[Bioperl-l] SVN and ...Re: Perltidy

Chris Fields cjfields at uiuc.edu
Sat Jun 16 15:18:06 EDT 2007

I think it's viable as an option if the code really needs it.  After  
100+ commits some of the code has schizy coding styles, so cleaning  
it up helps.  In those cases having a perltidy config file present  
wouldn't hurt.  However I agree that it shouldn't be applied across  
every module and should be done judiciously (the commit message, for  
instance, should actually state the code was tidied).


PS - Nice to see the ball is rolling on SVN!

On Jun 16, 2007, at 12:15 PM, rvos wrote:

> A brief word on the topic of perltidy: no. I like what it does, and  
> I sort of follow one of its settings (-syn -sob -b), but if you run  
> it on a whole source tree it'll screw up the diffs, and I'm still  
> worried about it breaking things (though really it shouldn't, it  
> creates a *.bak if something doesn't compile anymore).
> Rutger
> -----Original Message-----
>> Date: Sat Jun 16 10:09:18 PDT 2007
>> From: "rvos" <rvos at interchange.ubc.ca>
>> Subject: Re: [Bioperl-l] SVN and ...Re: Perltidy
>> To: "Hilmar Lapp" <hlapp at gmx.net>, "Sean Davis"  
>> <sdavis2 at mail.nih.gov>
>> CIPRES and Bio::Phylo use svn. As for the benefits, a lot of sales  
>> talk has been expended over it already, for my own purpose I like  
>> the integration with eclipse (through subclipse plugin) and  
>> komodo, in addition to the atomic commits (so I can ctrl+c if I  
>> goof up (again)).
>> For standalone use on osx I didn't use the fink one, but I forgot  
>> where I did get it from. It was very easy to set up, though. On  
>> windows there is a really nice standalone one (tortoisesvn) that  
>> integrates with the explorer so you can see on the file icons what  
>> the state of a file is. I know that there's a cvs2svn utility that  
>> converts your revision history (seems a requirement).
>> Rutger
>> -----Original Message-----
>>> Date: Sat Jun 16 07:55:09 PDT 2007
>>> From: "Hilmar Lapp" <hlapp at gmx.net>
>>> Subject: Re: [Bioperl-l] SVN and ...Re: Perltidy
>>> To: "Sean Davis" <sdavis2 at mail.nih.gov>
>>> On Jun 16, 2007, at 7:21 AM, Sean Davis wrote:
>>>> As for access, the typical access is over http (or https).
>>> We're using svn+ssh here (NESCent) so the password is the same as  
>>> the
>>> one you set for your account on the server, and you can use public/
>>> private key negotiation for authentication.
>>> I think the ability to not provide a password for every single
>>> interaction is a requirement. If that requires using svn+ssh or can
>>> be made to work through https too I don't know. On sf.net I have to
>>> use https for svn and it doesn't ask me for the password each time.
>>> Not sure how this works though, maybe some local caching?
>>> We should not be using http, or whatever other protocol that sends
>>> unencrypted passwords.
>>>>   Access controls can be set up on the server side while allowing
>>>> anonymous access for checkout.  There are many excellent SVN for
>>>> every OS, so that should not be a problem.
>>> On Mac OSX the most convenient way I have found is through fink. It
>>> does ask to install 30 other dependencies, which had me balk at
>>> first, but me doing it by hand is even worse than fink doing it,  
>>> so I
>>> finally gave in and it's really a breeze. I've not had a single  
>>> issue.
>>>   From a sysadmin perspective, what might be worth keeping in  
>>> mind is
>>> that svn is going to store everything in a database (BerkeleyDB I
>>> think). I.e., there is no such thing anymore as restoring individual
>>> source code files from backup if one gets accidentally corrupted on
>>> the server. It seems you have to restore the entire database, i.e.,
>>> the entire repository. I vaguely recall though that how svn manages
>>> the repository is actually configurable and that other storage than
>>> DB is possible too. Don't ask me for the pros and cons of one vs the
>>> other.
>>> 	-hilmar
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>> _______________________________________________
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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