[IPython-User] Various questions in regard to notebook

Fernando Perez fperez.net@gmail....
Mon Feb 3 15:47:53 CST 2014


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
> >>> 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
> _______________________________________________
> IPython-User mailing list
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> http://mail.scipy.org/mailman/listinfo/ipython-user
>



-- 
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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