[IPython-User] Various questions in regard to notebook

Brian Granger ellisonbg@gmail....
Mon Feb 3 15:11:39 CST 2014


I wasn't involved in that part of the publication process for that
paper, but I don't recall hearing that we got any trouble about it.

On Mon, Feb 3, 2014 at 1:05 PM, Adam Hughes <hughesadam87@gmail.com> wrote:
> 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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-- 
Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com


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