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Re: [h5md-user] Update on H5MD from Stuttgart

From: Pierre de Buyl
Subject: Re: [h5md-user] Update on H5MD from Stuttgart
Date: Sun, 21 Jul 2013 22:43:03 +0200
User-agent: Mutt/1.5.21 (2010-09-15)

Hi all,

A quick update on time-(in)dependent data.

On Wed, Jul 17, 2013 at 09:25:45PM +0200, Pierre de Buyl wrote:
> On Wed, Jul 17, 2013 at 11:30:54AM -0400, Peter Colberg wrote:
> > On Wed, Jul 17, 2013 at 02:28:28PM +0200, Pierre de Buyl wrote:
> > > 2.2 time (in)dependent data
> > > 
> > > A proposal is made to work in the following way: at any place in the 
> > > file, a
> > > data (such as /trajectory/protein/position) may be either:
> > > - A dataset (with shape [N]). It does not depend on time.
> > > - A H5MD time-dependent conforming group (see current spec).
> > 
> > That is a good idea.
> Glad to hear that. I am quite prudent about that but it would simplify the
> specification.

I pushed modifications and found a surprise issue. 

In the box specification, one stores edges and offset as attributes for time
independent boxes. This goes against the new idea that any data is a dataset or
a H5MD group. Still, datasets make sense in "/trajectory" (for species or
masses, say) but attributes are more appropriate for a box edges and offset.

I also updated https://github.com/pdebuyl/pyh5md (on branch time_data_optional)
and the code is (in my opinion) simpler than previously.

Still, almost all that was discussed is going well :-)


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