[Biopython-dev] curious error from HMM unit test

[Peter]

On Mon, Jan 17, 2011 at 4:17 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> It could have been an exotic bug in Jython (or its interactions with the
> JVM) where the JIT or garbage collector is removing local variables too
> early. I don't see how you could provide a "fix" for it in Biopython, since
> k definitely exists at that point in the loop in any valid Python and Jython
> almost always handles it correctly.
>

Good point - maybe that is the most likely explanation.

>
> Maybe you could seed the RNG at the start of the unit test to ensure the
> same paths are always taken?
>

We could do, but as part of that I'd want to increase the test coverage
to ensure most of the HMM code is actually covered in the single non-
stochastic run. As no-one is actively looking after it, so I'd rather not
touch the tests.

Peter