[Biopython-dev] Biopython 1.59 plans

[Peter Cock]

On Monday, February 20, 2012, Brandon Invergo wrote:

> 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?
>
>
I'm tied up in a workshop Monday (today) and Tuesday (tomorrow),
so Wednesday was the earliest date anyway. If you have these
extended unit tests done by Wednesday that would be great.

Thanks,

Peter