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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1271, in get return obj.loc[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 38, in __getitem__ return self._handle_both_axes(*indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1271, in get return obj.loc[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 42, in __getitem__ return self._slice_on_first_axis(self._obj, indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1271, in get return obj.loc[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 38, in __getitem__ return self._handle_both_axes(*indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1271, in get return obj.loc[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 42, in __getitem__ return self._slice_on_first_axis(self._obj, indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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_small (skbio.alignment.tests.test_tabular_msa.TestLoc) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1119, in test_bool_index_too_small self.get(msa, [False]) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1271, in get return obj.loc[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 42, in __getitem__ return self._slice_on_first_axis(self._obj, indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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_unhashable_index_both_axes (skbio.alignment.tests.test_tabular_msa.TestLoc) ---------------------------------------------------------------------- TypeError: unhashable type: 'list' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1461, in test_unhashable_index_both_axes self.get(msa, (s, 0)) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1271, in get return obj.loc[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 38, in __getitem__ return self._handle_both_axes(*indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 1926, in get_duplicates return self[self.duplicated()].unique() File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 4539, in duplicated return super(Index, self).duplicated(keep=keep) File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 1250, in duplicated return duplicated(self, keep=keep) File "/usr/lib/python3/dist-packages/pandas/core/algorithms.py", line 798, in duplicated return f(values, keep=keep) SystemError: <built-in function duplicated_object> returned a result with an error set ====================================================================== ERROR: test_unhashable_index_first_axis (skbio.alignment.tests.test_tabular_msa.TestLoc) ---------------------------------------------------------------------- TypeError: unhashable type: 'slice' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1433, in test_unhashable_index_first_axis self.get(msa, s, axis=0) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1273, in get return obj.loc(axis=axis)[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 29, in __getitem__ return self._slice_on_first_axis(self._obj, indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 1926, in get_duplicates return self[self.duplicated()].unique() File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 4539, in duplicated return super(Index, self).duplicated(keep=keep) File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 1250, in duplicated return duplicated(self, keep=keep) File "/usr/lib/python3/dist-packages/pandas/core/algorithms.py", line 798, in duplicated return f(values, keep=keep) SystemError: <built-in function duplicated_object> returned a result with an error set ====================================================================== ERROR: test_unhashable_index_second_axis (skbio.alignment.tests.test_tabular_msa.TestLoc) ---------------------------------------------------------------------- TypeError: unhashable type: 'slice' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1446, in test_unhashable_index_second_axis self.get(msa, [0, 1], axis=1) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 1273, in get return obj.loc(axis=axis)[indexable] File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py", line 31, in __getitem__ return self._slice_on_second_axis(self._obj, indexable) File "/<<PKGBUILDDIR>>/.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 "/<<PKGBUILDDIR>>/.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 1926, in get_duplicates return self[self.duplicated()].unique() File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 4539, in duplicated return super(Index, self).duplicated(keep=keep) File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 1250, in duplicated return duplicated(self, keep=keep) File "/usr/lib/python3/dist-packages/pandas/core/algorithms.py", line 798, in duplicated return f(values, keep=keep) SystemError: <built-in function duplicated_object> returned a result with an error set ====================================================================== FAIL: test_with_positional_metadata (skbio.alignment.tests.test_tabular_msa.TestIterPositions) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 2958, in test_with_positional_metadata 'bar': [np.nan, np.nan, 'bazz']})]) AssertionError: Lists differ: [Sequ[50 chars]o': 9.0 'pm1': 0.5 Positional metadata: [313 chars] C--] != [Sequ[50 chars]o': 9 'pm1': 0.5 Positional metadata: [309 chars] C--] First differing element 0: Seque[49 chars]o': 9.0 'pm1': 0.5 Positional metadata: [102 chars]0 AA- Seque[49 chars]o': 9 'pm1': 0.5 Positional metadata: [100 chars]0 AA- [Sequence --------------------------- Metadata: - 'foo': 9.0 ? -- + 'foo': 9 'pm1': 0.5 Positional metadata: + 'foo': <dtype: float64> 'bar': <dtype: object> - 'foo': <dtype: float64> Stats: length: 3 --------------------------- 0 AA-, Sequence --------------------------- Metadata: - 'foo': 99.0 ? -- + 'foo': 99 'pm1': 1.5 Positional metadata: + 'foo': <dtype: float64> 'bar': <dtype: object> - 'foo': <dtype: float64> Stats: length: 3 --------------------------- 0 C--] ====================================================================== FAIL: test_with_positional_metadata_reverse (skbio.alignment.tests.test_tabular_msa.TestIterPositions) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 2979, in test_with_positional_metadata_reverse 'bar': [np.nan, np.nan, 'baz']})]) AssertionError: Lists differ: [Sequ[51 chars]': 99.0 'pm1': 1.5 Positional metadata: [312 chars] AA-] != [Sequ[51 chars]': 99 'pm1': 1.5 Positional metadata: [308 chars] AA-] First differing element 0: Seque[50 chars]': 99.0 'pm1': 1.5 Positional metadata: [102 chars]0 C-- Seque[50 chars]': 99 'pm1': 1.5 Positional metadata: [100 chars]0 C-- [Sequence --------------------------- Metadata: - 'foo': 99.0 ? -- + 'foo': 99 'pm1': 1.5 Positional metadata: + 'foo': <dtype: float64> 'bar': <dtype: object> - 'foo': <dtype: float64> Stats: length: 3 --------------------------- 0 C--, Sequence --------------------------- Metadata: - 'foo': 9.0 ? -- + 'foo': 9 'pm1': 0.5 Positional metadata: + 'foo': <dtype: float64> 'bar': <dtype: object> - 'foo': <dtype: float64> Stats: length: 3 --------------------------- 0 AA-] ====================================================================== FAIL: test_how_outer (skbio.alignment.tests.test_tabular_msa.TestJoin) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 2770, in test_how_outer 'baz': [np.nan, np.nan, 'c', 'd', 'e']})) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py", line 2521, in assertEqualJoinedMSA self.assertEqual(msa1, msa2) AssertionError: Tabul[59 chars] 'bar': <dtype: object> 'baz': <dtype: [136 chars]----- != Tabul[59 chars] 'foo': <dtype: int64> 'bar': <dtype: o[136 chars]----- ====================================================================== FAIL: test_not_equal (skbio.util.tests.test_testing.TestAssertDataFrameAlmostEqual) ---------------------------------------------------------------------- Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/util/tests/test_testing.py", line 211, in test_not_equal assert_data_frame_almost_equal(df1, df2) AssertionError: AssertionError not raised ---------------------------------------------------------------------- Ran 2314 tests in 70.280s FAILED (SKIP=30, errors=8, failures=4)