[Bioperl-l] Clean-up of Bio::Root::IO

Hilmar Lapp hlapp at gmx.net
Wed Oct 4 14:43:54 UTC 2006

On Oct 4, 2006, at 1:21 AM, Torsten Seemann wrote:

> Bio::Root::IO has functions catfile(), tmpdir(), tmpfile(), rmtree()
> which currently dispatch to the File:: version, or try to emulate  
> it. We
> don't need to emulate anymore. Jason Stajich suggested in a previous
> post that they should be deprecated, and that users should use  
> directly
> the File:: functions themselves.

I don't think there's a need to deprecate - if the methods just plain  
delegate to whatever File:: module is appropriate their  
implementation (supposedly) will become very simple and hence won't  
pose a maintenance burden anymore.

One can still recommend for all new scripts or modules or code  
written to use the File:: modules directly, just I'm not sure there's  
a need to tell users that they should start changing their existing  

> I have an uncommitted simplified version of Bio::Root::IO which does
> this, and "all tests pass". The functions currently (silently)  
> dispatch
> directly to their native counterparts.
> The only tricky function is tempfile() which is *mostly* like
> File::Temp::tempfile(), but does some voodoo of converting
> (TEMPLATE=>'xxx') to the non-hash first parameter of the File::  
> version,
> so I'm hesitant to commit. It may do other magic - Hilmar?

Not that I would know of. If the tests pass (without having to change  
them!) I'd give it a try.


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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