[Biopython-dev] upgrade to python 3.1.2

Peter biopython at maubp.freeserve.co.uk
Wed Oct 27 15:33:05 UTC 2010

On Wed, Oct 27, 2010 at 4:19 PM, Dragoslav Zaric
<zaricdragoslav at gmail.com> wrote:
> Hi Peter,
> I did everything from scratch, get biopython with git, than tun those
> two commands for 2to3 from README file and at the end I run
> run_tests.py from Tests folder.
> I am sending you log file just to check am I on right track. I will
> continue to investigate errors.
> One error is related to numpy module, so I will try to install numpy
> for python 3.1.2
> Anyway, two test FAIL, test_SeqIO_online and test_Wise
> Kind regards

The problem with test_kNN.py was my mistake - it is meant to
be skipped when numpy is not installed. Fixed here:

The "IndexError: index out of range" problem on Python 3 with
test_SeqIO_online.py is the known failure I mentioned before.
This is to do with bytes versus unicode handles.

The output from test_Wise.py is unexpected through (I don't
have Wise installed on my Mac - I should do that):

FAIL: test_psw (test_Wise.TestWiseDryRun)
Call psw, and do a trivial check on its output.
Traceback (most recent call last):
  File "/home/maiev/work/biopython/Tests/test_Wise.py", line 31, in test_psw
    self.assertTrue(sys.stdout.getvalue().startswith("psw -kbyte 4
seq1.faa seq2.faa"))
AssertionError: False is not True

Hopefully with the following change we'll get a more useful message:

Could you update your Biopython and re-test? You'll have to
repeat the 2to3 conversion, e.g.

git reset --hard
2to3 ...


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