[Insight-developers] [ITK Community] Rendered SimpleITK Notebooks

[Matt McCormick]

Hi Brad, Jc,

Thanks for starting the discussion.  I think Brad's discussion
summaries the issue well.  I started going in that direction, but I
got distracted with other priorities.

In addition to storing the notebooks in version control and having
them rendered for online viewing, other concerns are downloading the
data needed to run them and running a test suite to ensure they are
working as expected.  For the latter, there are some notebook test
drivers [1].  For the data fetching task, a simple Python script might
do the job.

For a tutorial perspective, it would be nice to have the notebooks in
master saved without the output, so they can be interactively
generated by the student.  Maybe the very cool hooks Jc mentioned
could be used to grab the test data, run the tests and generate
output, run nbconvert, and publish the results to the gh-pages branch?

2 cents,
Matt

[1] https://github.com/TubeTK/TubeTK/blob/544961414e8194fdc9551444a81df1bf8c299f46/Utilities/Python/EvaluateIPythonNotebook.py

On Fri, Dec 6, 2013 at 1:52 PM, Jean-Christophe Fillion-Robin
<jchris.fillionr at kitware.com> wrote:
> Hi Brad,
>
> These look great.
>
> Independently of the solution, seems that setting a webhook [1][2] to
> "convert" and "re-publish" the updated notebook each time there are updated
> would be great.
>
> Jc
>
> [1] https://help.github.com/articles/post-receive-hooks
> [2] http://developer.github.com/v3/repos/hooks/
>
>
> On Fri, Dec 6, 2013 at 12:59 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>>
>> Hello,
>>
>> I took the first steps to getting the SimpleITK Python Notebooks available
>> as static web pages. They are linked from the Github Pages ( thanks for the
>> suggestion)  page:
>>
>> http://simpleitk.github.io/SimpleITK-Notebooks/
>>
>> I used nbconvert to change the ipynb to html. This is a separate manual
>> process and requites the committing of the html with data into the gh-pages
>> branch.
>>
>>
>> The alternative, would be to use nbviewer:
>>
>> http://nbviewer.ipython.org
>>
>> This would entail saving the output in the ipynb, and then using the
>> nbviewer like so:
>>
>>
>> http://nbviewer.ipython.org/github/SimpleITK/SimpleITK-Notebooks/blob/master/01_Image_Basics.ipynb
>>
>> This is much easier to maintain as no additional conversions or branches
>> are really needed. I thought the bulk of the image data would be a size
>> issue, but it's still in the repo with the pages approach.
>>
>> Does anyone have a thought on this choose? Would it be bad if the output
>> was saved in the ipynb files too? How would this effect giving tutorials
>> with the notebooks?
>>
>> Thanks for your thoughts,
>> Brad
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