[yt-dev] Soliciting opinions about how to handle data tables for spectral integrator port

[Cameron Hummels]

Agreed that these should stay out of the repo.  Trident has this issue as
well, and it automatically downloads them when the code is used the first
time.  It also has a permanent location where HPC users and such can
download them directly and put them in the appropriate directory.  I think
this is about as good as you can get to making it work for everyone.  Just
document it and hope people read the docs before using.

Cameron

On Thu, Dec 8, 2016 at 7:34 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi,
>
> I'm okay with this, but let's try to make it obvious where things go.
> (which you have all suggested.)
>
> I think astropy does this and has helper functions for it.
>
> Matt
>
> On Dec 8, 2016 9:28 AM, "Britton Smith" <brittonsmith at gmail.com> wrote:
>
> HI all,
>
> I agree that it would be best to keep the data files out of the repo.
> What about adding some config variables to control where the data gets
> stored?  We could even have it default to storing things in .config/yt.
> Perhaps, on the first import when the data is not there, you just get a
> notice with links to wget/curl them.
>
> Britton
>
> On Wed, Dec 7, 2016 at 12:12 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Wed, Dec 7, 2016 at 1:30 PM, John Zuhone <jzuhone at gmail.com> wrote:
>>
>>> Hi everyone,
>>>
>>> I just issued PR 2465 (https://bitbucket.org/yt_anal
>>> ysis/yt/pull-requests/2465/wip-port-the-spectral_integrator-analysis/)
>>> to port the spectral integrator analysis module (originally written by
>>> Britton) under yt.fields. spectral_integrator is an analysis module that
>>> creates X-ray emission fields in user-specified energy bands.
>>>
>>> The hitch is that spectral_integrator uses HDF5 tables to compute the
>>> emissivity, since they are not analytical functions. We currently host
>>> those tables on yt-project.org/data. spectral_integrator downloads them
>>> automatically if the analysis module is used and they are not present.
>>>
>>> There was some discussion on Slack as to whether or not this is the
>>> correct approach, since it’s not ideal for certain computing environments
>>> (e.g., HPC).
>>>
>>
>> Also a problem for e.g. packaging yt on linux distros.
>>
>>
>>> The files are a total of about 2.4 MB in size, so there is some
>>> reticence to bundling them with yt.
>>>
>>
>> So my main concern here is adding them to the repo. If you could figure
>> out a way to add them to the source distribution without including them in
>> the repo (and then issue an error with a URL for non-sdist builds of yt
>> [e.g. from the repo]), it wouldn't be a problem.
>>
>> This isn't really a generic solution for all binary files we might want
>> to send to users, but 2.4 MB isn't all that big to be part of an sdist or
>> wheel.
>>
>>
>>> There is also the issue that uploading new versions of the tables breaks
>>> backward-compatibility. I have sacrificed backwards-compatiblity for
>>> considerable simplification of code.
>>>
>>
>> I think the solution is just to use different names for the files or the
>> hdf5 datasets or groups here so the code can tell the difference.
>>
>>
>>>
>>> Does anyone have any ideas about the best way to handle this issue?
>>>
>>> Best,
>>>
>>> John Z
>>>
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>>>
>>>
>>
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-- 
Cameron Hummels
NSF Postdoctoral Fellow
Department of Astronomy
California Institute of Technology
http://chummels.org
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