[gmx-developers] libxml2 versus JSON

[David van der Spoel]

On 12/05/16 17:54, Mark Abraham wrote:
> Hi,
>
> What's the scope? If we want to write a wrapper layer around some JSON
> code so people can use it for parsing input files, while we have a way
> to replace the dependency with something else in the future, then that's
> pretty much fine by me.
>
> What I'm not keen on is the rabbit hole of converting all our existing
> parameter-like file formats to some JSON format. That amounts to
> re-writing lots of our setup tools. That would likely be a big
> improvement in code quality, but it's dozens of hours of input from
> quite a few people to agree on how it should look, and then a few coding
> months to write tests, re-implement the code, and get it reviewed. This
> create a bunch of friction for users, for no immediate gain. Who's got
> the resources for that, and what's the big payoff?

This would mainly be for new files, and for files without user 
interaction (e.g. atomprops). I have a patch on SAXS in limbo for a year 
because we cannot make up our minds.

>
> Mark
>
> On Thu, May 12, 2016 at 5:25 PM David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     On 12/05/16 14:16, Erik Lindahl wrote:
>      > Hi,
>      >
>      > While I’m all for JSON, the format per se isn’t critical. What is
>     needed is for somebody (or a couple of people) to sit down and start
>     working on a larger framework for writing and reading all sorts of
>     data, and how to handle this in an abstract way. Then the actual
>     file format is simply a module that can be replaced if we ever want
>     to change it.  But, this will require volunteers!
>      >
>     This is what we discussed in the gerrit patch, to have a module on top
>     of it that would form the API for the rest of the code. For me this is
>     the most important thing to decide in gmx development in the near
>     future.
>
>      > Just picking a format and then having dozens of modules all fire
>     away with creating their own data fields directly in that format
>     doesn’t bring any more portability than using raw text files, IMHO :-)
>      >
>      > Cheers,
>      >
>      > Erik
>      >
>      >
>      >
>      >
>      >> On 12 May 2016, at 12:40, David van der Spoel
>     <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>      >>
>      >> Hi,
>      >>
>      >> with the developer meeting coming up next week I would like to
>     once again bring up the issue of what file format to use for
>     database files. We have discussed this for over ten years and not
>     having a decision is stopping innovation.
>      >>
>      >> I propose we vote on it at the meeting next week if we can not
>     reach concensus. Personally I am beyond caring which of the two as
>     long as we make a decision - now we have nothing.
>      >>
>      >> Cheers,
>      >> --
>      >> David van der Spoel, Ph.D., Professor of Biology
>      >> Dept. of Cell & Molec. Biol., Uppsala University.
>      >> Box 596, 75124 Uppsala, Sweden. Phone:       +46184714205.
>      >> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>      >> --
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>
>     --
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
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>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se