[Biopython-dev] Post Biopython 1.62 release, clean-up after dropping Python 2.5

[Peter Cock]

On Thu, May 8, 2014 at 10:46 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, May 7, 2014 at 7:36 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Sat, Aug 31, 2013 at 10:31 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>
>>> If you'd like to try some context managers for the
>>> warnings in the unit tests (9), that would be great.
>>
>> If anyone was wondering, I've just fixed the obvious uses
>> of the global warnings filter, see this commit and its parents:
>> https://github.com/biopython/biopython/commit/2e30dc67920532906e5755098c90958a2e257a88
>>
>> Note the the TODO in test_PDB.py for test_1_warnings
>> which can now be rewritten to use warnings.catch_warnings
>> (the old hack was for Python 2.5 support).
>>
>> This should hopefully mean less harmless warnings
>> showing up in the full test suite where the default
>> filters accidentally got removed (which I suspect was
>> happening sometimes).
>
> Grrr. All the buildbot tests failed last night:
>
> $ python3.4 test_SeqIO_QualityIO.py
> --> fine
>
> $ python3.4 run_tests.py test_SeqIO_QualityIO.py
> --> fine
>
> $ python3.4 run_tests.py --offline
> Skipping any tests requiring internet access
> Python version: 3.4.0a4 (default, Nov  4 2013, 14:58:04)
> [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)]
> Operating system: posix darwin
> test_Ace ... ok
> ...
> test_SeqIO_PdbIO ... ok
> test_SeqIO_QualityIO ... FAIL
> test_SeqIO_SeqXML ... ok
> ...
> ======================================================================
> FAIL: test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests)
> Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Volumes/Hitachi-3TB-mirrored/repositories/biopython/Tests/test_SeqIO_QualityIO.py",
> line 696, in test_sanger_to_illumina
>     self.assertEqual(len(w), 1, w)
> AssertionError: 0 != 1 : []
>
> ======================================================================
> FAIL: test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests)
> Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Volumes/Hitachi-3TB-mirrored/repositories/biopython/Tests/test_SeqIO_QualityIO.py",
> line 659, in test_sanger_to_solexa
>     self.assertEqual(len(w), 1, w)
> AssertionError: 0 != 1 : []
>
> ----------------------------------------------------------------------
> Ran 226 tests in 178.329 seconds
>
> FAILED (failures = 1)
>
>
> I'm hunting down the remaining manipulations of the global
> warnings filter now... this problem has been lurking for a
> long time.

Well, I replaced a load more temporary warning filters with a
context manager (and found a couple of hidden issues), but did
not solve what filter is breaking test_SeqIO_QualityIO.py, thus:
https://github.com/biopython/biopython/commit/bdf3fca8264e5e34385a908455947193f3334954

Peter