[Biopython-dev] Releasing (a beta of) Biopython 1.62 this week?

[Michiel de Hoon]

Hi Bow,


> Would it be ok if we move parts that are used by SearchIO into their own private classes in
> Bio.SearchIO, while putting the BiopythonDeprecationWarning on the current files?

That sounds fine to me. Any other opinions, anybody?

Best,
-Michiel.



________________________________
 From: Wibowo Arindrarto <w.arindrarto at gmail.com>
To: Michiel de Hoon <mjldehoon at yahoo.com> 
Cc: Peter Cock <p.j.a.cock at googlemail.com>; Eric Talevich <eric.talevich at gmail.com>; Zheng Ruan <zruan1991 at gmail.com>; Biopython-Dev Mailing List <biopython-dev at biopython.org> 
Sent: Saturday, July 13, 2013 3:58 PM
Subject: Re: [Biopython-dev] Releasing (a beta of) Biopython 1.62 this week?
 

Hi Michiel,

There are two classes from Bio.Blast.NCBIStandalone still being used
by Bio.SearchIO internally (for the BLAST text parser): the
BlastParser and the Iterator classes. The BlastParser class itself
still relies on Bio.ParserSupport. Would it be ok if we move parts
that are used by SearchIO into their own private classes in
Bio.SearchIO, while putting the BiopythonDeprecationWarning on the
current files?

Best regards,
Bow

On Sat, Jul 13, 2013 at 3:52 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> The following pieces of code had a PendingDeprecationWarning in Biopython release 1.61, and can be upgraded to a BiopythonDeprecationWarning:
>
> Bio.Blast.NCBIStandalone (entire module). This module has had a PendingDeprecationWarning since September 2010.
>
> Bio.Motif (entire module). Its functionality is available from Bio.motifs, so Bio.Motif can be deprecated.
>
> Bio.ParserSupport (entire module). This module is currently only being used by Bio.Blast.NCBIStandalone, and has had a PendingDeprecationWarning since September 2011.
>
> Any final objections?
>
> Best,
> -Michiel
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