[AstroPy] Best practices for Python sample code in journal articles

[August (Gus) Muench]

As one of the ApJ/AJ journal data scientists, I just want to weigh in that
our view is that notebooks should be presented in a narrative form and not
just a supplementary file linked to the final articles. Until we can
support that fully formed narrative form, which we are investigating, it
seems like the best option is to host them in your github repo as Kevin
suggested and does so well for his paper.

Another example that I have to share is from Mingarelli et al. 2015:

https://ui.adsabs.harvard.edu/#abs/2015ApJ...814L..20M/abstract

and

https://github.com/ChiaraMingarelli/blackHoleBatteryFRBs/blob/master/transient.ipynb


- gus





----------
August (Gus) Muench
august.fly at gmail.com
@augustmuench

On Thu, Apr 28, 2016 at 10:51 AM, Kevin Gullikson <kevin.gullikson at gmail.com
> wrote:

> Leo,
>
> I just submitted a paper <http://arxiv.org/abs/1604.06456> that links to
> my github <https://github.com/kgullikson88/BinaryInference> with a bunch
> of jupyter notebooks with the analysis. The journal people mentioned that
> they are actually working on some way to host the notebooks on their
> website or something, but for now I think linking to your github is
> probably the way to go. If you want to show code in the actual article,
> I've heard minted is a good option but never used it myself.
>
> On Thu, Apr 28, 2016 at 9:13 AM Jo Bovy <bovy at astro.utoronto.ca> wrote:
>
>> Hi Leo,
>>
>> I'm not sure this is exactly what you're looking for, but in my paper
>> <http://adsabs.harvard.edu/abs/2015ApJS..216...29B> on galpy, I used
>> minted <https://github.com/gpoore/minted> to typeset Python code as
>> figures (and some inline). The only downside is that arXiv doesn't allow
>> this, because you need to run latex with -shell-escape (I got my paper
>> on arXiv in a very hacky way). ApJS didn't have any problems with getting
>> this in print.
>>
>> Best,
>>
>> Jo
>>
>> On Thu, Apr 28, 2016 at 10:00 AM, Singer, Leo P.
>> (GSFC-661.0)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] <
>> leo.p.singer at nasa.gov> wrote:
>>
>>> Hi,
>>>
>>> I am working on an ApJ submission that I would like to pair with a
>>> supplement paper that contains (among other things) some Astropy-based
>>> sample/tutorial Python code to acquaint the reader with an accompanying
>>> data release. Are there any established best practices for including Python
>>> in journal articles? Should code and output be presented docstring-style or
>>> should it look like an IPython session? Does anyone have nice examples of
>>> astronomy papers that include supplemental IPython notebooks?
>>>
>>> If anyone is interested, this is the article and data release:
>>> https://arxiv.org/abs/1603.07333
>>> http://asd.gsfc.nasa.gov/Leo.Singer/going-the-distance/
>>>
>>> Cheers,
>>> Leo
>>>
>>>
>>> Dr. Leo P. Singer
>>> NASA Postdoctoral Program Fellow
>>> Goddard Space Flight Center
>>> 8800 Greenbelt Rd., B34, Room S239
>>> Greenbelt, MD 20771
>>> _______________________________________________
>>> AstroPy mailing list
>>> AstroPy at scipy.org
>>> https://mail.scipy.org/mailman/listinfo/astropy
>>>
>>
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> --
> Kevin Gullikson
> PhD Candidate
> University of Texas Astronomy
>
>
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