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

rvos rvos at interchange.ubc.ca
Sat Jun 16 13:15:45 EDT 2007


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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