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Re: pycdf vs. scipy.io.netcdf vs. python-netcdf4



Ok,

So I forgot about python-netcdf and pupynere.

That adds up to 3 APIs from 5 packages I know of:

* pyCDF (circa 2007):
* Scientific.IO.NetCDF        : from python-netcdf or pupynere
* scipy.io.netcdf                : from scipy, or python-netcdf4

python-netcdf appears to work with netcdf4 these days,  or rather, it
uses netcdf4 libraries
and so will _read_ these files, but doesn't give an API to manage them
(eg. compression facilities, parallelism, etc)
to my knowledge.

The point is that we _don't_ want 2 APIs and 5 packages, but rather to
converge on one.
A package that I'm working on passes back a CDF object (originally from
pyCDF, planned now
to be a netcdf_file object from scipy.io.netcdf) to the user; ie. it
assumes the underlying netcdf package
I'm using is pyCDF. We're in danger of having code that uses multiple
netcdf libraries.

NetCDF is morphing from a simple file format to being a way of handling
large scientific data (especially using
HDF5 underneath, as in netcdf4). The files can easily be 10-100 GB in
size, and with netcdf using the opendap library
underneath to read the contents as-needed over a network, its important
to be able to pass netcdf objects around
without reading the contents of the underlying file unless necessary: ie
abstractions that involve hiding netcdf
by reading in the file into memory are not an option.

Is it possible to standardize on one python netcdf implementation, based
on the latest netcdf4 libraries?

[note: I'm having some difficulties posting to debian lists at the
moment. If this mail does not appear
on debian-science, can you please repost on my behalf? thanks]

regards
Alastair


> Hi Alaistair,
>
> I think that pupynere [1] could be interesting for your research packages
> to manipulate netCDF4.
> It only depends on numpy and obviously of python.
>
> Regards,
> Arnaldo.
> ---
> *Arnaldo D'Amaral Pereira Granja Russo*
> Lab. de Estudos dos Oceanos e Clima
> Instituto de Oceanografia - FURG
>
>
>
>
>
> 2012/4/18 Alastair McKinstry <alastair.mckinstry@ichec.ie>
>
>> Hi,
>>
>> I'm looking at the problem of netcdf-wrappers for python. Unfortunately
>> there seem to be multiple:
>> * pyCDF
>> * scipy (scipy.io.netcdf)
>> * python-netCDF4
>>
>> Of which only scipy is in Debian. pyCDF appears to have last been
>> updated in 2007. python-netcdf4
>> seems be 'compatible' with scipy, in that it is based on netcdf4 rather
>> than netcdf3, but otherwise
>> follows the same API. ( I don't believe the underlying objects are
>> compatible).
>>
>> I'm proposing to package python-netCDF4 for Debian, as some code depends
>> on it. Does anyone know
>> of plans to merge these projects?
>>
>>
>> Regards
>> Alastair
>>
>> --
>> Alastair McKinstry ,  Computational Scientist
>> <alastair.mckinstry@ichec.ie
>> >
>> ICHEC, Room 301, IT Building NUI Galway,  Galway , Ireland
>> tel: +353 91 495946
>>
>>
>>
>> --
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>>
>>
>



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