[Bioperl-l] All done with Bio::DB::Query

[Hilmar Lapp]

Good point. By removing I meant remove from POD. I.e., comment by '#', not by the tags POD uses. So it would still be in the code but people reading POD wouldn't see it.

	-hilmar

> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Monday, November 25, 2002 4:46 AM
> To: Hilmar Lapp
> Cc: bioperl-l@bioperl.org
> Subject: Re: [Bioperl-l] All done with Bio::DB::Query
> 
> 
> I'm not sure one should ever remove documentation.  Otherwise 
> people reading 
> through old code will have trouble when they hit the removed 
> method.  Isn't 
> it better to leave the documentation there with a note that 
> the method has 
> been superseded by something else?
> 
> Lincoln
> 
> On Monday 25 November 2002 02:14 am, Hilmar Lapp wrote:
> > I was just wondering why we need to deprecate it if it works nicely
> > using the new code. Also, if you really want to deprecate it, it
> > should become undocumented. My suggestion is to not deprecate it
> > (for 1.2), but remove documentation. This way new users won't pick
> > it up easily by accident, but old clients continue to run
> > undisturbed.
> >
> > As for module name clash, there is none yet. There might just be one
> > in the future, but frankly I don't think it's likely to happen. The
> > only thing that lets me favor a name change is that Bio::DB::Query
> > in bioperl-db is about object-relational queries, whereas
> > Bio::DB::Query in bioperl-live now is about (sequence-)databank
> > queries. Might be clearer for users who have both installed to have
> > them end up in different namespaces.
> >
> > 	-hilmar
> >
> > On Sunday, November 24, 2002, at 05:11 PM, Lincoln Stein wrote:
> > > get_stream_by_batch does use the new code; the method still works
> > > and is
> > > documented, but is marked as deprecated.  
> get_Stream_by_batch() was
> > > originally an optimized form of get_Stream_by_id().  Now that it
> > > doesn't
> > > contribute any performance improvement, I think we should 
> deprecate it.
> > >
> > > Sorry about the module name clash.  Perhaps we should rename as
> > > Bio::DB::SimpleQuery?
> > >
> > > Lincoln
> > >
> > > On Sunday 24 November 2002 04:46 pm, Hilmar Lapp wrote:
> > >> Cool Lincoln.
> > >>
> > >> Can't get_stream_by_batch rewritten to use the new code? Sorry if
> > >> the answer is obvious.
> > >>
> > >> I should have said that Bio::DB::Query is the namespace 
> that I also
> > >> use in bioperl-db for object-relational query modules. There's no
> > >> clash yet of module names, and the chance for one is 
> probably fairly
> > >> low; I just thought I mention this here. If you or 
> anyone else feels
> > >> we need to better protect from possible future clashes, 
> we need to
> > >> rename either in bioperl-live or bioperl-db.
> > >>
> > >> 	-hilmar
> > >>
> > >> On Friday, November 22, 2002, at 08:24 AM, Lincoln Stein wrote:
> > >>> Hi,
> > >>>
> > >>> I'm all done with the following modules:
> > >>>
> > >>> 	Bio::DB::QueryI
> > >>> 	Bio::DB::Query::WebDBQuery  # web utilities
> > >>> 	Bio::DB::Query::GenBank   # the only "real" one
> > >>>
> > >>> I have tested on a variety of Unix systems, but I need a Windows
> > >>> tester.  I
> > >>> used fork() in a couple of places in order to make 
> SeqIO streaming
> > >>> pipelineable (otherwise it has to download the whole 
> set of records
> > >>> before it
> > >>> can start processing the first one).  The code should 
> detect that
> > >>> it is not
> > >>> on a platform that supports fork-and-pipe and automatically fall
> > >>> back to the
> > >>> old way of doing things, but I'm not 100% certain it 
> will work as
> > >>> advertised.
> > >>>
> > >>> I've also done a touch up here and there on the 
> Bio::DB:: modules,
> > >>> mostly to
> > >>> deprecate Aaron Mackey's get_Stream_by_batch() methods, 
> which are
> > >>> superseded
> > >>> by the eutils interface.
> > >>>
> > >>> Let us all be glad that NCBI has committed to maintain eutils as
> > >>> its official
> > >>> interface.
> > >>>
> > >>> Lincoln
> > >>>
> > >>> --
> > >>> Lincoln Stein
> > >>> lstein@cshl.org
> > >>>
> > >>> _______________________________________________
> > >>> Bioperl-l mailing list
> > >>> Bioperl-l@bioperl.org
> > >>> http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> > > --
> > > Lincoln Stein
> > > lstein@cshl.org
> 
> -- 
> Lincoln Stein
> lstein@cshl.org
> 
>