[IPython-User] Various questions in regard to notebook

Adam Hughes hughesadam87@gmail....
Mon Feb 3 15:05:46 CST 2014


Brian,

I noticed one of your publications on here and see that you included a
"data availability" section with which you reference an external link to
the notebooks among other resources.  Did you find that journals were
amenable to link to external sources?  Or did you find that they tended to
try to force you to host all of the supplemental content through them?




On Mon, Feb 3, 2014 at 3:24 PM, Adam Hughes <hughesadam87@gmail.com> wrote:

> Thanks Brian.  You're the man.
>
>
> On Mon, Feb 3, 2014 at 3:21 PM, Brian Granger <ellisonbg@gmail.com> wrote:
>
>> > I have some notebook questions and hope it's ok to post them together.
>>  They
>> > range the full spectrum from big-picture to minor details.
>>
>> Sure!
>>
>> > 1. Supplemental materials in journals:  Is anyone aware of any accepted
>> > publications where notebooks were published as articles, or as
>> supplemental
>> > materials in peer-reviewed journals?  We are looking to publish some
>> results
>> > that are already heavily integrated with the notebook and are looking
>> for
>> > amenable journals.  I was directed to a discussion on AcitvePapers
>> > integration.  This looks really cool, but for the here and now, what the
>> > current approach.
>>
>> I don't know of any cases where notebook were part of the "official"
>> record of publication. But there are a number of article listed on our
>> gallery where notebooks were part of the publication effort:
>>
>>
>> https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks#wiki--reproducible-academic-publications
>>
>> > 2. Quick changing notebook styles:  I've followed a trail of blog posts
>> > about controlling the typography in a notebook.  This blog from february
>> > 2013 gives a copy-pasteable snippet which didn't seem to work on my
>> system
>> > (canopy v 1.1 ubuntu 10.04).   What the current "easy/recommended way"
>> to
>> > change a notebook style.  I'm really looking more for pre-defined styles
>> > rather than creating my own, and if anyone could direct me to the most
>> > recent musings on the topic, I'd be quite grateful.
>>
>> The ability to style a notebook using CSS is possible, but not part of
>> our official API yet. I don't know of any prepakaged CSS files, but I
>> do have this IPython magic that loads a css file onto the page:
>>
>> https://github.com/ellisonbg/talk-cplug2013/blob/master/load_style.py
>>
>> > PS, one problem with the linked solution is that it requires one to
>> fill an
>> > entire notebook cell.  I'd rather have this hidden if possible, I guess
>> in a
>> > config file.  Thus, is it common practice to share config files with
>> > readers?  What are you guys doing currently?
>>
>> Not currently possible to hide this easily. I suppose you could put it
>> into a config file, but it would run at the beginning of all ipython
>> sessions.
>>
>> You can also just put CSS into your
>> $IPYTHONDIR/profile_default/static/custom/custom.css file.
>>
>> > 3.  Updating the gallery of examples wiki:  I have a few examples that I
>> > think are flashy enough to fit in to the wiki, but do they need to be
>> > curated?  Is it ok to just clone and add a hyperlink, or is there a
>> > review/uploading process in place that I'm not seeing?  It's not clear
>> to me
>> > how to contribute an example (sorry if it is clear and I'm just dense).
>>  I
>> > would only be adding one link, which itself links all of the notebooks
>> I had
>> > in mind.
>>
>> Just go ahead and edit the page or submit a pull request. It is
>> "curated" by the entire community...
>>
>> > (...and for something completely unrelated...)
>> > 4.  Suppressing logging:  After some searching, I found this suggestion
>> as a
>> > way to supress logging in a notebook:
>> >
>> > import warnings
>> > warnings.filterwarnings('ignore')
>>
>> There is also a command line flag:
>>
>> ipython notebook --log-level=WARN
>>
>> Cheers,
>>
>> Brian
>>
>> >
>> > This suppresses some logging messages, but I still am getting Warnings
>> from
>> > the package I wrote.  It's possible that the custom logger I'm using is
>> > doing something non-standard, so it could just be my fault that the
>> above
>> > lines are not working.  What do you recommend to hide all logging
>> methods?
>> > This is mostly for keeping examples clean, so I'd take any solution, as
>> > hacky as it needs to be.  There's not magic for this, right?
>> >
>> > Thanks so much.
>> >
>> > _______________________________________________
>> > IPython-User mailing list
>> > IPython-User@scipy.org
>> > http://mail.scipy.org/mailman/listinfo/ipython-user
>> >
>>
>>
>>
>> --
>> Brian E. Granger
>> Cal Poly State University, San Luis Obispo
>> bgranger@calpoly.edu and ellisonbg@gmail.com
>> _______________________________________________
>> IPython-User mailing list
>> IPython-User@scipy.org
>> http://mail.scipy.org/mailman/listinfo/ipython-user
>>
>
>
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