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

[Wibowo Arindrarto]

Hi Michiel, Peter,

In preparation for the 1.62 release, I've made the following changes
to Bio.NCBIStandalone and Bio.ParserSupport:

* Migrated the two modules under Bio.SearchIO._legacy
* Upgraded their PendingDeprecationWarning to BiopythonDeprecationWarning

I've pushed the changes to this branch:
https://github.com/bow/biopython/tree/bio_blast_migrate

Tests seem to be running fine still, but now there is the awkward
situation where if users import Bio.NCBIStandalone and/or
Bio.ParserSupport directly they will be greeted with two warnings: the
BiopythonWarning for the modules' deprecation and the
BiopythonExperimentalWarning for SearchIO.

We could suppress the SearchIO warning in Bio.NCBIStandalone and
Bio.ParserSupport. But before this is done, I was wondering if we have
a defined timeline for removing a BiopythonExperimentalWarning? (i.e.
if it will be removed in this release, then we could do that instead).

Any opinions on this :)?

Cheers,
Bow

On Sat, Jul 13, 2013 at 12:54 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> 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
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>
>