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

[Thøger Emil Rivera-Thorsen]

PythonTeX uses the Fancyvrb package for syntax highlighting. The output 
is not as nice as minted, but nicer than listings.

Og course, PythonTeX requires one more step in the production, as it is 
a filter that runs on your document and either evaluates, typesets or 
both to your inline code, then outputs it as a .tex file to be typeset 
the normal way. But it might be a good solution in a case like this, as 
I believe it doesn't require the special settings that minted does.



On 04/28/2016 05:42 PM, Stuart Mumford wrote:
>
> Hi Jo,
>
> FWIW, I had this minted + Arxiv issue when I submitted the SunPy 
> paper, what I did in the end was swap to the much more boring looking 
> `listings` package for ArXiV and use minted for everything else.
>
> https://github.com/sunpy/sunpy-0.4-paper/commit/d91dd8809f469e7a4295c317feeded41aeca17c8
>
> Stuart
>
> On 28/04/16 15:12, Jo Bovy 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 <mailto: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
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>>
>>
>>
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-- 
----

Thøger Emil Rivera-Thorsen
Astrophysicist, Ph.D. candidate
Stockholm University, dept. of Astronomy
Sweden

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