[IPython-dev] How to load an extension into every notebook on a server

[Ted Liefeld]

*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
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