[Biopython-dev] Biopython under PyPy

[Peter Cock]

Hi all,

I've been trying Biopython under PyPy 1.6, and the unit tests for
a lot of things work fine. In the short term I'm skipping all the C
extensions (not clear how easy they will be under PyPy):
https://github.com/biopython/biopython/commit/2a26ceebed01508a69aefd6a3a6437245347a5a2

PyPy ships with a minimal numpy implementation, but it seems
to be very minimal - e.g. there is no dot function. This is actually
a bit annoying as "import numpy" works but you don't get everything!
Anyway, there are some easy checks we can add to individual
unit tests to skip them under pypy.

What is interesting is running the full test suite reports some
false positives (tests which when run on their own, or as part
of a smaller group pass), and the test suite itself never finishes:
error: Too many open files

I'm not sure what this is from... I fixed an obvious handle leak:
https://github.com/biopython/biopython/commit/f7ce81b3751745970c32cc813836507e93da3c30

I suspect the problem is some of the individual tests are
leaking handles - which we know already from warnings
under Python 3 etc.

Peter