[Biopython-dev] upgrade to python 3.1.2

[Peter]

On Wed, Oct 27, 2010 at 5:14 PM, Dragoslav Zaric
<zaricdragoslav at gmail.com> wrote:
>
> Ok, errors:
>
> test_SeqIO_online ... FAIL
> test_Wise ... FAIL
>
> ======================================================================
> ERROR: test_nuccore_X52960 (test_SeqIO_online.EntrezTests)
> Bio.Entrez.efetch(nuccore, X52960, ...)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> ...
> IndexError: index out of range
>
> ======================================================================
> ERROR: test_nucleotide_6273291 (test_SeqIO_online.EntrezTests)
> Bio.Entrez.efetch(nucleotide, 6273291, ...)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> ...
> IndexError: index out of range
>
> ======================================================================
> ERROR: test_protein_16130152 (test_SeqIO_online.EntrezTests)
> Bio.Entrez.efetch(protein, 16130152, ...)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> ...
> IndexError: index out of range


We're ignoring the above problem with test_SeqIO_online.py
on Python 3 for now.


> ======================================================================
> FAIL: test_dnal (test_Wise.TestWiseDryRun)
> Call dnal, and do a trivial check on its output.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/maiev/work/biopython/Tests/test_Wise.py", line 27, in test_dnal
>    self.assertTrue(output.startswith("dnal -kbyte 100000 seq1.fna
> seq2.fna"), output[:200])
> AssertionError: dnal -kbyte 100000 -quiet seq1.fna seq2.fna > /tmp/tmpEVkZM8
>
>
> ======================================================================
> 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 33, in test_psw
>    self.assertTrue(output.startswith("psw -kbyte 4 seq1.faa
> seq2.faa"), output[:200])
> AssertionError: psw -kbyte 4 -quiet seq1.faa seq2.faa > /tmp/tmpOJ3QL3

I remember this issue now:
http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007904.html
(very end)
...
http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007908.html

This was due to the psw/dnal wrappers sometimes automatically including
the command line switch -quiet switch. It happens if you redirect the unit
test output to a file. This change should solve it:

http://github.com/biopython/biopython/commit/4f430adad7a5b8bc021dec8b188963ca76612393

Thanks!

Peter