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Add '_FillValue' to set of valid_encodings for netCDF4 backend #1869

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Merged
shoyer merged 6 commits into from Feb 13, 2018
Merged

Add '_FillValue' to set of valid_encodings for netCDF4 backend #1869

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b8fd86d
Add '_FillValue' to set of valid_encodings for netCDF4 backend
czroth Jan 30, 2018
9210dfa
Add additional omit_fill_value tests
czroth Jan 30, 2018
5dc6802
Fix additional omit_fill_value tests
czroth Jan 30, 2018
b57851f
Fix scipy failure in additional omit_fill_value tests
czroth Jan 30, 2018
f840612
Added bug-fix documentation for pydata/xarray#1865
czroth Feb 7, 2018
8af7866
Merge branch 'master' into patch-1
czroth Feb 7, 2018
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2 changes: 1 addition & 1 deletion xarray/backends/netCDF4_.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,7 +160,7 @@ def _extract_nc4_variable_encoding(variable, raise_on_invalid=False,

safe_to_drop = set(['source', 'original_shape'])
valid_encodings = set(['zlib', 'complevel', 'fletcher32', 'contiguous',
'chunksizes', 'shuffle'])
'chunksizes', 'shuffle', '_FillValue'])
if lsd_okay:
valid_encodings.add('least_significant_digit')

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5 changes: 3 additions & 2 deletions xarray/backends/scipy_.py
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Expand Up @@ -188,8 +188,9 @@ def encode_variable(self, variable):
def prepare_variable(self, name, variable, check_encoding=False,
unlimited_dims=None):
if check_encoding and variable.encoding:
raise ValueError('unexpected encoding for scipy backend: %r'
% list(variable.encoding))
if variable.encoding != {'_FillValue': None}:
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@shoyer shoyer Jan 31, 2018

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Yeah, this is a little awkward.

I think this is probably OK (backend classes already need to know about encodings), but it would be good to think about why we don't already have validation for encodings with scipy. We should probably be raising an error if somebody attempts an encoding like {'zlib': True} but right now it looks like we don't do that.

raise ValueError('unexpected encoding for scipy backend: %r'
% list(variable.encoding))

data = variable.data
# nb. this still creates a numpy array in all memory, even though we
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20 changes: 20 additions & 0 deletions xarray/tests/test_backends.py
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Expand Up @@ -704,6 +704,26 @@ def test_explicitly_omit_fill_value(self):
with self.roundtrip(ds) as actual:
assert '_FillValue' not in actual.x.encoding

def test_explicitly_omit_fill_value_via_encoding_kwarg(self):
ds = Dataset({'x': ('y', [np.pi, -np.pi])})
kwargs = dict(encoding={'x': {'_FillValue': None}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert '_FillValue' not in actual.x.encoding
self.assertEqual(ds.y.encoding, {})

def test_explicitly_omit_fill_value_in_coord(self):
ds = Dataset({'x': ('y', [np.pi, -np.pi])}, coords={'y': [0.0, 1.0]})
ds.y.encoding['_FillValue'] = None
with self.roundtrip(ds) as actual:
assert '_FillValue' not in actual.y.encoding

def test_explicitly_omit_fill_value_in_coord_via_encoding_kwarg(self):
ds = Dataset({'x': ('y', [np.pi, -np.pi])}, coords={'y': [0.0, 1.0]})
kwargs = dict(encoding={'y': {'_FillValue': None}})
with self.roundtrip(ds, save_kwargs=kwargs) as actual:
assert '_FillValue' not in actual.y.encoding
self.assertEqual(ds.y.encoding, {})

def test_encoding_same_dtype(self):
ds = Dataset({'x': ('y', np.arange(10.0, dtype='f4'))})
kwargs = dict(encoding={'x': {'dtype': 'f4'}})
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