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

[Peter Cock]

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.

Peter