[IPython-User] Various questions in regard to notebook

Adam Hughes hughesadam87@gmail....
Tue Feb 4 10:08:28 CST 2014


Thanks Konrad.  That certainly clears up some of the haze for me.  It's
actually quite amazing how hard it is to find succinct explanations like
that from the journal sites themselves.

Brian, thanks.  I'm probably misunderstanding the logging facilities, but I
had assumed that if I had a library that has a logger and is outputting to
different streams (INFO, WARNING etc...) then the notebook would sort of
act as a screen to filter out various streams, say anything of WARNING or
below.

I know it's bad practice, but is there a way to divert standard error
completely via the notebook.  I would only run this for generating my
static notebooks which need to be clear of the warning messages to clean up
their presentation.




On Tue, Feb 4, 2014 at 3:13 AM, Konrad Hinsen <konrad.hinsen@fastmail.net>wrote:

> Adam Hughes writes:
>
>  > 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?
>
> My own experience says that no journal ever objected to links to
> external sources. In fact, it's rare to see any paper in my domain
> today that does not have some URLs in the reference list. A link to a
> notebook is just one more URL. You can also put it on figshare or
> Zenodo to get a DOI, which indicates more permanence than a URL.
>
> The difference to proper "supplementary material" is that the latter
> is part of what the reviewers are supposed to evaluate, whereas a link
> is just one more reference to previously published material. I have
> yet to see any reviewer comment on supplementary material that is not
> additional text or images, but it's supposed to happen.
>
> In my first two fully reproducible papers, published last years, I
> submitted the code and data as supplementary material, because that's
> where it morally belongs, and put it on figshare for visibility.
> There's still a lot of freedom for authors to choose what pleases
> them.
>
> Konrad.
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