[Biopython-dev] Biopython 1.59 plans

[Brandon Invergo]

Hi Peter,

After getting bitten by some subtle output differences between different
versions of the PAML programs, I've been writing much stricter unit
tests for the parsing routines. I have the big one, codeml, done, so I
just have to do the output for the two smaller programs, baseml and
yn00. 

So far, I've only had to change one line in a Bio.Phylo.PAML file to
accommodate a parsing mistake for the oldest supported codeml version.
It's related to a purely informational line in the output rather than to
any generated results. Combined, the insignificance of the changed line
and the extremely old software version that produces the difference mean
that this change in the code is not mission critical.

The testing code and the directory of PAML test resources is, however,
significantly different.

I can probably have the other two parts done by, say, Wednesday. The
question, though, is whether this is worth trying to pull in for
Biopython 1.59 or should I hold of on the pull request until after the
release?

Cheers,
Brandon

On Sat, 2012-02-18 at 09:15 +0000, Peter Cock wrote:
> Hello all,
> 
> Based on the typical release schedule, we're a little overdue
> for releasing Biopython 1.59 - I would have raised this earlier
> but January was busy for me. With the recent NCBI EFetch
> change, and the workaround for it, it would be especially
> good to get the release out soon.
> 
> I propose we release Biopython 1.59 in the second half of
> next week - essentially the master branch as it is.
> 
> Most of the unit tests are also passing under PyPy (bar
> the C extensions, and external dependencies like NumPy)
> with the exception of some XML issues with the standard
> library. If we mark these as known failures and include
> them in the buildbot before then, we can announce this
> release as having (partial) PyPy support.
> 
> Does anyone else want to do the release? If not, I can.
> 
> Any comments on this? I'll start a new thread for plans
> for Biopython 1.60 - there are several exciting chunks
> of new code that looks near ready for release.
> 
> Peter
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