[Biopython-dev] Python 2.3 [Was Re: [BioPython] GRAVY index program anyone?]

Andrew Dalke dalke at dalkescientific.com
Mon Aug 4 04:13:38 EDT 2003

I don't think there's a strong reason to move to 2.3.  Here's the most
relevant changes

sum and enumerate builtins - we can get by with old-style code.

The module I like most is 'datetime'.  As some point we should get our
database records to use this.

For the chemistry work I do, csv is nice, but surprisingly unused
in biology.

The bsddb and bz2 modules are nice for Mindy, but not essential.
(*sigh*, and I need to finish that off.)

The logging might be nice, but I'm just not a logging type of person.

I'm told that optparse is better than getopt, so we should move
scripts over to use the new API

sets is potentially useful, but will require API changes.  Eg,
we could return search results as a set rather than a list.  This
would allow us to do intersections and unions pretty easily.  But
then we lose native order.

socket timeout might be handy in a few cases.  I don't think so
though - the socket should be passed in to objects rather than
created internally.

zipimport suggests a nice way to distribute biopython (excepting
the C extensions)

A lot of ugly slice code can be fixed up with the new slice object


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