[Biopython-dev] Status of SearchIO

[Kai Blin]

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On 2012-10-26 11:33, Wibowo Arindrarto wrote:
> Hi Kai, Peter,
> 
> For the merge conflict, which branch are you using? Can you point
> to specific commits that cause the conflicts? I haven't tried
> merging / rebasing my own branch to the current master myself ~ so
> knowing this should help the process as well.

For merging, I think I had to change
.travis.yml
setup.py
and Tests/run_tests.py

.travis.yml and setup.py mainly had whitespace changes in comments, so
I just went with the version from master on those changes. As I said,
nothing really huge.

https://github.com/kblin/biopython/tree/searchio-merge is the merged tree.

The rebase had a number of things, I just gave up on that.

> 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'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.

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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