--- Begin Message ---
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)
--- End Message ---
