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ENH: Add default fill values for decode_cf #5680

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ENH: Add default fill values for decode_cf #5680

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4ebfb4d
Add f8 default fill value and test for it.
gcaria Aug 6, 2021
26f1b32
Add built-in dictionary for dtype to default fill value
gcaria Aug 8, 2021
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3 changes: 3 additions & 0 deletions xarray/coding/variables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from functools import partial
from typing import Any, Hashable

import netCDF4
import numpy as np
import pandas as pd

Expand Down Expand Up @@ -183,6 +184,8 @@ def decode(self, variable, name=None):
pop_to(attrs, encoding, attr, name=name)
for attr in ("missing_value", "_FillValue")
]

raw_fill_values.append(netCDF4.default_fillvals["f8"])
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I think we should vendor this dictionary to avoid adding netcdf4 as a required dependency.

{'S1': '\x00',
 'i1': -127,
 'u1': 255,
 'i2': -32767,
 'u2': 65535,
 'i4': -2147483647,
 'u4': 4294967295,
 'i8': -9223372036854775806,
 'u8': 18446744073709551614,
 'f4': 9.969209968386869e+36,
 'f8': 9.969209968386869e+36}

We'll also have to pick the appropriate one based on dtype.

if raw_fill_values:
encoded_fill_values = {
fv
Expand Down
7 changes: 7 additions & 0 deletions xarray/tests/test_conventions.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import contextlib
import warnings

import netCDF4
import numpy as np
import pandas as pd
import pytest
Expand Down Expand Up @@ -232,6 +233,12 @@ def test_decode_cf_with_multiple_missing_values(self):
assert_identical(expected, actual)
assert "has multiple fill" in str(w[0].message)

def test_decode_standard_missing_value(self):
original = Variable(["t"], [netCDF4.default_fillvals["f8"], 1, 2], {})
expected = Variable(["t"], [np.nan, 1, 2], {})
actual = conventions.decode_cf_variable("t", original)
assert_identical(expected, actual)

def test_decode_cf_with_drop_variables(self):
original = Dataset(
{
Expand Down