[Bioperl-l] added a perltidy profile file

[Heikki Lehvaslaiho]

De facto coding style standard for BioPerl has been emacs using cperl
mode and bioperl.list file. As long as this configuration does not
change the conventions used, I see this as great way in helping to
format code from other editors.


   -Heikki

2009/8/23 Hilmar Lapp <hlapp at gmx.net>:
> Consistent coding style is in principle a good thing.
>
> It's also worth to keep in mind one of the old BioPerl principles - don't
> change working code purely to change style. In my interpretation of the
> rule, however, this has always applied to code writing style, and not code
> formatting style. I'm assuming the goal here is only to make the formatting
> consistent.
>
>        -hilmar
>
> On Aug 21, 2009, at 5:55 PM, Dan Bolser wrote:
>
>> Cheers Rob,
>>
>> Whatever objectons may arise from style x or style y, I think it's a
>> great idea to at least have one style or another recognized as being
>> 'standard'. I know TMTOWTDI, but on a project like this, with so many
>> contributors and users, it's essential to at least have a
>> recommendation. I'll try to use this on any contribs.
>>
>> As you pointed out [1], its probably best to provide two patches for
>> any change involving a formating clean up: one to change the fomat to
>> the standard and one to commit the actual code changes.
>>
>>
>> All the best,
>> Dan.
>>
>> [1] irc://irc.freenode.net/#bioperl
>>
>>
>> 2009/8/21 Robert Buels <rmb32 at cornell.edu>:
>>>
>>> This one is copied from the parrot project.  I added it in
>>> maintenance/perltidy.conf.
>>> Have a look, tweak as you see fit.
>>>
>>> The idea with perltidy profile files is to use them to enforce coding
>>> style
>>> rules.  So this perltidy profile file would be the place to codify the
>>> BioPerl coding standards, such as indentation, use of cuddled elses, etc.
>>>
>>> So here is one, let's customize it for our needs.  The way I usually run
>>> perltidy is with -b to modify a file in-place, and with the '-pro='
>>> option
>>> to specify a profile file.
>>>
>>> Example:
>>>  perltidy -b -pro=maintenance/perltidy.conf Bio/SimpleAlign.pm
>>>
>>> Rob
>>>
>>> --
>>> Robert Buels
>>> Bioinformatics Analyst, Sol Genomics Network
>>> Boyce Thompson Institute for Plant Research
>>> Tower Rd
>>> Ithaca, NY  14853
>>> Tel: 503-889-8539
>>> rmb32 at cornell.edu
>>> http://www.sgn.cornell.edu
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
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>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
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>



-- 
     -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
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