placing div elements containing JS9
classes on a page. Will users want to do that? I think that partly depends
on what Jupyter users are accustomed to doing in general -- I have no idea
about that. Hopefully Gijs will have a better feel for how the astronomical
community uses Jupyter ... but comments are welcome ...

Finally, if the JS9 js and css files are installed and loaded locally,
possibilities open up for adding locally tailored data analysis. That might
be something to move toward. But again, it depends on how people might want
to use it.



--
View this message in context: http://python.6.x6.nabble.com/embedding-js9-into-a-notebook-tp5173096p5178827.html
Sent from the IPython - Development mailing list archive at Nabble.com.


From markbak at gmail.com  Wed Dec  9 03:21:43 2015
From: markbak at gmail.com (Mark Bakker)
Date: Wed, 9 Dec 2015 09:21:43 +0100
Subject: [IPython-dev] Python tutorials based on notebook
Message-ID: <CAEX=yaaG-Kw+arbMXo1Q8yruTWAs8D_J6R_ezN1+6RvYbT_fyw@mail.gmail.com>

I put the Notebooks of my Introductory Programming class online. Maybe
those help:

https://mbakker7.github.io/exploratory_computing_with_python/

On 2015/12/03 8:34 PM, Fr?d?ric Mantegazza wrote:
> Hi!
>
> I was wondering is there are some Python tutorials based on notebook?
> Something I could re-use to make an nice intriduction to Python...
>
> Thanks,
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151209/21f3236b/attachment.html>

From mantegazza at ill.fr  Wed Dec  9 03:33:54 2015
From: mantegazza at ill.fr (=?UTF-8?B?RnLDqWTDqXJpYw==?= Mantegazza)
Date: Wed, 9 Dec 2015 09:33:54 +0100
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <CAEX=yaaG-Kw+arbMXo1Q8yruTWAs8D_J6R_ezN1+6RvYbT_fyw@mail.gmail.com>
References: <CAEX=yaaG-Kw+arbMXo1Q8yruTWAs8D_J6R_ezN1+6RvYbT_fyw@mail.gmail.com>
Message-ID: <20151209093354.5cf0a860@ill.fr>

Le 09/12/2015, Mark a ?crit :

> I put the Notebooks of my Introductory Programming class online. Maybe
> those help:
> 
> https://mbakker7.github.io/exploratory_computing_with_python/

Yes, very helpfull for our scientists! I'll transmit them your link.

Thanks,

-- 
    Fr?d?ric
    76 17


From pietro.terna at unito.it  Wed Dec  9 03:52:55 2015
From: pietro.terna at unito.it (Pietro Terna)
Date: Wed, 9 Dec 2015 09:52:55 +0100
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <20151209093354.5cf0a860@ill.fr>
References: <CAEX=yaaG-Kw+arbMXo1Q8yruTWAs8D_J6R_ezN1+6RvYbT_fyw@mail.gmail.com>
 <20151209093354.5cf0a860@ill.fr>
Message-ID: <5667EBE7.2010903@unito.it>

     Wonderful, I'll diffuse it, best, Pietro

Il 09/12/15 09:33, Fr?d?ric Mantegazza ha scritto:
> Le 09/12/2015, Mark a ?crit :
>
>> I put the Notebooks of my Introductory Programming class online. Maybe
>> those help:
>>
>> https://mbakker7.github.io/exploratory_computing_with_python/
> Yes, very helpfull for our scientists! I'll transmit them your link.
>
> Thanks,
>

-- 
The world is full of interesting problems to be solved!

NEW home page: http://terna.to.it

A new book on ABMs: http://www.palgrave.com/page/detail/agentbased-models-of-the-economy-/?K=9781137339805
SLAPP shell for ABMs: https://github.com/terna/SLAPP/



From vsego at vsego.org  Wed Dec  9 08:43:55 2015
From: vsego at vsego.org (Vedran Sego)
Date: Wed, 9 Dec 2015 13:43:55 +0000
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <20151204073435.59787326@ill.fr>
References: <20151204073435.59787326@ill.fr>
Message-ID: <CAOvnjKRC8rd=Hhoeyaxrd5NNhGLOsS3WO6Q0rh5-=Bs9q=f9hA@mail.gmail.com>

Frederic,

Here is the course that I gave in previous semester:
http://www.maths.manchester.ac.uk/~vsego/teaching.php

The materials will be removed at some point, because someone else will
be teaching it in this academic year.

Cheers,

Vedran


From zvoros at gmail.com  Wed Dec  9 08:47:09 2015
From: zvoros at gmail.com (=?UTF-8?B?Wm9sdMOhbiBWw7Zyw7Zz?=)
Date: Wed, 9 Dec 2015 14:47:09 +0100
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <CAOvnjKRC8rd=Hhoeyaxrd5NNhGLOsS3WO6Q0rh5-=Bs9q=f9hA@mail.gmail.com>
References: <20151204073435.59787326@ill.fr>
 <CAOvnjKRC8rd=Hhoeyaxrd5NNhGLOsS3WO6Q0rh5-=Bs9q=f9hA@mail.gmail.com>
Message-ID: <566830DD.10505@gmail.com>

Vedran,

If you think it's worth it, why don't you upload it to github? It is 
really annoying, when one finds orphaned links, and your comment 
indicates, that this is what is going to happen here.

Cheers,

Zolt?n

On 12/09/2015 02:43 PM, Vedran Sego wrote:
> Frederic,
>
> Here is the course that I gave in previous semester:
> http://www.maths.manchester.ac.uk/~vsego/teaching.php
>
> The materials will be removed at some point, because someone else will
> be teaching it in this academic year.
>
> Cheers,
>
> Vedran
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev



From carl.input at gmail.com  Wed Dec  9 08:51:56 2015
From: carl.input at gmail.com (Carl Smith)
Date: Wed, 09 Dec 2015 13:51:56 +0000
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <566830DD.10505@gmail.com>
References: <20151204073435.59787326@ill.fr>
 <CAOvnjKRC8rd=Hhoeyaxrd5NNhGLOsS3WO6Q0rh5-=Bs9q=f9hA@mail.gmail.com>
 <566830DD.10505@gmail.com>
Message-ID: <CAP-uhDfZyoK896WFML=o2MvquFq_c7ZNpw5-4jaE8skP6sSeNg@mail.gmail.com>

It is a real shame to see valuable resources go offline. GitHub is an
excellent place to archive that stuff. Other people can find it, and can
easily start a fork if they want to develop it further. It's totally free
for open source projects too.

On Wed, 9 Dec 2015 13:47 Zolt?n V?r?s <zvoros at gmail.com> wrote:

> Vedran,
>
> If you think it's worth it, why don't you upload it to github? It is
> really annoying, when one finds orphaned links, and your comment
> indicates, that this is what is going to happen here.
>
> Cheers,
>
> Zolt?n
>
> On 12/09/2015 02:43 PM, Vedran Sego wrote:
> > Frederic,
> >
> > Here is the course that I gave in previous semester:
> > http://www.maths.manchester.ac.uk/~vsego/teaching.php
> >
> > The materials will be removed at some point, because someone else will
> > be teaching it in this academic year.
> >
> > Cheers,
> >
> > Vedran
> > _______________________________________________
> > IPython-dev mailing list
> > IPython-dev at scipy.org
> > https://mail.scipy.org/mailman/listinfo/ipython-dev
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151209/8482178e/attachment.html>

From jonathan.taylor at stanford.edu  Thu Dec 10 02:00:35 2015
From: jonathan.taylor at stanford.edu (Jonathan Taylor)
Date: Wed, 9 Dec 2015 23:00:35 -0800
Subject: [IPython-dev] not sure where to report this
Message-ID: <CANmCCuSUY58HneSxbg5HF39zRUOYGwXxBbjguLRpPcP4ou5sNQ@mail.gmail.com>

I have a gist (https://gist.github.com/jonathan-taylor/04cc0306a08fb15c4c30
) with
some MathJax that renders fine on chrome and safari but not on firefox.
Same problem on two different macs. Possibly other browsers as well (Rob?)

Machine #1: chrome (47.0.2526.80), safari (9.0.1), firefox (42.0). OS X
(10.10.5)

Machine #2: chrome ( 47.0.2526.73), safari (9.0.1), firefox (42.0). OS X
(10.11.1)

(I presume OS is not relevant but including it just in case)

-- 
Jonathan Taylor
Dept. of Statistics
Sequoia Hall, 137
390 Serra Mall
Stanford, CA 94305
Tel:   650.723.9230
Fax:   650.725.8977
Web: http://www-stat.stanford.edu/~jtaylo
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151209/549bf52d/attachment.html>

From fperez.net at gmail.com  Thu Dec 10 02:29:04 2015
From: fperez.net at gmail.com (Fernando Perez)
Date: Wed, 9 Dec 2015 23:29:04 -0800
Subject: [IPython-dev] not sure where to report this
In-Reply-To: <CANmCCuSUY58HneSxbg5HF39zRUOYGwXxBbjguLRpPcP4ou5sNQ@mail.gmail.com>
References: <CANmCCuSUY58HneSxbg5HF39zRUOYGwXxBbjguLRpPcP4ou5sNQ@mail.gmail.com>
Message-ID: <CAHAreOpEKP_fzGgN3u_zYMWEyi649_N_x7mGrAsQ+D6Usaz9UQ@mail.gmail.com>

On Wed, Dec 9, 2015 at 11:00 PM, Jonathan Taylor <
jonathan.taylor at stanford.edu> wrote:

> I have a gist (
> https://gist.github.com/jonathan-taylor/04cc0306a08fb15c4c30 ) with some
> MathJax that renders fine on chrome and safari but not on firefox. Same
> problem on two different macs. Possibly other browsers as well (Rob?)
>
> Machine #1: chrome (47.0.2526.80), safari (9.0.1), firefox (42.0). OS X
> (10.10.5)
>
> Machine #2: chrome ( 47.0.2526.73), safari (9.0.1), firefox (42.0). OS X
> (10.11.1)
>
> (I presume OS is not relevant but including it just in case)
>

Mmh, the issue is actually that on github, the math renderer is *not* the
full MathJax, but an internal library with different and more limited
capabilities.

If you render this same gist on nbviewer, which does use the full MathJax,
it works fine also on Firefox (I just tested, and I do see the problem on
the github-based render):

http://nbviewer.jupyter.org/gist/jonathan-taylor/04cc0306a08fb15c4c30

These bugs aren't in our renderer, so they should be sent directly to
support at github.com so they can fix them in the github renderer itself...

Cheers

f



-- 
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151209/43101f5c/attachment.html>

From jonathan.taylor at stanford.edu  Fri Dec 11 13:34:05 2015
From: jonathan.taylor at stanford.edu (Jonathan Taylor)
Date: Fri, 11 Dec 2015 10:34:05 -0800
Subject: [IPython-dev] not sure where to report this
In-Reply-To: <CAHAreOpEKP_fzGgN3u_zYMWEyi649_N_x7mGrAsQ+D6Usaz9UQ@mail.gmail.com>
References: <CANmCCuSUY58HneSxbg5HF39zRUOYGwXxBbjguLRpPcP4ou5sNQ@mail.gmail.com>
 <CAHAreOpEKP_fzGgN3u_zYMWEyi649_N_x7mGrAsQ+D6Usaz9UQ@mail.gmail.com>
Message-ID: <CANmCCuRdeg8mEcwRLgBDVYY69T+=sH7=8YQ_VQtu+LOse7nHHA@mail.gmail.com>

Thanks. I thought it was probably github's implementation of LaTeX but
wasn't sure where to send it.

On Wed, Dec 9, 2015 at 11:29 PM, Fernando Perez <fperez.net at gmail.com>
wrote:

>
> On Wed, Dec 9, 2015 at 11:00 PM, Jonathan Taylor <
> jonathan.taylor at stanford.edu> wrote:
>
>> I have a gist (
>> https://gist.github.com/jonathan-taylor/04cc0306a08fb15c4c30 ) with some
>> MathJax that renders fine on chrome and safari but not on firefox. Same
>> problem on two different macs. Possibly other browsers as well (Rob?)
>>
>> Machine #1: chrome (47.0.2526.80), safari (9.0.1), firefox (42.0). OS X
>> (10.10.5)
>>
>> Machine #2: chrome ( 47.0.2526.73), safari (9.0.1), firefox (42.0). OS X
>> (10.11.1)
>>
>> (I presume OS is not relevant but including it just in case)
>>
>
> Mmh, the issue is actually that on github, the math renderer is *not* the
> full MathJax, but an internal library with different and more limited
> capabilities.
>
> If you render this same gist on nbviewer, which does use the full MathJax,
> it works fine also on Firefox (I just tested, and I do see the problem on
> the github-based render):
>
> http://nbviewer.jupyter.org/gist/jonathan-taylor/04cc0306a08fb15c4c30
>
> These bugs aren't in our renderer, so they should be sent directly to
> support at github.com so they can fix them in the github renderer itself...
>
> Cheers
>
> f
>
>
>
> --
> Fernando Perez (@fperez_org; http://fperez.org)
> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
> fernando.perez-at-berkeley: contact me here for any direct mail
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>


-- 
Jonathan Taylor
Dept. of Statistics
Sequoia Hall, 137
390 Serra Mall
Stanford, CA 94305
Tel:   650.723.9230
Fax:   650.725.8977
Web: http://www-stat.stanford.edu/~jtaylo
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151211/f1587355/attachment.html>

From bussonniermatthias at gmail.com  Fri Dec 11 13:39:18 2015
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Fri, 11 Dec 2015 19:39:18 +0100
Subject: [IPython-dev] Notebook 4.1.0 beta out.
Message-ID: <A4C572EA-52D8-48BB-9BB1-657C9EA88789@gmail.com>

Cf annouce on Jupyter ML: 

https://groups.google.com/forum/#!topic/jupyter/szzD8arkDv0 <https://groups.google.com/forum/#!topic/jupyter/szzD8arkDv0>

TL;DR: 

Please backup your files, install the notebook 4.1-beta with 

python -m pip install notebook --pre --upgrade 

and then send us feedback. 

-- 
M
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151211/2e015ed6/attachment.html>

From bussonniermatthias at gmail.com  Mon Dec 14 06:58:32 2015
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Mon, 14 Dec 2015 12:58:32 +0100
Subject: [IPython-dev] Should we do an IPython 4.1 soon ?
Message-ID: <C93A8E76-5C60-4FA9-91F7-73DC683C6723@gmail.com>

Hi all, 

With the separation of the multiple project, as of The Big Split, 
the pace on IPython terminal itself has been much slower than usual, with 
relatively low number of new features, but still a few bug fixes and improvement
here and there that users are waiting for. 

For example no PR merged in 13 days as of this writing, and nothing especially important for 4.1.

I propose that we release a 4.1 mostly bug fix soon (monthish ? Earlier ?), and try to keep now a relatively
slow moving, regular minor release for the 4.x branch, like one minor release every 8 weeks. 
I?ve already put a 4.1 release for mid January in GitHub, and 4.2 2 month after that. 

I think a regular release schedule would be welcomed for us (we tend to live of master and forget that end user
experience bugs) and for end user to know what to expect. 

That would likely mean that any API breakage PR would be targeted as 5.0 branch. 

Thoughts  ?
-- 
M



From benjaminrk at gmail.com  Mon Dec 14 07:39:12 2015
From: benjaminrk at gmail.com (MinRK)
Date: Mon, 14 Dec 2015 13:39:12 +0100
Subject: [IPython-dev] Should we do an IPython 4.1 soon ?
In-Reply-To: <C93A8E76-5C60-4FA9-91F7-73DC683C6723@gmail.com>
References: <C93A8E76-5C60-4FA9-91F7-73DC683C6723@gmail.com>
Message-ID: <CAHNn8BVDVLvem6wMYOb2C1S4G7dP4_CYteHrGqfr+Tx1GWpxDQ@mail.gmail.com>

Given the resources involved in getting notebook-4.1 out the door, I think
we should probably focus on that and wait on starting the IPython release
process until notebook-4.1 ships, but I think we can start IPython 4.1
immediately after we ship the notebook release. I think IPython's in a
pretty releasable state right now, so it shouldn't take long to ship
IPython 4.1.

-MinRK

On Mon, Dec 14, 2015 at 12:58 PM, Matthias Bussonnier <
bussonniermatthias at gmail.com> wrote:

> Hi all,
>
> With the separation of the multiple project, as of The Big Split,
> the pace on IPython terminal itself has been much slower than usual, with
> relatively low number of new features, but still a few bug fixes and
> improvement
> here and there that users are waiting for.
>
> For example no PR merged in 13 days as of this writing, and nothing
> especially important for 4.1.
>
> I propose that we release a 4.1 mostly bug fix soon (monthish ? Earlier
> ?), and try to keep now a relatively
> slow moving, regular minor release for the 4.x branch, like one minor
> release every 8 weeks.
> I?ve already put a 4.1 release for mid January in GitHub, and 4.2 2 month
> after that.
>
> I think a regular release schedule would be welcomed for us (we tend to
> live of master and forget that end user
> experience bugs) and for end user to know what to expect.
>
> That would likely mean that any API breakage PR would be targeted as 5.0
> branch.
>
> Thoughts  ?
> --
> M
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151214/e6f6d331/attachment.html>

From ellisonbg at gmail.com  Mon Dec 14 11:47:58 2015
From: ellisonbg at gmail.com (Brian Granger)
Date: Mon, 14 Dec 2015 08:47:58 -0800
Subject: [IPython-dev] Should we do an IPython 4.1 soon ?
In-Reply-To: <CAHNn8BVDVLvem6wMYOb2C1S4G7dP4_CYteHrGqfr+Tx1GWpxDQ@mail.gmail.com>
References: <C93A8E76-5C60-4FA9-91F7-73DC683C6723@gmail.com>
 <CAHNn8BVDVLvem6wMYOb2C1S4G7dP4_CYteHrGqfr+Tx1GWpxDQ@mail.gmail.com>
Message-ID: <CAH4pYpRqaVwReCpB6rD-BAbQuS=REzX6wVntEWBcbho1sfFLvg@mail.gmail.com>

I agree that we should release it soon, but let's get the notebook out
the door first.

On Mon, Dec 14, 2015 at 4:39 AM, MinRK <benjaminrk at gmail.com> wrote:
> Given the resources involved in getting notebook-4.1 out the door, I think
> we should probably focus on that and wait on starting the IPython release
> process until notebook-4.1 ships, but I think we can start IPython 4.1
> immediately after we ship the notebook release. I think IPython's in a
> pretty releasable state right now, so it shouldn't take long to ship IPython
> 4.1.
>
> -MinRK
>
> On Mon, Dec 14, 2015 at 12:58 PM, Matthias Bussonnier
> <bussonniermatthias at gmail.com> wrote:
>>
>> Hi all,
>>
>> With the separation of the multiple project, as of The Big Split,
>> the pace on IPython terminal itself has been much slower than usual, with
>> relatively low number of new features, but still a few bug fixes and
>> improvement
>> here and there that users are waiting for.
>>
>> For example no PR merged in 13 days as of this writing, and nothing
>> especially important for 4.1.
>>
>> I propose that we release a 4.1 mostly bug fix soon (monthish ? Earlier
>> ?), and try to keep now a relatively
>> slow moving, regular minor release for the 4.x branch, like one minor
>> release every 8 weeks.
>> I?ve already put a 4.1 release for mid January in GitHub, and 4.2 2 month
>> after that.
>>
>> I think a regular release schedule would be welcomed for us (we tend to
>> live of master and forget that end user
>> experience bugs) and for end user to know what to expect.
>>
>> That would likely mean that any API breakage PR would be targeted as 5.0
>> branch.
>>
>> Thoughts  ?
>> --
>> M
>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at scipy.org
>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>



-- 
Brian E. Granger
Associate Professor of Physics and Data Science
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger at calpoly.edu and ellisonbg at gmail.com


From faltet at gmail.com  Tue Dec 15 04:10:23 2015
From: faltet at gmail.com (Francesc Alted)
Date: Tue, 15 Dec 2015 10:10:23 +0100
Subject: [IPython-dev] Editing a table in the notebook
Message-ID: <CAFrp1vrur15+V6-FD1BU81Wm5xj-Cdqc33Nr9KzrPC6zf_Qy+w@mail.gmail.com>

Hi,

I am trying to see if there is an easy way to edit a table (pandas
dataframe or whatever that can be seen as tabular data) inside the jupyter
notebook.

Right now, I am trying to make the handsontable (http://handsontable.com/)
widget to work using this recipe by Cyrille Rossant:
https://gist.github.com/rossant/9463955.  However, after spending a couple
of hours, I still cannot do that with a recent version of Jupyter (1.0.0)
and ipywidgets (4.1.0).

I think the problem is the location of where to put the .js and .css
files.  So following the recipe above, I copied a couple of handsontable
files in:

$ ll ~/.ipython/profile_default/static/custom
total 1048
drwxrwxr-x 2 faltet faltet    4096 dic 15 09:22 ./
drwxrwxr-x 3 faltet faltet    4096 dic 15 09:15 ../
-rw-rw-r-- 1 faltet faltet      47 dic 15 09:22 custom.css
-rw-rw-r-- 1 faltet faltet      50 dic 15 09:22 custom.js
-rw-rw-r-- 1 faltet faltet   27378 dic 15 09:17 handsontable.full.css
-rw-rw-r-- 1 faltet faltet 1024388 dic 15 09:17 handsontable.full.js
$ cat ~/.ipython/profile_default/static/custom/custom.css
@import "/static/custom/handsontable.full.css"
$ cat ~/.ipython/profile_default/static/custom/custom.js
require(['/static/custom/handsontable.full.js']);

But I keep getting the next messages in the console:

[W 09:48:26.860 NotebookApp] 404 GET /static/custom/handsontable.full.css
(127.0.0.1) 7.69ms referer=http://localhost:8888/custom/cu
stom.css
[W 09:48:27.267 NotebookApp] Notebook handsondataframe.ipynb is not trusted
[W 09:48:27.292 NotebookApp] 404 GET
/static/custom/handsontable.full.js?v=20151215094826 (127.0.0.1) 2.03ms
referer=http://localhos
t:8888/notebooks/handsondataframe.ipynb

so, 404 is a clear indication that the files have not been found.

My guess is that the place to put .css and .js files has changed in newer
versions of IPython/Jupyter notebook.

Hints?

-- 
Francesc Alted
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151215/2d864e20/attachment.html>

From kikocorreoso at gmail.com  Tue Dec 15 04:26:39 2015
From: kikocorreoso at gmail.com (Kiko)
Date: Tue, 15 Dec 2015 10:26:39 +0100
Subject: [IPython-dev] Editing a table in the notebook
In-Reply-To: <CAFrp1vrur15+V6-FD1BU81Wm5xj-Cdqc33Nr9KzrPC6zf_Qy+w@mail.gmail.com>
References: <CAFrp1vrur15+V6-FD1BU81Wm5xj-Cdqc33Nr9KzrPC6zf_Qy+w@mail.gmail.com>
Message-ID: <CAB-sx61TT3-8so3o3ibG0P33nongjair3n0auP4RQA_dw1GnQQ@mail.gmail.com>

2015-12-15 10:10 GMT+01:00 Francesc Alted <faltet at gmail.com>:

> Hi,
>
> I am trying to see if there is an easy way to edit a table (pandas
> dataframe or whatever that can be seen as tabular data) inside the jupyter
> notebook.
>

Hi, Francesc.

I think qgrid does what you want. If not, at least can provide you some
hints:
https://github.com/quantopian/qgrid


>
> Right now, I am trying to make the handsontable (http://handsontable.com/)
> widget to work using this recipe by Cyrille Rossant:
> https://gist.github.com/rossant/9463955.  However, after spending a
> couple of hours, I still cannot do that with a recent version of Jupyter
> (1.0.0) and ipywidgets (4.1.0).
>
> I think the problem is the location of where to put the .js and .css
> files.  So following the recipe above, I copied a couple of handsontable
> files in:
>
> $ ll ~/.ipython/profile_default/static/custom
> total 1048
> drwxrwxr-x 2 faltet faltet    4096 dic 15 09:22 ./
> drwxrwxr-x 3 faltet faltet    4096 dic 15 09:15 ../
> -rw-rw-r-- 1 faltet faltet      47 dic 15 09:22 custom.css
> -rw-rw-r-- 1 faltet faltet      50 dic 15 09:22 custom.js
> -rw-rw-r-- 1 faltet faltet   27378 dic 15 09:17 handsontable.full.css
> -rw-rw-r-- 1 faltet faltet 1024388 dic 15 09:17 handsontable.full.js
> $ cat ~/.ipython/profile_default/static/custom/custom.css
> @import "/static/custom/handsontable.full.css"
> $ cat ~/.ipython/profile_default/static/custom/custom.js
> require(['/static/custom/handsontable.full.js']);
>
> But I keep getting the next messages in the console:
>
> [W 09:48:26.860 NotebookApp] 404 GET /static/custom/handsontable.full.css
> (127.0.0.1) 7.69ms referer=http://localhost:8888/custom/cu
> stom.css
> [W 09:48:27.267 NotebookApp] Notebook handsondataframe.ipynb is not
> trusted
> [W 09:48:27.292 NotebookApp] 404 GET
> /static/custom/handsontable.full.js?v=20151215094826 (127.0.0.1) 2.03ms
> referer=http://localhos
> t:8888/notebooks/handsondataframe.ipynb
>
> so, 404 is a clear indication that the files have not been found.
>
> My guess is that the place to put .css and .js files has changed in newer
> versions of IPython/Jupyter notebook.
>
> Hints?
>
> --
> Francesc Alted
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151215/b405e8b0/attachment.html>

From faltet at gmail.com  Tue Dec 15 05:29:25 2015
From: faltet at gmail.com (Francesc Alted)
Date: Tue, 15 Dec 2015 11:29:25 +0100
Subject: [IPython-dev] Editing a table in the notebook
In-Reply-To: <CAB-sx61TT3-8so3o3ibG0P33nongjair3n0auP4RQA_dw1GnQQ@mail.gmail.com>
References: <CAFrp1vrur15+V6-FD1BU81Wm5xj-Cdqc33Nr9KzrPC6zf_Qy+w@mail.gmail.com>
 <CAB-sx61TT3-8so3o3ibG0P33nongjair3n0auP4RQA_dw1GnQQ@mail.gmail.com>
Message-ID: <CAFrp1vrCD2mWCs46Li-1qSs9MDz8DCxBYDOVnyQsGsJ+ChUshw@mail.gmail.com>

2015-12-15 10:26 GMT+01:00 Kiko <kikocorreoso at gmail.com>:

>
>
> 2015-12-15 10:10 GMT+01:00 Francesc Alted <faltet at gmail.com>:
>
>> Hi,
>>
>> I am trying to see if there is an easy way to edit a table (pandas
>> dataframe or whatever that can be seen as tabular data) inside the jupyter
>> notebook.
>>
>
> Hi, Francesc.
>
> I think qgrid does what you want. If not, at least can provide you some
> hints:
> https://github.com/quantopian/qgrid
>

Wow, qgrid works like a charm.  Initially I thought there was not provision
for editing the table and propagate the changes back to the dataframe, but
actually it does, so woohoo!

Just for the record, I noticed that qgrid does install the .js and .css
files in:

$ ls ~/.local/share/jupyter/nbextensions/qgridjs/
__init__.py   lib        qgrid.datefilter.js  qgrid.filterbase.js
 qgrid.securityfilter.js  qgrid.textfilter.js
__init__.pyc  qgrid.css  qgrid.editors.js     qgrid.js
            qgrid.sliderfilter.js    qgrid.widget.js

and not in ~/.ipython/profile_default/static/custom .  I suppose this
change of configuration paths in newer IPython/Jupyter is responsible for
my previous attempts with the handsontable and the recipe in
https://gist.github.com/rossant/9463955 to fail in my setup.

Thank you!

-- 
Francesc Alted
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151215/32c0fb7b/attachment.html>

From takowl at gmail.com  Tue Dec 15 06:03:26 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Tue, 15 Dec 2015 11:03:26 +0000
Subject: [IPython-dev] Editing a table in the notebook
In-Reply-To: <CAFrp1vrCD2mWCs46Li-1qSs9MDz8DCxBYDOVnyQsGsJ+ChUshw@mail.gmail.com>
References: <CAFrp1vrur15+V6-FD1BU81Wm5xj-Cdqc33Nr9KzrPC6zf_Qy+w@mail.gmail.com>
 <CAB-sx61TT3-8so3o3ibG0P33nongjair3n0auP4RQA_dw1GnQQ@mail.gmail.com>
 <CAFrp1vrCD2mWCs46Li-1qSs9MDz8DCxBYDOVnyQsGsJ+ChUshw@mail.gmail.com>
Message-ID: <CAOvn4qh+Ka=m6TiXkvgihoLB=7ru7Qi92Du_XtD4mCEQx7QoLw@mail.gmail.com>

On 15 December 2015 at 10:29, Francesc Alted <faltet at gmail.com> wrote:

> Just for the record, I noticed that qgrid does install the .js and .css
> files in:
>
> $ ls ~/.local/share/jupyter/nbextensions/qgridjs/
> __init__.py   lib        qgrid.datefilter.js  qgrid.filterbase.js
>  qgrid.securityfilter.js  qgrid.textfilter.js
> __init__.pyc  qgrid.css  qgrid.editors.js     qgrid.js
>             qgrid.sliderfilter.js    qgrid.widget.js
>
> and not in ~/.ipython/profile_default/static/custom .  I suppose this
> change of configuration paths in newer IPython/Jupyter is responsible for
> my previous attempts with the handsontable and the recipe in
> https://gist.github.com/rossant/9463955 to fail in my setup.
>

You suppose correctly. :-) The notebook, along with all the other language
independent parts, comes under the Jupyter name. You can see where it looks
for different kinds of files on your system by running:

jupyter --paths

Notebook extensions are looked up in the set of paths marked 'data'.

Best wishes,
Thomas
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151215/b61780df/attachment.html>

From fperez.net at gmail.com  Tue Dec 15 18:13:06 2015
From: fperez.net at gmail.com (Fernando Perez)
Date: Tue, 15 Dec 2015 15:13:06 -0800
Subject: [IPython-dev] Should we do an IPython 4.1 soon ?
In-Reply-To: <CAH4pYpRqaVwReCpB6rD-BAbQuS=REzX6wVntEWBcbho1sfFLvg@mail.gmail.com>
References: <C93A8E76-5C60-4FA9-91F7-73DC683C6723@gmail.com>
 <CAHNn8BVDVLvem6wMYOb2C1S4G7dP4_CYteHrGqfr+Tx1GWpxDQ@mail.gmail.com>
 <CAH4pYpRqaVwReCpB6rD-BAbQuS=REzX6wVntEWBcbho1sfFLvg@mail.gmail.com>
Message-ID: <CAHAreOpKq9f0xgf1EieabPLFVkuuEcXr1UMSQZtOwdFiSZgkYg@mail.gmail.com>

On Mon, Dec 14, 2015 at 8:47 AM, Brian Granger <ellisonbg at gmail.com> wrote:

> I agree that we should release it soon, but let's get the notebook out
> the door first.
>

Please :)


-- 
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151215/3b46ce25/attachment.html>

From ceball at gmail.com  Wed Dec 16 08:10:35 2015
From: ceball at gmail.com (Chris Ball)
Date: Wed, 16 Dec 2015 13:10:35 +0000
Subject: [IPython-dev] No information about exceptions available from
	nbconvert output?
Message-ID: <1450271435.334570.469024073.0F5C7205@webmail.messagingengine.com>

Hi

If a notebook cell causes an exception, there doesn't seem to be any way
to see the traceback in the output of nbconvert. For instance, with the
command ``jupyter nbconvert --execute --to html hello.ipynb`` I get the
following output for various combinations of nbconvert version and
options, but the output never includes the actual traceback...

4.0.0:
```
$ jupyter nbconvert --execute --to html hello.ipynb
[...]
[NbConvertApp] ERROR | failed to run cell: CellExecutionError()
[NbConvertApp] ERROR | raise NotImplementedError('hello')
[NbConvertApp] ERROR | Error while converting 'hello.ipynb'
Traceback (most recent call last):
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/nbconvertapp.py",
  line 332, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename,
    resources=resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 166, in from_filename
    return self.from_notebook_node(nbformat.read(f, as_version=4),
    resources=resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/html.py",
  line 65, in from_notebook_node
    return super(HTMLExporter, self).from_notebook_node(nb, resources,
    **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/templateexporter.py",
  line 198, in from_notebook_node
    nb_copy, resources = super(TemplateExporter,
    self).from_notebook_node(nb, resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 131, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 303, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 47, in __call__
    return self.preprocess(nb,resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 83, in preprocess
    nb, resources = super(ExecutePreprocessor, self).preprocess(nb,
    resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 70, in preprocess
    nb.cells[index], resources = self.preprocess_cell(cell, resources,
    index)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 97, in preprocess_cell
    outputs = self.run_cell(cell)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 129, in run_cell
    raise CellExecutionError(msg['content']['traceback'])
CellExecutionError
```

4.0.0 with ``--Application.log_level=DEBUG``:
```
[...]
[NbConvertApp] Executing cell:
raise NotImplementedError('hello')
[NbConvertApp] ERROR | failed to run cell: CellExecutionError()
[NbConvertApp] ERROR | raise NotImplementedError('hello')
[NbConvertApp] ERROR | Error while converting 'hello.ipynb'
Traceback (most recent call last):
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/nbconvertapp.py",
  line 332, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename,
    resources=resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 166, in from_filename
    return self.from_notebook_node(nbformat.read(f, as_version=4),
    resources=resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/html.py",
  line 65, in from_notebook_node
    return super(HTMLExporter, self).from_notebook_node(nb, resources,
    **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/templateexporter.py",
  line 198, in from_notebook_node
    nb_copy, resources = super(TemplateExporter,
    self).from_notebook_node(nb, resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 131, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 303, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 47, in __call__
    return self.preprocess(nb,resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 83, in preprocess
    nb, resources = super(ExecutePreprocessor, self).preprocess(nb,
    resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 70, in preprocess
    nb.cells[index], resources = self.preprocess_cell(cell, resources,
    index)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 97, in preprocess_cell
    outputs = self.run_cell(cell)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 129, in run_cell
    raise CellExecutionError(msg['content']['traceback'])
CellExecutionError
```

Current master (71e80ef6f4930a06087b8bd32f0e209af1393e59):
```
[...]
[NbConvertApp] ERROR | Error while converting 'hello.ipynb'
Traceback (most recent call last):
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/nbconvertapp.py",
  line 335, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename,
    resources=resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 165, in from_filename
    return self.from_notebook_node(nbformat.read(f, as_version=4),
    resources=resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/html.py",
  line 65, in from_notebook_node
    return super(HTMLExporter, self).from_notebook_node(nb, resources,
    **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/templateexporter.py",
  line 196, in from_notebook_node
    nb_copy, resources = super(TemplateExporter,
    self).from_notebook_node(nb, resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 130, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 302, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 47, in __call__
    return self.preprocess(nb,resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 83, in preprocess
    nb, resources = super(ExecutePreprocessor, self).preprocess(nb,
    resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 70, in preprocess
    nb.cells[index], resources = self.preprocess_cell(cell, resources,
    index)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 112, in preprocess_cell
    raise CellExecutionError(msg)
CellExecutionError
```

Current master with with ``--Application.log_level=DEBUG``:
```
[...]
[NbConvertApp] Executing cell:
raise NotImplementedError('hello')
[NbConvertApp] output: status
[NbConvertApp] output: execute_input
[NbConvertApp] output: error
[NbConvertApp] output: status
[NbConvertApp] ERROR | Error while converting 'hello.ipynb'
Traceback (most recent call last):
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/nbconvertapp.py",
  line 335, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename,
    resources=resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 165, in from_filename
    return self.from_notebook_node(nbformat.read(f, as_version=4),
    resources=resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/html.py",
  line 65, in from_notebook_node
    return super(HTMLExporter, self).from_notebook_node(nb, resources,
    **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/templateexporter.py",
  line 196, in from_notebook_node
    nb_copy, resources = super(TemplateExporter,
    self).from_notebook_node(nb, resources, **kw)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 130, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/exporters/exporter.py",
  line 302, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 47, in __call__
    return self.preprocess(nb,resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 83, in preprocess
    nb, resources = super(ExecutePreprocessor, self).preprocess(nb,
    resources)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/base.py",
  line 70, in preprocess
    nb.cells[index], resources = self.preprocess_cell(cell, resources,
    index)
  File
  "/x/y/anaconda230/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py",
  line 112, in preprocess_cell
    raise CellExecutionError(msg)
CellExecutionError
```

Am I doing something wrong, or does what I'm looking for make no sense?

I could run nbconvert with ``--allow-errors`` and then inspect the html,
but that seems like a difficult way to obtain the information (e.g. on a
build server where nbconvert is being used to test a notebook).


Thanks
Chris


From vsego at vsego.org  Tue Dec 22 09:05:46 2015
From: vsego at vsego.org (Vedran Sego)
Date: Tue, 22 Dec 2015 14:05:46 +0000
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <566830DD.10505@gmail.com>
References: <20151204073435.59787326@ill.fr>
 <CAOvnjKRC8rd=Hhoeyaxrd5NNhGLOsS3WO6Q0rh5-=Bs9q=f9hA@mail.gmail.com>
 <566830DD.10505@gmail.com>
Message-ID: <CAOvnjKRfsfy9Eo+yy2RQZm+HFdDV52KJRP4bQxv089jvBSGK5w@mail.gmail.com>

On 9 December 2015 at 13:47, Zolt?n V?r?s <zvoros at gmail.com> wrote:
> If you think it's worth it, why don't you upload it to github? It is really
> annoying, when one finds orphaned links, and your comment indicates, that
> this is what is going to happen here.

Sorry for the delay, I had to check with the University if it's OK to
publish it. Here:
https://github.com/vsego/python-lecture-notes

Cheers,

V.


From steve at holdenweb.com  Tue Dec 22 13:30:42 2015
From: steve at holdenweb.com (Steve Holden)
Date: Tue, 22 Dec 2015 18:30:42 +0000
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <566830DD.10505@gmail.com>
References: <20151204073435.59787326@ill.fr>
 <CAOvnjKRC8rd=Hhoeyaxrd5NNhGLOsS3WO6Q0rh5-=Bs9q=f9hA@mail.gmail.com>
 <566830DD.10505@gmail.com>
Message-ID: <4A865A8A-E23B-4927-B488-402FED3FFB5E@holdenweb.com>

Great idea! S

Sent from my iPhone

> On 9 Dec 2015, at 13:47, Zolt?n V?r?s <zvoros at gmail.com> wrote:
> 
> Vedran,
> 
> If you think it's worth it, why don't you upload it to github? It is really annoying, when one finds orphaned links, and your comment indicates, that this is what is going to happen here.
> 
> Cheers,
> 
> Zolt?n
> 
>> On 12/09/2015 02:43 PM, Vedran Sego wrote:
>> Frederic,
>> 
>> Here is the course that I gave in previous semester:
>> http://www.maths.manchester.ac.uk/~vsego/teaching.php
>> 
>> The materials will be removed at some point, because someone else will
>> be teaching it in this academic year.
>> 
>> Cheers,
>> 
>> Vedran
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at scipy.org
>> https://mail.scipy.org/mailman/listinfo/ipython-dev
> 
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev


From fperez.net at gmail.com  Tue Dec 22 14:15:43 2015
From: fperez.net at gmail.com (Fernando Perez)
Date: Tue, 22 Dec 2015 11:15:43 -0800
Subject: [IPython-dev] [ANN-JOB] Project Jupyter is hiring a Project Manager
 - position at UC Berkeley
Message-ID: <CAHAreOp66RGiMz50-SHZvHUw_HwsAWUqQgoqC2=y1rdoYXxFzw@mail.gmail.com>

Hi all,

[ please direct all replies directly to me ]

Project Jupyter is announcing the opening of a position for a full-time
project manager, who will help us coordinate our technical development,
engage the open source community and work with our multiple stakeholders in
academia and industry.

If you have experience leading technical teams in open source communities,
we'd love to hear from you! In the last few years the project has rapidly
grown in multiple directions, and this presents both challenges and
opportunities. We are looking for someone who can help us harness the
energy and activity from our many contributors that include those funded by
our research grants, our industry partners, and the entire open source
community.

The role of the project manager is to help us maintain this activity
focused into a solid whole, so we can deliver timely and robust releases,
evolve our architecture coherently, ensure our documentation and
communication matches our technical foundation, and continue engaging a
wide range of stakeholders to evolve the project in new, interesting and
valuable directions.

This position will be hosted at the Berkeley Institute for Data Science,
working locally with Fernando Perez, Matthias Bussonnier, and our new
postdoctoral scholars. But the scope of this role is the entire project, so
we are looking for a candidate who will be regularly communicating with
project stakeholders from all locations, traveling to conferences,
development workshops and other project activities.

For specific details on the position and to apply, you can learn more at
jobs.berkeley.edu, Job ID #20975:

https://hrw-vip-prod.is.berkeley.edu/psc/JOBSPROD/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_CE.GBL?Page=HRS_CE_JOB_DTL&Action=A&JobOpeningId=20975&SiteId=1&PostingSeq=1&

Note that while the application review date is listed as January 1, 2016,
we will be considering applicants past that date (that is the cutoff for us
to be allowed to look at incoming applications). The search will remain
open until filled.

-- 
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151222/5a6b6aa0/attachment.html>

From zvoros at gmail.com  Wed Dec 23 02:51:05 2015
From: zvoros at gmail.com (=?UTF-8?B?Wm9sdMOhbiBWw7Zyw7Zz?=)
Date: Wed, 23 Dec 2015 08:51:05 +0100
Subject: [IPython-dev] Python tutorials based on notebook
In-Reply-To: <CAOvnjKRfsfy9Eo+yy2RQZm+HFdDV52KJRP4bQxv089jvBSGK5w@mail.gmail.com>
References: <20151204073435.59787326@ill.fr>
 <CAOvnjKRC8rd=Hhoeyaxrd5NNhGLOsS3WO6Q0rh5-=Bs9q=f9hA@mail.gmail.com>
 <566830DD.10505@gmail.com>
 <CAOvnjKRfsfy9Eo+yy2RQZm+HFdDV52KJRP4bQxv089jvBSGK5w@mail.gmail.com>
Message-ID: <567A5269.20706@gmail.com>

Vedran,

Many thanks! This way it won't sink into oblivion:)

Cheers,
Zolt?n


On 12/22/2015 03:05 PM, Vedran Sego wrote:
> On 9 December 2015 at 13:47, Zolt?n V?r?s <zvoros at gmail.com> wrote:
>> If you think it's worth it, why don't you upload it to github? It is really
>> annoying, when one finds orphaned links, and your comment indicates, that
>> this is what is going to happen here.
> Sorry for the delay, I had to check with the University if it's OK to
> publish it. Here:
> https://github.com/vsego/python-lecture-notes
>
> Cheers,
>
> V.
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev



From ewm at redtetrahedron.org  Wed Dec 23 12:30:22 2015
From: ewm at redtetrahedron.org (Eric Moore)
Date: Wed, 23 Dec 2015 12:30:22 -0500
Subject: [IPython-dev] (no subject)
Message-ID: <CAGeA38kBythXAFNJph4JpZzUK0EcLECrfXS4GEmPk63Cs8T06w@mail.gmail.com>

Hi,

I'm using the qtconsole, version 4.0.1.  It was installed using conda from
miniconda for windows (64 bit), running on windows 7 64 bit.

Sometimes when the current entry is at the bottom of the window, the window
does not scroll to display all of the output. I'm also occasionally seeing
the output overlaping with the next input. E.g. "IOut[19]: n [20]:" is
printed followed by the output on the next line with the cursor on the last
line of the output. Sometimes when this happens just pressing enter will
give me a clean input prompt on the next line.  Other times it seems to
hang and recover after a few seconds.  Still other times it hangs
completely and will not accept any more input.

Given the big split, I'm not sure where to start looking and I don't really
have any guesses about what the problem might be.

Eric
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151223/9e8f646e/attachment.html>

From bussonniermatthias at gmail.com  Wed Dec 23 12:37:13 2015
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Wed, 23 Dec 2015 18:37:13 +0100
Subject: [IPython-dev] (no subject)
In-Reply-To: <CAGeA38kBythXAFNJph4JpZzUK0EcLECrfXS4GEmPk63Cs8T06w@mail.gmail.com>
References: <CAGeA38kBythXAFNJph4JpZzUK0EcLECrfXS4GEmPk63Cs8T06w@mail.gmail.com>
Message-ID: <D5CCCA56-7391-4324-857B-E54B2AD5B9B8@gmail.com>


> On Dec 23, 2015, at 18:30, Eric Moore <ewm at redtetrahedron.org> wrote:
> 
> Hi, 
> 
> I'm using the qtconsole, version 4.0.1.  It was installed using conda from miniconda for windows (64 bit), running on windows 7 64 bit.
> 
> Sometimes when the current entry is at the bottom of the window, the window does not scroll to display all of the output. I'm also occasionally seeing the output overlaping with the next input. E.g. "IOut[19]: n [20]:" is printed followed by the output on the next line with the cursor on the last line of the output. Sometimes when this happens just pressing enter will give me a clean input prompt on the next line.  Other times it seems to hang and recover after a few seconds.  Still other times it hangs completely and will not accept any more input.  



> 
> Given the big split, I'm not sure where to start looking and I don't really have any guesses about what the problem might be.


Hi Eric, 

That seem QtConsole  specific, so that will be this repo:

https://github.com/jupyter/qtconsole <https://github.com/jupyter/qtconsole>

I?m not sure what can cause this though. 

-- 
M


> 
> Eric
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151223/dc0eccb8/attachment.html>

From liefeld at broadinstitute.org  Wed Dec 23 17:06:59 2015
From: liefeld at broadinstitute.org (Ted Liefeld)
Date: Wed, 23 Dec 2015 14:06:59 -0800
Subject: [IPython-dev] How to load an extension into every notebook on a
	server
Message-ID: <CADqKjdQo8+-D8zAGYHr5MW1xUqyGQSrk+GKuhWHhgO=eN8QGww@mail.gmail.com>

I am building a Docker image to have a Jupyter server with the GenePattern
notebook extension in it.  So far so good except that in every notebook I
have to enter

     %reload_ext genepattern

into the first cell to make the extension active.  I have been prowling
through the docs and have tried putting this command in lots of places,
none of which have worked (e.g. ~/.jupyter/jupyter_notebook_config.py,
 ~/.ipython/profile_default/startup/ipython_notebook_config.py) both
normally (ie as above) and also as a config setting
        c.InteractiveShellApp.exec_lines = ['%reload_ext genepattern']

It seems with all the layers of config I am not finding the right one to
insert this at. Can anyone point me in the right direction?  My current
container is using Jupyter 4.0.6, IPython 4.0.1 and Python 3.4.3.

Thanks

Ted


-- 
Ted Liefeld                                      UC San Diego
Mesirov Lab                                    liefeld at ucsd.edu

Office 2A24, BRF-II                        858-534-2010
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151223/d497225d/attachment.html>

From takowl at gmail.com  Wed Dec 23 17:27:00 2015
From: takowl at gmail.com (Thomas Kluyver)
Date: Wed, 23 Dec 2015 22:27:00 +0000
Subject: [IPython-dev] How to load an extension into every notebook on a
	server
In-Reply-To: <CADqKjdQo8+-D8zAGYHr5MW1xUqyGQSrk+GKuhWHhgO=eN8QGww@mail.gmail.com>
References: <CADqKjdQo8+-D8zAGYHr5MW1xUqyGQSrk+GKuhWHhgO=eN8QGww@mail.gmail.com>
Message-ID: <CAOvn4qgeSpaVVRW4h+jzn19gB6tTXkuY=QvfK2JLDmqso9MFaQ@mail.gmail.com>

Looking at the Genepattern code [1], it's using display() to publish data.
The notebook interface will only actually use the Javascript that sends if
it's coming from code run in a cell, so that part of the loading can't work
at startup.

I think we'd probably encourage you to keep putting the command to load the
extension at the top of every notebook, by analogy with a similar situation
we had with pylab. It used to be possible to run "ipython notebook
--pylab", and have a lot of numpy & matplotlib functions pre-loaded into
the namespace. But this produces notebooks which can only be run by someone
starting the notebook server in the same way. We found it better to use a
'%pylab' magic inside the notebook when we want the namespace set up like
that. I think loading the genepattern extension is a similar thing: it's
clearer what's going on when that lives inside the notebook, rather than
hidden in your config.

[1]
https://github.com/genepattern/genepattern-notebook/blob/master/profile/extensions/genepattern.py

Thomas

On 23 December 2015 at 22:06, Ted Liefeld <liefeld at broadinstitute.org>
wrote:

> I am building a Docker image to have a Jupyter server with the GenePattern
> notebook extension in it.  So far so good except that in every notebook I
> have to enter
>
>      %reload_ext genepattern
>
> into the first cell to make the extension active.  I have been prowling
> through the docs and have tried putting this command in lots of places,
> none of which have worked (e.g. ~/.jupyter/jupyter_notebook_config.py,
>  ~/.ipython/profile_default/startup/ipython_notebook_config.py) both
> normally (ie as above) and also as a config setting
>         c.InteractiveShellApp.exec_lines = ['%reload_ext genepattern']
>
> It seems with all the layers of config I am not finding the right one to
> insert this at. Can anyone point me in the right direction?  My current
> container is using Jupyter 4.0.6, IPython 4.0.1 and Python 3.4.3.
>
> Thanks
>
> Ted
>
>
> --
> Ted Liefeld                                      UC San Diego
> Mesirov Lab                                    liefeld at ucsd.edu
>
> Office 2A24, BRF-II                        858-534-2010
>
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151223/c4d8af59/attachment.html>

From liefeld at broadinstitute.org  Thu Dec 24 08:13:25 2015
From: liefeld at broadinstitute.org (Ted Liefeld)
Date: Thu, 24 Dec 2015 05:13:25 -0800
Subject: [IPython-dev] How to load an extension into every notebook on a
	server
In-Reply-To: <CADqKjdQo8+-D8zAGYHr5MW1xUqyGQSrk+GKuhWHhgO=eN8QGww@mail.gmail.com>
References: <CADqKjdQo8+-D8zAGYHr5MW1xUqyGQSrk+GKuhWHhgO=eN8QGww@mail.gmail.com>
Message-ID: <CADqKjdT=E4pQzOUpNyuYVNmS5_r+2VcDnF7j4ukcyh7irQ80kA@mail.gmail.com>

*Aside:  Wish I knew how to reply to a thread in the digest on mailman
too...*

Thomas

what you says makes sense about having the magic be explicit in the
notebook.  For the Docker server though I'd still like to not have to make
users remember to insert it themselves  because they have just started the
GP-noteook-jupyter container so they (or at least I) would expect it to
just work.

So whats your opinion of if I were to modify the jupyter in the container
(assuming its possible) to make the default empty python 3 notebook have
one cell at its top with the magic line in it?

Ted



Date: Wed, 23 Dec 2015 22:27:00 +0000
From: Thomas Kluyver <takowl at gmail.com>
To: IPython developers list <ipython-dev at scipy.org>
Subject: Re: [IPython-dev] How to load an extension into every
        notebook on a   server
Message-ID:
        <CAOvn4qgeSpaVVRW4h+jzn19gB6tTXkuY=QvfK2JLDmqso9MFaQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Looking at the Genepattern code [1], it's using display() to publish data.
The notebook interface will only actually use the Javascript that sends if
it's coming from code run in a cell, so that part of the loading can't work
at startup.

I think we'd probably encourage you to keep putting the command to load the
extension at the top of every notebook, by analogy with a similar situation
we had with pylab. It used to be possible to run "ipython notebook
--pylab", and have a lot of numpy & matplotlib functions pre-loaded into
the namespace. But this produces notebooks which can only be run by someone
starting the notebook server in the same way. We found it better to use a
'%pylab' magic inside the notebook when we want the namespace set up like
that. I think loading the genepattern extension is a similar thing: it's
clearer what's going on when that lives inside the notebook, rather than
hidden in your config.

[1]
https://github.com/genepattern/genepattern-notebook/blob/master/profile/extensions/genepattern.py

Thomas

On 23 December 2015 at 22:06, Ted Liefeld <liefeld at broadinstitute.org>
wrote:

> I am building a Docker image to have a Jupyter server with the GenePattern
> notebook extension in it.  So far so good except that in every notebook I
> have to enter
>
>      %reload_ext genepattern
>
> into the first cell to make the extension active.  I have been prowling
> through the docs and have tried putting this command in lots of places,
> none of which have worked (e.g. ~/.jupyter/jupyter_notebook_config.py,
>  ~/.ipython/profile_default/startup/ipython_notebook_config.py) both
> normally (ie as above) and also as a config setting
>         c.InteractiveShellApp.exec_lines = ['%reload_ext genepattern']
>
> It seems with all the layers of config I am not finding the right one to
> insert this at. Can anyone point me in the right direction?  My current
> container is using Jupyter 4.0.6, IPython 4.0.1 and Python 3.4.3.
>
> Thanks
>
> Ted
>
>


On Wed, Dec 23, 2015 at 2:06 PM, Ted Liefeld <liefeld at broadinstitute.org>
wrote:

> I am building a Docker image to have a Jupyter server with the GenePattern
> notebook extension in it.  So far so good except that in every notebook I
> have to enter
>
>      %reload_ext genepattern
>
> into the first cell to make the extension active.  I have been prowling
> through the docs and have tried putting this command in lots of places,
> none of which have worked (e.g. ~/.jupyter/jupyter_notebook_config.py,
>  ~/.ipython/profile_default/startup/ipython_notebook_config.py) both
> normally (ie as above) and also as a config setting
>         c.InteractiveShellApp.exec_lines = ['%reload_ext genepattern']
>
> It seems with all the layers of config I am not finding the right one to
> insert this at. Can anyone point me in the right direction?  My current
> container is using Jupyter 4.0.6, IPython 4.0.1 and Python 3.4.3.
>
> Thanks
>
> Ted
>
>
> --
> Ted Liefeld                                      UC San Diego
> Mesirov Lab                                    liefeld at ucsd.edu
>
> Office 2A24, BRF-II                        858-534-2010
>
>


-- 
Ted Liefeld                                      UC San Diego
Mesirov Lab                                    liefeld at ucsd.edu

Office 2A24, BRF-II                        858-534-2010
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20151224/f530ab56/attachment.html>