Re: Bug#942106: Adding Python 3.8 as a supported Python3 version

2019-11-14 Thread Matthias Klose 
On 12.11.19 23:39, Matthias Klose wrote:
> On 07.11.19 15:08, Matthias Klose wrote:
>> This weekend, I am planning to upload python3-defaults, adding python3.8 as a
>> supported Python3 version.  This may introduce some churn in unstable until 
>> the
>> basic binNMUs are available as well.
>>
>> Details for the addition can be found at [1], known issues and patches are 
>> filed
>> [2].  There was no test rebuild in Debian itself, but the addition was made 
>> in
>> the current Ubuntu development series.  Things look good, and from my point 
>> of
>> view don't block any unrelated transition work.  python3-defaults will get a 
>> RC
>> issue to stay in unstable until the packages build-depending on 
>> python3-all-dev
>> are built, and after doing a test rebuild with the two supported Python3
>> versions.  Earlier test rebuilds don't make sense.
>>
>> There are a few packages, where the upstream versions used in Ubuntu diverge
>> from the ones currently in unstable (not naming those already updated in
>> unstable by the DPMT):
>>
>>  - hypothesis #942693, not sure if this is really needed,
>>    the testsuite stack might be fixed by the new pluggy
>>    version as well.
>>
>>  - python-xarray #944044. 1.4 is already broken with Python 3.7. For
>>    Ubuntu I fell back to 1.2.1. 1.2.3 might work as well, still seeing
>>    one or two test failures.
>>
>>  - Using numpy from experimental, and only building the Python2 numpy
>>    packages from the python-numpy source.
>>
>>  - Using python-scipy from experimental, building the Python3 packages,
>>    and renaming the python-scipy package to python2-scipy, only building
>>    the Python2 packages.
>>
>>  - matplotlib and pandas don't have Python2 packages in Ubuntu
>>    anymore, so I can't tell much what is needed here. Pandas needs
>>    a new upstream for 3.8.
>>
>> Packages building on top of numpy/scipy/pandas, like the PyAstro stack, 
>> continue
>> to work with these updates, despite some new test failures.
> 
> So this upload didn't happen, but thanks to Rebecca we now have an almost
> Python2 free pandas in unstable. And apologies to the science team for the 
> 1-day
> delayed NMUs for patsy and scikit-learn.
> 
> Now planning the python3-defaults upload for Thursday or Friday.

python3-defaults with 3.8 as a supported Python3 version is now built in
unstable.  Release team, please schedule binNMUs fpr stage1 and then stage2.
I'll raise severity of the 3.8 issues, and follow-up with 2-days delayed NMUs.

Matthias

Help needed to adapt python-skbio to Python3(?) / Pandas

2019-11-14 Thread Andreas Tille 
Control: tags -1 help
Control: tags -1 upstream
Control: forwarded -1 https://github.com/biocore/scikit-bio/issues/1678

Hi Rebecca,

thanks a lot for working on the Pandas migration.

On Wed, Nov 13, 2019 at 10:19:56PM +, Rebecca N. Palmer wrote:
> The ones that are blocking pandas [1] are python-skbio,
> 
> [1] https://qa.debian.org/excuses.php?package=pandas (cnvkit since fixed)

I've checked the issue with some patch from upstream[1] but failed.  I
also tried to build HEAD from upstream which also leaves three remaining
errors which I reported in issue #1678[2]:


==
ERROR: test_munging_invalid_type_to_self_type 
(skbio.sequence.tests.test_sequence.TestDistance)
--
Traceback (most recent call last):
  File 
"/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/tests/test_sequence.py",
 line 2369, in test_munging_invalid_type_to_self_type
Sequence("ACGT").distance(42)
  File 
"/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py",
 line 1539, in distance
other = self._munge_to_self_type(other, 'distance')
  File 
"/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py",
 line 2161, in _munge_to_self_type
return self.__class__(other)
  File 
"/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py",
 line 622, in __init__
s = np.frombuffer(sequence, dtype=np.uint8)
TypeError: a bytes-like object is required, not 'int'

==
ERROR: test_init_invalid_sequence 
(skbio.sequence.tests.test_sequence.TestSequence)
--
Traceback (most recent call last):
  File 
"/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/tests/test_sequence.py",
 line 465, in test_init_invalid_sequence
Sequence(('a', 'b', 'c'))
  File 
"/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py",
 line 622, in __init__
s = np.frombuffer(sequence, dtype=np.uint8)
TypeError: a bytes-like object is required, not 'tuple'

==
FAIL: test_no_variation_pearson 
(skbio.stats.distance.tests.test_mantel.MantelTests)
--
Traceback (most recent call last):
  File 
"/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/stats/distance/tests/test_mantel.py",
 line 247, in test_no_variation_pearson
npt.assert_equal(obs, (np.nan, np.nan, 3))
  File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 
355, in assert_equal
assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k, err_msg), verbose)
  File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 
427, in assert_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
item=0

 ACTUAL: 0.0
 DESIRED: nan

--
Ran 2352 tests in 44.011s

FAILED (SKIP=30, errors=2, failures=1)


I somehow suspect that the two errors above might be caused by a broken
Python3 conversion - any help to fix this would be welcome.

Kind regards

   Andreas.

[1] 
https://github.com/biocore/scikit-bio/commit/9c061da7e2746aee403b41621f71b118ce5c52f8
[2] https://github.com/biocore/scikit-bio/issues/1678

-- 
http://fam-tille.de