Re: How to load an extension into every notebook on a server

It occurs to me that one could use JavaScript in custom.js to create a cell and load the magic in that situation (with some complex event handling to make sure everything is loaded and that the kernel is started successfully), but there may be a better way of which I'm not aware.

Thorin

On Dec 24, 2015 8:13 AM, Ted Liefeld <[email protected]> wrote:

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 <[email protected] >

To: IPython developers list <[email protected] >

Subject: Re: [IPython-dev] How to load an extension into every

notebook on a server

Message-ID:

<CAOvn4qgeSpaVVRW4h+jzn19gB6tTXkuY=QvfK2JLDmqso9MFaQ@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 <[email protected] >

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 <[email protected] > 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 [email protected]
Office 2A24, BRF-II 858-534-2010





--

Ted Liefeld UC San Diego

Mesirov Lab [email protected]
Office 2A24, BRF-II 858-534-2010

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