[gmx-developers] mdp option names

[Szilárd Páll]

Looks good to me, could you submit it to gerrit?

Thanks!
--
Szilárd



On Wed, Nov 23, 2011 at 12:32 PM, Alexey Shvetsov
<alexxy at omrb.pnpi.spb.ru> wrote:
> Here is a patch for manual
> It should fix all renamed mdp option names
>
> Mark Abraham писал 22.11.2011 17:18:
>>
>> On 23/11/2011 1:04 AM, Alexey Shvetsov wrote:
>>>
>>> Szilárd Páll писал 22.11.2011 13:58:
>>>>
>>>> On Tue, Nov 22, 2011 at 10:11 AM, Alexey Shvetsov
>>>> <alexxy at omrb.pnpi.spb.ru> wrote:
>>>>>
>>>>> Szilárd Páll писал 21.11.2011 23:45:
>>>>>>
>>>>>> On Mon, Nov 21, 2011 at 9:22 PM, Alexey Shvetsov
>>>>>> <alexxy at omrb.pnpi.spb.ru> wrote:
>>>>>>>
>>>>>>> Szilárd Páll писал 21.11.2011 16:24:
>>>>>>>>
>>>>>>>> I was about to approve the patch in gerrit, but I realized that
>>>>>>>> there
>>>>>>>> is one thing we might have overlooked: mdp option names should be
>>>>>>>> consistent across standard output, the man pages, and manual.
>>>>>>>>
>>>>>>>> Questions:
>>>>>>>>
>>>>>>>> i) Are there more references to mdp options in the code (e.g. help
>>>>>>>> header text, warning/error
>>>>>>>> messages)?
>>>>>>>>
>>>>>>> I'm not sure about manual. If its generated automaticaly then there
>>>>>>> should
>>>>>>
>>>>>> The man pages are generated from the help messages in the code, the
>>>>>> manual is a separate a latex document (source located here:
>>>>>> git at git.gromacs.org:manual.git).
>>>>>
>>>>> Ok. Then man pages should be fine. I'll check manual today.
>>>>
>>>> That would be great! Thanks Alexey!
>>>
>>> Seems like this part of manual is generated fro source. :) so it shouldnt
>>> be problem
>>
>> There are certainly chunks of the manual not generated from source,
>> which we should check. If we have a list of names of .mdp options,
>> grepping should do the trick.
>>
>> Mark
>>
>>>
>>>> -- Szilárd
>>>>
>>>>>>
>>>>>> -- Szilárd
>>>>>>
>>>>>>> be no problem.
>>>>>>> All error messages are fixed in patch. As well as output to md.log.
>>>>>>> Seems
>>>>>>> all other messages were fixed in patch.
>>>>>>>
>>>>>>>> ii) Should we file a separate task in Redmine for fixes in the
>>>>>>>> manual
>>>>>>>> and get the patch approves as soon as i) is clarified?
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> -- Szilárd
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Oct 21, 2011 at 1:04 AM, Szilárd Páll
>>>>>>>> <szilard.pall at cbr.su.se>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Although in Gromacs hyphen and underscore are interchangeable, I do
>>>>>>>>> think Alexey's suggestion is good. It improves consistency and
>>>>>>>>> starting the change by generating and documenting only options with
>>>>>>>>> hyphen only could enable us to maybe brake this non-differentiation
>>>>>>>>> in
>>>>>>>>> later versions (say 5+ as the option parsing will be reworked)
>>>>>>>>> without
>>>>>>>>> causing too much trouble.
>>>>>>>>>
>>>>>>>>> -- Szilárd
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Oct 20, 2011 at 9:23 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> Aren't the hyphen and underscore interchangeable, such that either
>>>>>>>>>> is
>>>>>>>>>> already accepted?
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>>> Alexey Shvetsov wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hi all!
>>>>>>>>>>>
>>>>>>>>>>> Seems it will be good idea to have all mdp option names
>>>>>>>>>>> consistent.
>>>>>>>>>>> In
>>>>>>>>>>> its
>>>>>>>>>>> current state some of them has '-' in its names like E-t while
>>>>>>>>>>> some
>>>>>>>>>>> other
>>>>>>>>>>> options has '_' in their names like init_step. It will be good if
>>>>>>>>>>> all
>>>>>>>>>>> options
>>>>>>>>>>> will have same naming scheme like only '_' in names or only '-'
>>>>>>>>>>> in
>>>>>>>>>>> its
>>>>>>>>>>> names.
>>>>>>>>>>> Also it will simplyfy mdp file generation and parsing  by
>>>>>>>>>>> external
>>>>>>>>>>> software.
>>>>>>>>>>>
>>>>>>>>>>> I prepared two patches in gerrit
>>>>>>>>>>>
>>>>>>>>>>> https://gerrit.gromacs.org/229 <- it replaces '_' to '-' in mdp
>>>>>>>>>>> option
>>>>>>>>>>> names
>>>>>>>>>>>
>>>>>>>>>>> https://gerrit.gromacs.org/229 <- it changes mdp.html and
>>>>>>>>>>> mdp_opt.html
>>>>>>>>>>>
>>>>>>>>>>> PS currently we use such mdp file parser for gromacs grid ui in
>>>>>>>>>>> nnn
>>>>>>>>>>> grid
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -- ========================================
>>>>>>>>>>
>>>>>>>>>> Justin A. Lemkul
>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>> ICTAS Doctoral Scholar
>>>>>>>>>> MILES-IGERT Trainee
>>>>>>>>>> Department of Biochemistry
>>>>>>>>>> Virginia Tech
>>>>>>>>>> Blacksburg, VA
>>>>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>>>>>
>>>>>>>>>> ========================================
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>> -- Best Regards,
>>>>>>> Alexey 'Alexxy' Shvetsov
>>>>>>> Petersburg Nuclear Physics Institute, Russia
>>>>>>> Department of Molecular and Radiation Biophysics
>>>>>>> Gentoo Team Ru
>>>>>>> Gentoo Linux Dev
>>>>>>> mailto:alexxyum at gmail.com
>>>>>>> mailto:alexxy at gentoo.org
>>>>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>>>>> -- gmx-developers mailing list
>>>>>>> gmx-developers at gromacs.org
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> interface
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>>>>>>>
>>>>>
>>>>> -- Best Regards,
>>>>> Alexey 'Alexxy' Shvetsov
>>>>> Petersburg Nuclear Physics Institute, Russia
>>>>> Department of Molecular and Radiation Biophysics
>>>>> Gentoo Team Ru
>>>>> Gentoo Linux Dev
>>>>> mailto:alexxyum at gmail.com
>>>>> mailto:alexxy at gentoo.org
>>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>>> -- gmx-developers mailing list
>>>>> gmx-developers at gromacs.org
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>>>>>
>>>
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexxyum at gmail.com
> mailto:alexxy at gentoo.org
> mailto:alexxy at omrb.pnpi.spb.ru
> --
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