[Biopython-dev] Status of SearchIO

[Peter Cock]

On Fri, Oct 26, 2012 at 11:38 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
>>> Also, I think there are still some issues that need to be dealt
>>
>> >> with before we put SearchIO into master, notably with Bio.BLAST
>> >> module. If not the official deprecation notice, at least the the
>> >> tutorial has to be updated (let Bio.BLAST readers know about the
>> >> plan with SearchIO). I've written a short tutorial here:
>> >> http://bow.web.id/biopython/Tutorial.html. This is still a draft,
>> >> but you can already see that there are some obvious overlaps
>> >> between Bio.BLAST and Bio.SearchIO, which is confusing to new
>> >> readers.
>> >
>> > Personally I wouldn't let this consideration block the inclusion of a
>> > module as useful like that. Of course I need this code, so I'm biased.
>>
>> I'm also OK with merging the code before updating the Tutorial
>> chapter on BLAST (which would probably become a broader
>> chapter on BLAST and other tools using SearchIO). As discussed
>> before, the long term aim would be to remove Bio.BLAST.
>
> Ah, ok then :). There are other things I'm still working on at the
> moment (BLAST plain text writer, details about migrating from
> Bio.Blast), but I consider these to be less urgent than the tutorial.
> If everyone is ok for merging, then I'm good too :). I suppose we are
> going to use the 'beta' new feature warning here, right?

Yes to the 'beta' warning. I'd like to get some wider testing with
community feedback on the API, while giving us the option to
change it before declaring it stable.

>> > I'll have to read up on the namespace discussion. While I see the
>> > benefit of using PEP8 names, intuitively I don't like bio.seq.search
>> > much. Then again, I started my life in Bio* with BioPerl, and like the
>> > pretty similar module layout BioPython has so far.
>>
>> Yeah - the current naming of SeqIO and AlignIO was directly
>> inspired by BioPerl, and give the working name of SearchIO.
>>
>> Peter
>
> Reaching a unanimous decision on name preference seems difficult :/.
> We now have:
>
> 1. Bio.seq.search (in line with the namespace change)
> 2. Bio.seqsearch (top-level module, separate from Bio.seq. This used
> to be Bio.SeqSearch, now adjusted for PEP8 compliance)
> 3. Bio.search (same reasoning + explanation like Bio.seqsearch).
> 4. Bio.SearchIO / Bio.searchio
> 5. Bio.psearch (p for pairwise)
>
> Any other suggestions? Should we put it to a vote?

I'd like a consensus first on the larger question of should we
adopt lower case module names automatically under Python 3.
In that case, option (1) about would be bio.seq.search under
Python 3, and so on.

Peter