[Biopython-dev] Martel in CVS

[Jeffrey Chang]

> Want to make sure about the configuration before I do the
> final commit.  As I recall we said that
>   - Martel is a sibling to Bio

Do you mean that "Bio" and "Martel" live in the same namespace?  If so,
that sounds fine to me.

>   - Martel should be able to be distributed w/ or w/o the read of
> biopython

Definitely.


>   - Biopython should allow distributions w/ or w/o Martel, as determined
>       by a flag Brad added to setup.py

Sure.  However, I think that by 1.0 is released, Martel will be a
bona-fide requirement.  Biopython will be usable without Martel, but won't
be a lot of fun (like Windows without a mouse).


> There are some things I need to do to make things integrate nicely.
>
>   Martel needs its own setup.py for independent distribution.  I
>   assume it should be independent from the main setup.py (that is,
>   there will be a Martel/setup.py).

Yes.


>   I'm planning to move the format definitions to biopython proper,
>   and pull most (all?) of them out of Martel/formats.  Where
>   should they go?  It looks like they will be scattered about,
>   so they go into the directory associated with that datatype.

Covered in previous email.


>   Where do the tests go?  There are two types of tests.  Some are
>   integral to Martel and should stay with a Martel distribution.
>   Others are related to the formats.  I'm thinking of putting
>   the format tests under Tests, which would only contain tests
>   related to syntax matching like Martel already has.  The
>   problem there would be in upping the namespace pollution of
>   putting all the tests in one spot.  But we've only a couple
>   dozen so far so it isn't a serious problem.
>
>   I'm going to make all the core Martel tests use the Python 2.1
>   unittest and the other biopython tests (in Test) use
>   Test/unittest.py.  I hope they aren't too different.

Yes, me too.  Biopython will not require Python 2.1 for some time from
now.  Can we use the Python 2.1 unittest in biopython?  This would make
the migration easier when it happens, and it sounds like it would make
your work easier too.


>   Where should the documentation go?  I think it's okay to
>   leave it in Martel/doc since nearly everything that is there
>   is specific to Martel the parser, and not the format definitions
>   for biopython.

Sounds good.


>   I will scatter the files in the Martel/builders/ directory
>   to the appropriate parts of biopython.
>
>   This all means there will be two different ways to parse
>   the same data files.  How should that changeover be managed,
>   since the two styles of processing are somewhat different?

Will this change the API, or can we just change the code out from under
the current Parser and Iterator classes?  If the API needs to change, we
should do this sooner rather than later, and definitely before 1.0 is
released.  In fact, we won't release 1.0 until there are no planned API
changes.

Jeff


> 					Andrew
> 					dalke at acm.org
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