TST: don't catch, but supress warnings in panel4d/panelnd (pandas-dev#15705)

Author: jreback

pandas/core/categorical.py

@@ -550,8 +550,8 @@ def _validate_categories(cls, categories, fastpath=False):
             # we don't allow NaNs in the categories themselves
 
             if categories.hasnans:
-                # NaNs in cats deprecated in 0.17,
-                # remove in 0.18 or 0.19 GH 10748
+                # NaNs in cats deprecated in 0.17
+                # GH 10748
                 msg = ('\nSetting NaNs in `categories` is deprecated and '
                        'will be removed in a future version of pandas.')
                 warn(msg, FutureWarning, stacklevel=3)

pandas/io/pytables.py

@@ -2094,7 +2094,17 @@ def convert(self, values, nan_rep, encoding):
 
                 # we have a categorical
                 categories = self.metadata
-                self.data = Categorical.from_codes(self.data.ravel(),
+                codes = self.data.ravel()
+
+                # if we have stored a NaN in the categories
+                # then strip it; in theory we could have BOTH
+                # -1s in the codes and nulls :<
+                mask = isnull(categories)
+                if mask.any():
+                    categories = categories[~mask]
+                    codes[codes != -1] -= mask.astype(int).cumsum().values
+
+                self.data = Categorical.from_codes(codes,
                                                    categories=categories,
                                                    ordered=self.ordered)
 
@@ -3404,10 +3414,12 @@ def create_axes(self, axes, obj, validate=True, nan_rep=None,
                 if existing_table is not None:
                     indexer = len(self.non_index_axes)
                     exist_axis = existing_table.non_index_axes[indexer][1]
-                    if append_axis != exist_axis:
+                    if not array_equivalent(np.array(append_axis),
+                                            np.array(exist_axis)):
 
                         # ahah! -> reindex
-                        if sorted(append_axis) == sorted(exist_axis):
+                        if array_equivalent(np.array(sorted(append_axis)),
+                                            np.array(sorted(exist_axis))):
                             append_axis = exist_axis
 
                 # the non_index_axes info