[Debian-med-packaging] Bug#950930: python-skbio: FTBFS with pandas 1.0: test failures

Rebecca N. Palmer rebecca_palmer at zoho.com
Sat Feb 8 14:11:28 GMT 2020


Package: python3-skbio
Version: 0.5.5-3
Control: block 950430 by -1

With pandas 1.0 from experimental:

======================================================================
ERROR: test_how_left (skbio.alignment.tests.test_tabular_msa.TestJoin)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/alignment/tests/test_tabular_msa.py", 
line 2745, in test_how_left
     joined = msa1.join(msa2, how='left')
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/alignment/_tabular_msa.py", 
line 2260, in join
     joined_positional_metadata = pd.concat(
TypeError: concat() got an unexpected keyword argument 'join_axes'

======================================================================
ERROR: test_how_right (skbio.alignment.tests.test_tabular_msa.TestJoin)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/alignment/tests/test_tabular_msa.py", 
line 2771, in test_how_right
     joined = msa1.join(msa2, how='right')
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/alignment/_tabular_msa.py", 
line 2260, in join
     joined_positional_metadata = pd.concat(
TypeError: concat() got an unexpected keyword argument 'join_axes'

======================================================================
ERROR: test_preprocess_input_raises_error 
(skbio.stats.distance.tests.test_base.CategoricalStatsHelperFunctionTests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/tests/test_base.py", 
line 948, in test_preprocess_input_raises_error
     _preprocess_input(self.dm, self.df_missing_id, 'Group')
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_base.py", 
line 1007, in _preprocess_input
     grouping = _df_to_vector(distance_matrix, grouping, column)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_base.py", 
line 1071, in _df_to_vector
     grouping = df.loc[distance_matrix.ids, column]
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1760, in __getitem__
     return self._getitem_tuple(key)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1270, in _getitem_tuple
     return self._getitem_lowerdim(tup)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1387, in _getitem_lowerdim
     section = self._getitem_axis(key, axis=i)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1952, in _getitem_axis
     return self._getitem_iterable(key, axis=axis)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1593, in _getitem_iterable
     keyarr, indexer = self._get_listlike_indexer(key, axis, 
raise_missing=False)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1550, in _get_listlike_indexer
     self._validate_read_indexer(
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1652, in _validate_read_indexer
     raise KeyError(
KeyError: 'Passing list-likes to .loc or [] with any missing labels is 
no longer supported, see 
https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike'

======================================================================
ERROR: test_bioenv_missing_distance_matrix_ids 
(skbio.stats.distance.tests.test_bioenv.BIOENVTests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/tests/test_bioenv.py", 
line 174, in test_bioenv_missing_distance_matrix_ids
     bioenv(self.dm, df)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_bioenv.py", 
line 170, in bioenv
     vars_df = data_frame.loc[distance_matrix.ids, columns]
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1760, in __getitem__
     return self._getitem_tuple(key)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1270, in _getitem_tuple
     return self._getitem_lowerdim(tup)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1387, in _getitem_lowerdim
     section = self._getitem_axis(key, axis=i)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1952, in _getitem_axis
     return self._getitem_iterable(key, axis=axis)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1593, in _getitem_iterable
     keyarr, indexer = self._get_listlike_indexer(key, axis, 
raise_missing=False)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1550, in _get_listlike_indexer
     self._validate_read_indexer(
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1652, in _validate_read_indexer
     raise KeyError(
KeyError: 'Passing list-likes to .loc or [] with any missing labels is 
no longer supported, see 
https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike'

======================================================================
ERROR: test_confirm_betadispr_results 
(skbio.stats.distance.tests.test_permdisp.testPERMDISP)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/tests/test_permdisp.py", 
line 230, in test_confirm_betadispr_results
     obs_med_mp = permdisp(mp_dm, mp_mf,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 232, in permdisp
     stat, p_value = _run_monte_carlo_stats(test_stat_function, grouping,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_base.py", 
line 1085, in _run_monte_carlo_stats
     stat = test_stat_function(grouping)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 247, in _compute_groups
     centroids = samples.groupby('grouping').aggregate(_config_med)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 960, in aggregate
     result = self._aggregate_multiple_funcs([func], _axis=self.axis)
   File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 532, 
in _aggregate_multiple_funcs
     new_res = colg.aggregate(arg)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 253, in aggregate
     ret = self._aggregate_multiple_funcs(func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 321, in _aggregate_multiple_funcs
     results[name] = obj.aggregate(func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 265, in aggregate
     return self._python_agg_general(func, *args, **kwargs)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/groupby.py", 
line 936, in _python_agg_general
     result, counts = self.grouper.agg_series(obj, f)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/ops.py", 
line 635, in agg_series
     return self._aggregate_series_fast(obj, func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/ops.py", 
line 660, in _aggregate_series_fast
     result, counts = grouper.get_result()
   File "pandas/_libs/reduction.pyx", line 375, in 
pandas._libs.reduction.SeriesGrouper.get_result
   File "pandas/_libs/reduction.pyx", line 192, in 
pandas._libs.reduction._BaseGrouper._apply_to_group
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/groupby.py", 
line 913, in <lambda>
     f = lambda x: func(x, *args, **kwargs)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 264, in _config_med
     X = x.values[:, :-1]
IndexError: too many indices for array

======================================================================
ERROR: test_median_normal 
(skbio.stats.distance.tests.test_permdisp.testPERMDISP)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/tests/test_permdisp.py", 
line 191, in test_median_normal
     obs = permdisp(self.unifrac_dm, self.unif_grouping, test='median',
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 232, in permdisp
     stat, p_value = _run_monte_carlo_stats(test_stat_function, grouping,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_base.py", 
line 1085, in _run_monte_carlo_stats
     stat = test_stat_function(grouping)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 247, in _compute_groups
     centroids = samples.groupby('grouping').aggregate(_config_med)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 960, in aggregate
     result = self._aggregate_multiple_funcs([func], _axis=self.axis)
   File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 532, 
in _aggregate_multiple_funcs
     new_res = colg.aggregate(arg)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 253, in aggregate
     ret = self._aggregate_multiple_funcs(func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 321, in _aggregate_multiple_funcs
     results[name] = obj.aggregate(func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 265, in aggregate
     return self._python_agg_general(func, *args, **kwargs)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/groupby.py", 
line 936, in _python_agg_general
     result, counts = self.grouper.agg_series(obj, f)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/ops.py", 
line 635, in agg_series
     return self._aggregate_series_fast(obj, func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/ops.py", 
line 660, in _aggregate_series_fast
     result, counts = grouper.get_result()
   File "pandas/_libs/reduction.pyx", line 375, in 
pandas._libs.reduction.SeriesGrouper.get_result
   File "pandas/_libs/reduction.pyx", line 192, in 
pandas._libs.reduction._BaseGrouper._apply_to_group
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/groupby.py", 
line 913, in <lambda>
     f = lambda x: func(x, *args, **kwargs)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 264, in _config_med
     X = x.values[:, :-1]
IndexError: too many indices for array

======================================================================
ERROR: test_no_permuations 
(skbio.stats.distance.tests.test_permdisp.testPERMDISP)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/tests/test_permdisp.py", 
line 214, in test_no_permuations
     obs = permdisp(self.eq_mat, self.grouping_eq, permutations=0)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 232, in permdisp
     stat, p_value = _run_monte_carlo_stats(test_stat_function, grouping,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_base.py", 
line 1085, in _run_monte_carlo_stats
     stat = test_stat_function(grouping)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 247, in _compute_groups
     centroids = samples.groupby('grouping').aggregate(_config_med)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 960, in aggregate
     result = self._aggregate_multiple_funcs([func], _axis=self.axis)
   File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 532, 
in _aggregate_multiple_funcs
     new_res = colg.aggregate(arg)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 253, in aggregate
     ret = self._aggregate_multiple_funcs(func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 321, in _aggregate_multiple_funcs
     results[name] = obj.aggregate(func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/generic.py", 
line 265, in aggregate
     return self._python_agg_general(func, *args, **kwargs)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/groupby.py", 
line 936, in _python_agg_general
     result, counts = self.grouper.agg_series(obj, f)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/ops.py", 
line 635, in agg_series
     return self._aggregate_series_fast(obj, func)
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/ops.py", 
line 660, in _aggregate_series_fast
     result, counts = grouper.get_result()
   File "pandas/_libs/reduction.pyx", line 375, in 
pandas._libs.reduction.SeriesGrouper.get_result
   File "pandas/_libs/reduction.pyx", line 192, in 
pandas._libs.reduction._BaseGrouper._apply_to_group
   File "/usr/lib/python3/dist-packages/pandas/core/groupby/groupby.py", 
line 913, in <lambda>
     f = lambda x: func(x, *args, **kwargs)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/distance/_permdisp.py", 
line 264, in _config_med
     X = x.values[:, :-1]
IndexError: too many indices for array

======================================================================
ERROR: test_get_plot_point_colors_invalid_input 
(skbio.stats.ordination.tests.test_ordination_results.TestOrdinationResults)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py", 
line 200, in test_get_plot_point_colors_invalid_input
     self.min_ord_results._get_plot_point_colors(
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/ordination/_ordination_results.py", 
line 324, in _get_plot_point_colors
     col_vals = df.loc[ids, column]
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1760, in __getitem__
     return self._getitem_tuple(key)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1270, in _getitem_tuple
     return self._getitem_lowerdim(tup)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1419, in _getitem_lowerdim
     return getattr(section, self.name)[new_key]
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1766, in __getitem__
     return self._getitem_axis(maybe_callable, axis=axis)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1952, in _getitem_axis
     return self._getitem_iterable(key, axis=axis)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1593, in _getitem_iterable
     keyarr, indexer = self._get_listlike_indexer(key, axis, 
raise_missing=False)
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1550, in _get_listlike_indexer
     self._validate_read_indexer(
   File "/usr/lib/python3/dist-packages/pandas/core/indexing.py", line 
1652, in _validate_read_indexer
     raise KeyError(
KeyError: 'Passing list-likes to .loc or [] with any missing labels is 
no longer supported, see 
https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike'

======================================================================
ERROR: get_trajectories returns the results of all categories
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 799, in test_get_trajectories_all
     obs = av.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 651, in _compute_trajectories_results
     trajectory = np.array([np.linalg.norm(row[1].get_values() - center)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 651, in <listcomp>
     trajectory = np.array([np.linalg.norm(row[1].get_values() - center)
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: get_trajectories returns the results of the provided category
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 837, in test_get_trajectories_single
     obs = av.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 651, in _compute_trajectories_results
     trajectory = np.array([np.linalg.norm(row[1].get_values() - center)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 651, in <listcomp>
     trajectory = np.array([np.linalg.norm(row[1].get_values() - center)
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: get_trajectories returns the correct weighted results
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 866, in test_get_trajectories_weighted
     obs = av.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 651, in _compute_trajectories_results
     trajectory = np.array([np.linalg.norm(row[1].get_values() - center)
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 651, in <listcomp>
     trajectory = np.array([np.linalg.norm(row[1].get_values() - center)
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: test_get_trajectories 
(skbio.stats.tests.test_gradient.FirstDifferenceGradientANOVATests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 942, in test_get_trajectories
     obs = dv.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 750, in _compute_trajectories_results
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 750, in <listcomp>
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: test_get_trajectories_weighted 
(skbio.stats.tests.test_gradient.FirstDifferenceGradientANOVATests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 966, in test_get_trajectories_weighted
     obs = dv.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 750, in _compute_trajectories_results
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 750, in <listcomp>
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: test_get_trajectories 
(skbio.stats.tests.test_gradient.TrajectoryGradientANOVATests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 894, in test_get_trajectories
     obs = tv.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 700, in _compute_trajectories_results
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 700, in <listcomp>
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: test_get_trajectories_weighted 
(skbio.stats.tests.test_gradient.TrajectoryGradientANOVATests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 917, in test_get_trajectories_weighted
     obs = tv.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 700, in _compute_trajectories_results
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 700, in <listcomp>
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: test_get_trajectories 
(skbio.stats.tests.test_gradient.WindowDifferenceGradientANOVATests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 990, in test_get_trajectories
     obs = wdv.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 835, in _compute_trajectories_results
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 835, in <listcomp>
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
ERROR: test_get_trajectories_weighted 
(skbio.stats.tests.test_gradient.WindowDifferenceGradientANOVATests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_gradient.py", 
line 1017, in test_get_trajectories_weighted
     obs = wdv.get_trajectories()
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 479, in get_trajectories
     self._get_group_trajectories(group, cat_groups[group]))
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 594, in _get_group_trajectories
     return self._compute_trajectories_results(group_name,
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 835, in _compute_trajectories_results
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/gradient.py", 
line 835, in <listcomp>
     np.array([np.linalg.norm(trajectories.iloc[i+1].get_values() -
   File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 
5273, in __getattr__
     return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'get_values'

======================================================================
FAIL: test_nj_dm1 (skbio.tree.tests.test_nj.NjTests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/tree/tests/test_nj.py", 
line 83, in test_nj_dm1
     self.assertEqual(actual_TreeNode.compare_tip_distances(
AssertionError: 1.6653345369377348e-16 != 0.0

----------------------------------------------------------------------
Ran 2340 tests in 53.194s

FAILED (SKIP=38, errors=17, failures=1)



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