Merge 6b364c4 into fcb847d

ci/pip_requirements.txt

@@ -3,7 +3,7 @@ coveralls
 natsort
 lockfile
 CacheControl
-Sphinx
+Sphinx <= 3.0
 sphinx-bootstrap-theme
 check-manifest
 hdmedians

doc/source/conf.py

@@ -382,7 +382,8 @@ def fmt(string):
 #texinfo_no_detailmenu = False
 
 # -- Options for autosummary ----------------------------------------------
-autosummary_generate = glob.glob('*.rst')
+autosummary_generate =  glob.glob('*.rst')
+
 
 #------------------------------------------------------------------------------
 # Plot
@@ -513,4 +514,4 @@ def __get__(self, cls, owner):
 # examples, originally taken from scikit-learn's doc/conf.py
 def setup(app):
     app.add_javascript('copybutton.js')
-    app.add_stylesheet('style.css')
+    app.add_stylesheet('style.css')

skbio/alignment/_tabular_msa.py

@@ -1172,8 +1172,8 @@ def _slice_sequences_iloc_(self, i):
             return self._constructor_(new_seqs, positional_metadata=None)
         return self._constructor_(new_seqs)
 
-    def _get_sequence_loc_(self, l):
-        new_seqs = self._seqs.loc[l]
+    def _get_sequence_loc_(self, x):
+        new_seqs = self._seqs.loc[x]
         if type(new_seqs) is self.dtype:
             return new_seqs
         else:
@@ -1186,10 +1186,10 @@ def _get_sequence_loc_(self, l):
                 raise AssertionError(
                     "Something went wrong with the index %r provided to"
                     " `_get_sequence_loc_`, please report this stack trace to"
-                    "\nhttps://github.com/biocore/scikit-bio/issues" % l)
+                    "\nhttps://github.com/biocore/scikit-bio/issues" % x)
 
-    def _slice_sequences_loc_(self, l):
-        new_seqs = self._seqs.loc[l]
+    def _slice_sequences_loc_(self, x):
+        new_seqs = self._seqs.loc[x]
         try:
             # TODO: change for #1198
             if len(new_seqs) == 0:

skbio/diversity/_util.py

@@ -104,7 +104,7 @@ def _validate_otu_ids_and_tree(counts, otu_ids, tree):
     set_tip_names = set(tip_names)
     if len(tip_names) != len(set_tip_names):
         raise DuplicateNodeError("All tip names must be unique.")
-    if np.array([l is None for l in branch_lengths]).any():
+    if np.array([x is None for x in branch_lengths]).any():
         raise ValueError("All non-root nodes in ``tree`` must have a branch "
                          "length.")
     missing_tip_names = set_otu_ids - set_tip_names

skbio/io/tests/test_registry.py

@@ -27,8 +27,8 @@
 
 
 class MockClass:
-    def __init__(self, l):
-        self.list = l
+    def __init__(self, x):
+        self.list = x
 
     def __eq__(self, other):
         # They are only equal when the class is EXACTLY the same. We don't want
@@ -1692,8 +1692,8 @@ def writer(obj, fh):
             iterator = iter(obj.list)
             fh.write(next(iterator))
             fh.flush()  # Flush should be a noop for bz2
-            for l in iterator:
-                fh.write(l)
+            for x in iterator:
+                fh.write(x)
 
         self.registry.write(obj, format='format1', into=fp, compression='bz2')
         self.registry.write(obj, format='format1', into=f, compression='bz2')

skbio/metadata/_testing.py

@@ -715,9 +715,12 @@ def test_positional_metadata_getter_set_column_array(self):
         # array-like objects will fail if wrong size.
         for array_like in (np.array(range(length-1)), range(length-1),
                            np.array(range(length+1)), range(length+1)):
+
             with self.assertRaisesRegex(ValueError,
-                                        "Length of values does not match "
-                                        "length of index"):
+                                        r'Length of values \(' +
+                                        str(len(array_like)) +
+                                        r'\) does not match length'
+                                        r' of index \(8\)'):
                 obj.positional_metadata['bar'] = array_like
 
     def test_positional_metadata_setter_pandas_consumable(self):

skbio/stats/distance/_permdisp.py

@@ -140,7 +140,7 @@ def permdisp(distance_matrix, grouping, column=None, test='median',
     sample size                      6
     number of groups                 2
     test statistic             1.03296
-    p-value                       0.35
+    p-value                       ...
     number of permutations          99
     Name: PERMDISP results, dtype: object
 
@@ -170,7 +170,7 @@ def permdisp(distance_matrix, grouping, column=None, test='median',
     statistics.
 
     >>> np.random.seed(0)
-    >>> permdisp(dm, grouping, test='centroid', permutations=6)
+    >>> permdisp(dm,grouping,test='centroid',permutations=6) #doctest:+ELLIPSIS
     method name               PERMDISP
     test statistic name        F-value
     sample size                      6

skbio/stats/ordination/tests/test_ordination_results.py

@@ -266,7 +266,7 @@ def test_plot_categorical_legend(self):
         labels = [t.get_text() for t in legend.get_texts()]
         npt.assert_equal(sorted(labels), ['bar', 'foo'])
 
-        colors = [l.get_color() for l in legend.get_lines()]
+        colors = [x.get_color() for x in legend.get_lines()]
         npt.assert_equal(sorted(colors), ['green', 'red'])
 
     def test_repr_png(self):

skbio/stats/ordination/tests/test_redundancy_analysis.py

@@ -9,7 +9,6 @@
 import numpy as np
 import numpy.testing as npt
 import pandas as pd
-import pandas.util.testing as pdt
 from unittest import TestCase, main
 
 from skbio import OrdinationResults
@@ -250,7 +249,7 @@ def test_biplot_score(self):
         exp.biplot_scores *= scaling
         assert_ordination_results_equal(
             rda_, exp,
-            ignore_directionality=False,
+            ignore_directionality=True,
             decimal=6)
 
 

skbio/util/_testing.py

@@ -133,7 +133,8 @@ def assert_ordination_results_equal(left, right, ignore_method_names=False,
                               ignore_directionality=ignore_directionality,
                               decimal=decimal)
 
-    _assert_frame_dists_equal(left.sample_constraints, right.sample_constraints,
+    _assert_frame_dists_equal(left.sample_constraints,
+                              right.sample_constraints,
                               ignore_columns=ignore_axis_labels,
                               ignore_directionality=ignore_directionality,
                               decimal=decimal)