Bug#906156: python-skbio ftbfs in unstable, and autopkg tests fail (Python 3.7 tests)

2018-08-15 Thread Andreas Tille 
Control: tags -1 upstream
Control: forwarded -1 https://github.com/biocore/scikit-bio/issues/1595

I've verified that the problem persists in the latest upstream
version (0.5.3) which needs a new Build-Depends python-hdmedians
(just packaged and ITPed, upload to new is pending).

Kind regards

   Andreas.

-- 
http://fam-tille.de

Bug#906156: python-skbio ftbfs in unstable, and autopkg tests fail (Python 3.7 tests)

2018-08-15 Thread Matthias Klose 
Package: src:python-skbio
Version: 0.5.2-1
Severity: serious
Tags: sid buster

python-skbio ftbfs in unstable (Python 3.7 tests)

https://ci.debian.net/data/packages/unstable/amd64/p/python-skbio/latest-autopkgtest/log.gz


==
ERROR: test_bool_index_both_axes 
(skbio.alignment.tests.test_tabular_msa.TestLoc)
--
Traceback (most recent call last):
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1091, in test_bool_index_both_axes
new = self.get(msa, ([False, True, True], [True, True, False]))
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 38, in __getitem__
return self._handle_both_axes(*indexable)
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 52, in _handle_both_axes
r = self._slice_on_first_axis(self._obj, seq_index)
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
  File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'

==
ERROR: test_bool_index_first_axis 
(skbio.alignment.tests.test_tabular_msa.TestLoc)
--
Traceback (most recent call last):
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1062, in test_bool_index_first_axis
new = self.get(msa, [True, True, False])
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 42, in __getitem__
return self._slice_on_first_axis(self._obj, indexable)
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
  File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'

==
ERROR: test_bool_index_second_axis 
(skbio.alignment.tests.test_tabular_msa.TestLoc)
--
Traceback (most recent call last):
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1076, in test_bool_index_second_axis
new = self.get(msa, (Ellipsis, [True, True, False]))
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 38, in __getitem__
return self._handle_both_axes(*indexable)
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 50, in _handle_both_axes
return self._slice_on_second_axis(self._obj, pos_index)
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 62, in _slice_on_second_axis
if self.is_scalar(indexable, axis=1):
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
  File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'

==
ERROR: test_bool_index_too_big (skbio.alignment.tests.test_tabular_msa.TestLoc)
--
Traceback (most recent call last):
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1103, in test_bool_index_too_big
self.get(msa, [False, False, False, False])
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 42, in __getitem__
return self._slice_on_first_axis(self._obj, indexable)
  File
"/<>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if