Re: [SED-ML-discuss] The 'numberOfPoints' attribute

[David N. <dav...@gm...>]

My preference is also option 1.

Cheers,
David.

On 27 June 2017 at 14:58, Bergmann, Frank T. <fbe...@ca...> wrote:
> I’d prefer option 1.
>
> Cheers
> Frank
>
>
> On Jun 27, 2017, at 2:03 PM, Kyle Medley <me...@co...> wrote:
>
> I was under the mistaken in impression that this change was going to impact
> SED-ML L1V2 retroactively, but it's actually slated for L1V3 and won't
> affect libsedml's ability to read older versions, so I also agree with
> Herbert (i.e. option 2).
>
> J Kyle Medley, PhD Candidate
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
>
> On 6/27/17 1:47 PM, Moraru,Ion wrote:
>
> I agree with Herbert.
> Ion
>
> From: Herbert Sauro [mailto:uw....@gm...]
> Sent: Tuesday, June 27, 2017 4:21 PM
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] The 'numberOfPoints' attribute
>
> Given that the sedml community is still very small, it would be better to
> get it right at this early stage, hence I prefer option
>
> 2) change the name to set thing else, e.g. numberOfSteps
>
> For those clinging to earlier versions they can check the version of the
> sedml and interpret numberofpoints in the old way. In that sense I don't
> think it affects backward compatibility.
>
> Herbett
>
>
> On Tue, Jun 27, 2017 at 1:08 PM Kyle Medley <me...@co...> wrote:
>
> It seems to me that breaking backwards compatibility defeats one of the
> major advantages of having a standard encoding, so I would prefer option 1.
> If people are not happy with that, I have a different suggestion:
>
> 4) Allow 'numberOfPoints', and do not change its meaning, but also create a
> new attribute 'numberOfSteps' with the same semantics. 'numberOfPoints'
> would not be deprecated.
>
> Cheers,
>
> Kyle
>
> J Kyle Medley, PhD Candidate
>
> Bioengineering/BPSD, Sauro Lab
>
> University of Washington, Seattle
>
> skype: jkylemedley
>
> On 6/27/17 12:46 PM, Lucian Smith wrote:
>
> At HARMONY, the issue was brought up that the 'numberOfPoints' attribute is
> confusing, because the literal number of expected points in the output file
> is one more than that: the initial conditions, and the number of *computed*
> points.
>
> It was proposed that we fix this for SED-ML Level 1 Version 3.  There are a
> few options:
>
> 1) No change:  simply make it more clear in the spec that 'numberOfPoints'
> means 'number of computed points' aka 'number of steps'.
>
> 2) Change the name of the attribute to 'numberOfSteps' or possibly
> 'numberOfComputedPoints'.
>
> 3) Deprecate but allow 'numberOfPoints', and make a new 'numberOfSteps'
> attribute that people are encouraged to use instead.
>
> Any opinions?  It seems like the advantage is preventing future confusion,
> and the cost is having a non-backwards-compatible spec, and the cost of
> implementation changes for the groups that currently support SED-ML.
>
> -Lucian
>
>
>
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David Nickerson
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