[Biopython-dev] Release blockers? PAML?

Brandon Invergo b.invergo at gmail.com
Tue Aug 16 20:06:24 UTC 2011

Hi everyone,

I wrote some tests for the presence of the PAML binaries and I've run
all the unit tests in Python 2.7 on Windows 7 and they all pass.


On Mon, 2011-08-15 at 11:04 +0100, Peter Cock wrote:
> 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
> ways?
> What else should be addressed before the next release?
> There are some open bugs, but at first glance nothing
> critical.
> Regards,
> Peter

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