[Biopython-dev] test_PopGen_GenePop_EasyController.py failure on Jython

[Peter Cock]

Hi all,

I've exchanged a few emails with Tiago off list regarding an inconsistent
test_PopGen_GenePop_EasyController.py problem (most visible on
Jython), giving error "Unable to open file genepop.txt".

I've just had it from Python 2.7 on a 32bit Linux machine:

======================================================================
ERROR: test_get_avg_fst_pair (test_PopGen_GenePop_EasyController.AppTest)
Test get pairwise Fst.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/pjcock/repositories/biopython/Tests/test_PopGen_GenePop_EasyController.py",
line 98, in test_get_avg_fst_pair
    pop_fis =  self.ctrl.get_avg_fst_pair()
  File "/home/pjcock/repositories/biopython/build/lib.linux-i686-2.7/Bio/PopGen/GenePop/EasyController.py",
line 162, in get_avg_fst_pair
    return self._controller.calc_fst_pair(self._fname)[1]
  File "/home/pjcock/repositories/biopython/build/lib.linux-i686-2.7/Bio/PopGen/GenePop/Controller.py",
line 819, in calc_fst_pair
    self._run_genepop([".ST2", ".MIG"], [6,2], fname)
  File "/home/pjcock/repositories/biopython/build/lib.linux-i686-2.7/Bio/PopGen/GenePop/Controller.py",
line 296, in _run_genepop
    % (ret, e_out.strip().split("\n",1)[0]))
IOError: GenePop error -11, Unable to open file genepop.txt

======================================================================
ERROR: test_get_avg_fst_pair_locus (test_PopGen_GenePop_EasyController.AppTest)
Test get average Fst for pairwise pops on a locus.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/pjcock/repositories/biopython/Tests/test_PopGen_GenePop_EasyController.py",
line 93, in test_get_avg_fst_pair_locus
    self.assertEqual(len(self.ctrl.get_avg_fst_pair_locus("Locus4")), 45)
  File "/home/pjcock/repositories/biopython/build/lib.linux-i686-2.7/Bio/PopGen/GenePop/EasyController.py",
line 166, in get_avg_fst_pair_locus
    iter = self._controller.calc_fst_pair(self._fname)[0]
  File "/home/pjcock/repositories/biopython/build/lib.linux-i686-2.7/Bio/PopGen/GenePop/Controller.py",
line 819, in calc_fst_pair
    self._run_genepop([".ST2", ".MIG"], [6,2], fname)
  File "/home/pjcock/repositories/biopython/build/lib.linux-i686-2.7/Bio/PopGen/GenePop/Controller.py",
line 296, in _run_genepop
    % (ret, e_out.strip().split("\n",1)[0]))
IOError: GenePop error -11, Unable to open file genepop.txt

----------------------------------------------------------------------


This failed twice in a row, then passed four times in a row (Linux, Python 2.7).
I suspect the issue was related to machine IO load - during the first
tests I had
something compiling at the same time. I can't reproduce it on demand :(

I've also seen it on the Mac with Apple's Python 2.6 (although usually it is
usually fine).

However, I'm seeing this (consistently?) with Jython 2.5.1 on the Mac.

Peter