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Hello Chris,

On Mon, 21 Sep 2009 11:39:46 -0600
"Chris J. Myers" <myers@ece.utah.edu> wrote:

> >
> > If a developer wants as minimal impact on his code as possible
> > they are
> > free to keep coding towards L2 for which libsml provides well
> > defined default values. For L3 support one can use the excellent
> > libsbml conversion facilities to read and write.
> >
> I'd really like to stop hearing this argument being made. I don't
> think we should be advocating continued use of L2 but rather
> developing an L3 that people are happy with. If the answer to all
> suggestions is if you don't like it, use L2, then L3 will never gain
> acceptance. In which case, why is L3 being developed? What good is
> a clean language if no one uses it?

I agree with that completely. However I do not understand why you want
to water down the achievements by reintroducing the defaults in the
libsbml API for convenience.

>
> A better approach, in my opinion, is to come up with ways that
> people can use L3 for their needs. Case in point is my suggestion of
> adding a readSBML that provides defaults to required entries. Or, a
> readAndConvert function which would also need to provide defaults
> since L2 had defaults. I really think it is problematic to allow
> SBML files to be read that have missing, unspecified, required
> entries.

I agree again. However, I do not advocate to introduce the fix
functions you suggest. An L3 file which does not contain mandatory
elements is not valid and can not be fixed.

A convenient method for writing L2 or even L1V2 files which
explicitly spells out all defaults would help even the older
Levels to gain clarity.

Thanks,
Stefan


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility II
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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