[IPython-User] Various questions in regard to notebook

Adam Hughes hughesadam87@gmail....
Mon Feb 3 16:33:32 CST 2014


Thanks guys, I feel more confident approaching journals with this in mind.


On Mon, Feb 3, 2014 at 4:47 PM, Fernando Perez <fperez.net@gmail.com> wrote:

> This was a microbiology journal from the Nature group (ISME), and I don't
> recall any particular issues with it.  This was a rapid communication and
> one of our co-authors, a biologist, was in touch with the Journal's editor
> regarding the submission, but as far as I know there weren't particular
> issues.
>
> We wrote up the manuscript and submitted it like any other for review, and
> put up those external links (that include not only notebooks, but also the
> Amazon virtual machine image).
>
> I think this is something that will be changing slowly over time. I've
> been in conversations with a couple of journal publishers (both from
> professional societies and standalone entities) that are interested in
> making this a more 'official' part of the publication record. Given that a
> notebook is just a file, and that it can even be converted to static PDF if
> desired, I don't think there are major issues to overcome here.
>
> The more complex discussion points are:
>
>  - hosting of data, virtual machine images and other potentially large
> resources.
>
> - versioning of these resources: what to do regarding version control
> repositories, what does the journal host vs. what's on say github, etc...
>
> These are things we'll need to figure out both as a community of
> practitioners and in collaboration with the publishers themselves.
>
> Cheers
>
> f
>
>
> On Mon, Feb 3, 2014 at 1:11 PM, Brian Granger <ellisonbg@gmail.com> wrote:
>
>> 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
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>> >>
>> >>
>> >
>> >
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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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>
>
>
> --
> Fernando Perez (@fperez_org; http://fperez.org)
> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
> fernando.perez-at-berkeley: contact me here for any direct mail
>
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