only use bottleneck version 1.0 and later (#1190)

* only use bottleneck version 1.0 and later

* move bottleneck version warning to Rolling.__init__

Author: Joe Hamman

doc/installing.rst

@@ -30,6 +30,7 @@ For accelerating xarray
 
 - `bottleneck <https://github.com/kwgoodman/bottleneck>`__: speeds up
   NaN-skipping and rolling window aggregations by a large factor
+  (1.0 or later)
 - `cyordereddict <https://github.com/shoyer/cyordereddict>`__: speeds up most
   internal operations with xarray data structures (for python versions < 3.5)
 

doc/whats-new.rst

@@ -74,7 +74,8 @@ Breaking changes
   ``vmax`` when these kwargs are explicitly provided (:issue:`1191`). The
   automated level selection logic also slightly changed.
   By `Fabien Maussion <https://github.com/fmaussion>`_.
-- xarray no longer supports python 3.3 or versions of dask prior to v0.9.0.
+- xarray no longer supports python 3.3, versions of dask prior to v0.9.0,
+  or versions of bottleneck prior to v1.0.
 
 Deprecations
 ~~~~~~~~~~~~

xarray/backends/common.py

@@ -18,6 +18,7 @@
 except ImportError:
     from threading import Lock
 
+
 # Create a logger object, but don't add any handlers. Leave that to user code.
 logger = logging.getLogger(__name__)
 

xarray/core/ops.py

@@ -6,6 +6,7 @@
 import inspect
 import operator
 import warnings
+from distutils.version import StrictVersion
 
 import numpy as np
 import pandas as pd
@@ -504,6 +505,9 @@ def inject_bottleneck_rolling_methods(cls):
 
     # bottleneck rolling methods
     if has_bottleneck:
+        if StrictVersion(bn.__version__) < StrictVersion('1.0'):
+            return
+
         for bn_name, method_name in BOTTLENECK_ROLLING_METHODS.items():
             f = getattr(bn, bn_name)
             func = cls._bottleneck_reduce(f)

xarray/core/rolling.py

@@ -2,11 +2,13 @@
 from __future__ import division
 from __future__ import print_function
 import numpy as np
+import warnings
+from distutils.version import StrictVersion
 
 from .pycompat import OrderedDict, zip
 from .common import ImplementsRollingArrayReduce, full_like
 from .combine import concat
-from .ops import inject_bottleneck_rolling_methods
+from .ops import inject_bottleneck_rolling_methods, has_bottleneck, bn
 
 
 class Rolling(object):
@@ -48,6 +50,13 @@ def __init__(self, obj, min_periods=None, center=False, **windows):
         rolling : type of input argument
         """
 
+        if (has_bottleneck and
+                (StrictVersion(bn.__version__) < StrictVersion('1.0'))):
+            warnings.warn('xarray requires bottleneck version of 1.0 or '
+                          'greater for rolling operations. Rolling '
+                          'aggregation methods will use numpy instead'
+                          'of bottleneck.')
+
         if len(windows) != 1:
             raise ValueError('exactly one dim/window should be provided')
 

xarray/test/__init__.py

@@ -3,6 +3,7 @@
 from __future__ import print_function
 import warnings
 from contextlib import contextmanager
+from distutils.version import StrictVersion
 
 import numpy as np
 from numpy.testing import assert_array_equal
@@ -68,6 +69,8 @@
 
 try:
     import bottleneck
+    if StrictVersion(bottleneck.__version__) < StrictVersion('1.0'):
+        raise ImportError('Fall back to numpy')
     has_bottleneck = True
 except ImportError:
     has_bottleneck = False
@@ -76,6 +79,7 @@
 # Generally `pytest.importorskip('package')` inline is even easier
 requires_matplotlib = pytest.mark.skipif(not has_matplotlib, reason='requires matplotlib')
 
+
 def requires_scipy(test):
     return test if has_scipy else pytest.mark.skip('requires scipy')(test)
 
@@ -192,16 +196,18 @@ def assertDataArrayIdentical(self, ar1, ar2):
     def assertDataArrayAllClose(self, ar1, ar2, rtol=1e-05, atol=1e-08):
         assert_xarray_allclose(ar1, ar2, rtol=rtol, atol=atol)
 
+
 def assert_xarray_equal(a, b):
     import xarray as xr
     ___tracebackhide__ = True  # noqa: F841
     assert type(a) == type(b)
     if isinstance(a, (xr.Variable, xr.DataArray, xr.Dataset)):
         assert a.equals(b), '{}\n{}'.format(a, b)
-    else:  
+    else:
         raise TypeError('{} not supported by assertion comparison'
                         .format(type(a)))
 
+
 def assert_xarray_identical(a, b):
     import xarray as xr
     ___tracebackhide__ = True  # noqa: F841
@@ -215,6 +221,7 @@ def assert_xarray_identical(a, b):
         raise TypeError('{} not supported by assertion comparison'
                         .format(type(a)))
 
+
 def assert_xarray_allclose(a, b, rtol=1e-05, atol=1e-08):
     import xarray as xr
     ___tracebackhide__ = True  # noqa: F841
@@ -241,6 +248,7 @@ def assert_xarray_allclose(a, b, rtol=1e-05, atol=1e-08):
         raise TypeError('{} not supported by assertion comparison'
                         .format(type(a)))
 
+
 class UnexpectedDataAccess(Exception):
     pass
 

xarray/test/test_dataarray.py

@@ -2381,7 +2381,9 @@ def da(request):
         return da
 
     if request.param == 2:
-        return DataArray([0, np.nan, 1, 2, np.nan, 3, 4, 5, np.nan, 6, 7], dims='time')
+        return DataArray([0, np.nan, 1, 2, np.nan, 3, 4, 5, np.nan, 6, 7],
+                         dims='time')
+
 
 def test_rolling_iter(da):
 
@@ -2393,8 +2395,9 @@ def test_rolling_iter(da):
     for i, (label, window_da) in enumerate(rolling_obj):
         assert label == da['time'].isel(time=i)
 
+
 def test_rolling_properties(da):
-    pytest.importorskip('bottleneck')
+    pytest.importorskip('bottleneck', minversion='1.0')
 
     rolling_obj = da.rolling(time=4)