[Biopython-dev] Release blockers? PAML?

Peter Cock p.j.a.cock at googlemail.com
Mon Aug 15 10:04:41 UTC 2011

Hi all,

We're about due to make a Biopython release, and I could
do it early this week - but then I'm away for a fortnight. I am
fortunate to be attending the BioHackathon 2011 in Kyoto
next week, http://2011.biohackathon.org/

I think we're in a good position with the code on the trunk to
release Biopython 1.58, bar the PAML code which has not
yet been tested on Windows. Also, I'd be keen for Tiago and
Brandon to take a look at the application calling code to see
if the is any scope for a more common approach between
the PAML wrappers and the PopGen tools. Note that both
sets of tools are not 'nicely behaved' Unix style tools (which
is what the Bio.Applications API targets). To do anything
useful with these tools you have to do nasty things like
switch the current working directory and so on.

If we want to do the release this week, we could just warn
that the PAML code is consider to be "in beta" and that
the API may well change in non-backwards compatible

What else should be addressed before the next release?

There are some open bugs, but at first glance nothing



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