[Biopython-dev] upgrade to python 3.1.2

[Peter]

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:
http://github.com/biopython/biopython/commit/2ae15f94e7e90b237e982145f9697157ed1f801e

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:
http://github.com/biopython/biopython/commit/811f5ced0305fa41539b8867c594a119135ef682

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

git reset --hard
2to3 ...
etc

Peter