[IPython-dev] Developing a MOOC with IPython notebooks

William Stein wstein at gmail.com
Tue Dec 23 11:48:24 EST 2014


On Tue, Dec 23, 2014 at 8:00 AM, William Stein <wstein at gmail.com> wrote:
> On Tue, Dec 23, 2014 at 4:46 AM, Anton Akhmerov
> <anton.akhmerov at gmail.com> wrote:
>>  On Mon, Dec 22, 2014 at 7:39 PM, William Stein <wstein at gmail.com> wrote:
>>> Hi,
>>>
>>> I just (seconds ago) added the ability to publish IPython notebooks
>>> from SageMathCloud (https://cloud.sagemath.com).
>>
>> Actually I should've considered SMC. Looking at the FAQ, it seems that
>> it is suitable for most our needs, the only unclear thing being the
>> software setup.
>> Basically in addition to the regular scipy-stack we also need the
>> kwant package (http://kwant-project.org), which is in pypi.
>
> Since it was so easy, kwant is now installed for all SMC projects:
>
>   https://cloud.sagemath.com/projects/4a5f0542-5873-4eed-a85c-a18c706e8bcd/files/support/2014-12-23-kwant.html
>
>
> Note: on import of kwant, it says "RuntimeWarning: The installed SciPy
> does not use UMFPACK. Instead, SciPy will use the version of SuperLu
> it is shipped with. Performance can be very poor in this case."   Can
> you run tests and let me know if this is a problem?  If you know how
> to rebuild scipy so it uses UMFPACK, I can fix this, of course.  (With
> Sage -- which I know much better than scipy -- there are a million
> subtle performance dependencies like this, and it's best to get
> feedback from an expert when one hits one of them.)

Hi,

I removed the pip version and installed Kwant system-wide using the
Ubuntu Packages suggested at http://kwant-project.org/install

Now kwant works fine without the UMFPACK warning.

 --  William

>
>
>> Unfortunately it also requires the MUMPS linear algebra package, so
>> overall the installation process would be somewhat involved I imagine.
>>
>> Do you know if we would be able to set it up, so that the course users
>> wouldn't have a need to install Kwant separately?
>
> Regarding kwant -- done!
>
> Regarding MUMPS, is that this somewhat strange seeming "public-domain"
> library, where you fill out a form and get an email link?
>
>     http://mumps.enseeiht.fr/index.php?page=dwnld#license
>
> Anyway, my model with SMC is to pre-install a very wide range of
> packages, available for everybody, motivated by what people need.    I
> have a script [1] that installs everything into a custom Python
> install (=Sage), each time I upgrade to a new version (though I leave
> the old versions in case people need them).
>
>> Some extra questions: Is it possible use single cell servers with
>> custom code pre-executed?
>>  Is it possible to embed those in an IFrame?
>
> I don't know -- I've cc'd Andrey and Jason, the single cell server
> devs, and the sage-cell mailng list.
>
> [1] https://github.com/sagemath/cloud/blob/master/build.py
>
> William
>
>>
>> Thanks,
>> Anton
>>
>>> On Mon, Dec 22, 2014 at 9:53 AM, Andrew Odewahn <odewahn at oreilly.com> wrote:
>>>> Hi, Anton.  I've been working on something along a similar line: running a
>>>> Notebook kernel in a Docker container via tmpnb and then connecting to it
>>>> via a widget.  This presentation has some of the details:
>>>>
>>>> http://odewahn.github.io/publishing-workflows-for-jupyter/#1
>>>>
>>>> Like Cyrille Rossant's work, it's still very experimental, but I've been
>>>> pleased with the results so far.  The biggest issues have been around
>>>> getting it running for version 2 of the Notebook (currently it only works
>>>> for version 1) and getting the CORS headers set up for tmpnb.
>>>>
>>>> Andrew
>>>>
>>>> ps -- here are a few examples of the output.  (It only works in Chrome right
>>>> now due to the CORS issues):
>>>>
>>>> http://sites.oreilly.com/odewahn/ipython-tutorial2/ch01.html
>>>>
>>>> http://sites.oreilly.com/odewahn/jem-test/ch01.html
>>>>
>>>>
>>>>
>>>> On Mon, Dec 22, 2014 at 11:47 AM, Cyrille Rossant
>>>> <cyrille.rossant at gmail.com> wrote:
>>>>>
>>>>> Hi Anton,
>>>>>
>>>>> > * What are the best practices for keeping notebooks in git? We've
>>>>> > found nbdiff, but it seems limited: for example it doesn't do anything
>>>>> > to diff markdown cells. Is there a better way?
>>>>>
>>>>> I am currently working on a solution that basically replaces JSON
>>>>> .ipynb by regular Markdown .md. You loose all metadata and outputs,
>>>>> but you keep Markdown cells and the input of code cells. It is still
>>>>> highly experimental and unstable, you'll find the code here:
>>>>> https://github.com/rossant/ipymd/tree/support-atlas -- let me know if
>>>>> you're interested in trying it out or contributing.
>>>>>
>>>>> > * What are the current options for creating rich graphic content that
>>>>> > doesn't rely on having a live kernel? I know of mpld3, ipywidgets, and
>>>>> > bokeh. For us ipywidgets seem like the best solution so far, but it's
>>>>> > a pet project of Jake Vanderplas that didn't see any action in around
>>>>> > half a year. So I wonder if there is anything more alive in that
>>>>> > respect, that'd be great. Perhaps in v3?
>>>>>
>>>>> I'm also very interested in this use case, but as far as I know
>>>>> there's nothing ready yet... We plan to support this in VisPy, but we
>>>>> haven't started to work on it yet.
>>>>>
>>>>> I suppose you could work something out based on tmpnb.org -- you get a
>>>>> temporary live kernel in the cloud launched just for you.
>>>>>
>>>>> Cyrille
>>>>> _______________________________________________
>>>>> IPython-dev mailing list
>>>>> IPython-dev at scipy.org
>>>>> http://mail.scipy.org/mailman/listinfo/ipython-dev
>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> William Stein
>>> Professor of Mathematics
>>> University of Washington
>>> http://wstein.org
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>
>
>
> --
> William Stein
> Professor of Mathematics
> University of Washington
> http://wstein.org



-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org



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