TST: Fix warnings in np 1.9

These break our tests

Author: GaelVaroquaux

sklearn/cluster/tests/test_hierarchical.py

@@ -209,6 +209,9 @@ def test_ward_agglomeration():
     assert_warns(DeprecationWarning, WardAgglomeration)
     with warnings.catch_warnings(record=True) as warning_list:
         warnings.simplefilter("always", DeprecationWarning)
+        if hasattr(np, 'VisibleDeprecationWarning'):
+            # Let's not catch the numpy internal DeprecationWarnings
+            warnings.simplefilter('ignore', np.VisibleDeprecationWarning)
         ward = WardAgglomeration(n_clusters=5, connectivity=connectivity)
         ward.fit(X)
         assert_equal(len(warning_list), 1)

sklearn/utils/fixes.py

@@ -15,6 +15,7 @@
 import numpy as np
 import scipy.sparse as sp
 
+from .testing import ignore_warnings
 
 np_version = []
 for x in np.__version__.split('.'):
@@ -102,7 +103,10 @@ def astype(array, dtype, copy=True):
 
 
 try:
-    sp.csr_matrix([1.0, 2.0, 3.0]).max(axis=0)
+    with ignore_warnings():
+        # Don't raise the numpy deprecation warnings that appear in
+        # 1.9
+        sp.csr_matrix([1.0, 2.0, 3.0]).max(axis=0)
 except (TypeError, AttributeError):
     # in scipy < 14.0, sparse matrix min/max doesn't accept an `axis` argument
     # the following code is taken from the scipy 0.14 codebase

sklearn/utils/testing.py

@@ -193,6 +193,9 @@ def assert_warns_message(warning_class, message, func, *args, **kw):
     with warnings.catch_warnings(record=True) as w:
         # Cause all warnings to always be triggered.
         warnings.simplefilter("always")
+        if hasattr(np, 'VisibleDeprecationWarning'):
+            # Let's not catch the numpy internal DeprecationWarnings
+            warnings.simplefilter('ignore', np.VisibleDeprecationWarning)
         # Trigger a warning.
         result = func(*args, **kw)
         # Verify some things