[gmx-developers] libxml2 versus JSON

[Erik Lindahl]

Hi,

Rome wasn't built in a day, so no - I don't want the kitchen sink
initially. However, it would be good if we could decide on some high-level
principles and roughly how formats should later be implemented
hierarchically.

Where should comments and metadata go? Can we get a format where it is
trivial to combine multiple files if a new analysis tools suddenly needs
multiple types of data already implemented for other programs (without
writing a new parser)?  For instance, if we were to rewrite pdb2gmx,
roughly how should all those files be organized?

With a bit of thought and a common parsing layer, it feels like it should
be much easier for any developer to start adding/changing formats
one-by-one instead of having a large discussion involving everybody each
time somebody needs to add a file type!

Cheers,

Erik


On Thu, May 12, 2016 at 4:54 PM, Mark Abraham <mark.j.abraham at gmail.com>
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?
>
> Mark
>
> On Thu, May 12, 2016 at 5:25 PM David van der Spoel <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>
>> 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    http://folding.bmc.uu.se
>> >> --
>> >> Gromacs Developers mailing list
>> >>
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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
>> --
>> Gromacs Developers mailing list
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>
>
> --
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-- 
--
Erik Lindahl <erik.lindahl at gmail.com>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
University
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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