Merge pull request #97 from pacificclimate/fix-fill-value

Fix fill value

.github/workflows/python-ci.yml

@@ -8,7 +8,11 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
     - uses: actions/checkout@v2

nchelpers/__init__.py

@@ -231,7 +231,7 @@ class CFDataset(Dataset):
 
     Some of this class replaces the functionality of helper functions defined
     in pacificclimate/modelmeta. The following list maps those functions to
-    \properties/methods of this class.
+    properties/methods of this class.
 
     get_file_metadata -> metadata.<global attribute>
         - <global attribute> is the unified name for actual CF standard global
@@ -1047,7 +1047,7 @@ def dependent_varnames(self, dim_names=set()):
         """
         if isinstance(dim_names, six.string_types):
             dim_names = {dim_names}
-        elif isinstance(dim_names, collections.Iterable):
+        elif isinstance(dim_names, collections.abc.Iterable):
             dim_names = {d for d in dim_names if isinstance(d, six.string_types)}
         else:
             raise ValueError(
@@ -1110,14 +1110,16 @@ def var_range(self, var_name, chunksize=2 ** 20):
         :param var_name: (str) name of variable
         :return (tuple) (min, max) minimum and maximum values
         """
-        # TODO: What about fill values?
+        # Temporarily mask fill values
+        self.set_auto_mask(True)
         variable = self.variables[var_name]
         range_min = float("inf")
         range_max = float("-inf")
         chunk_shape = opt_chunk_shape(variable.shape, chunksize)
         for chunk in chunks(variable, chunk_shape):
             range_min = min(range_min, np.nanmin(chunk))
             range_max = max(range_max, np.nanmax(chunk))
+        self.set_auto_mask(False)
         return range_min, range_max
 
     ###########################################################################

nchelpers/date_utils.py

@@ -117,7 +117,7 @@ def to_datetime(value):
     """
     # TODO: Convert time values in case of 360_day calendar?
     # See https://github.com/pacificclimate/modelmeta/blob/master/db/index_netcdf.r#L468-L479
-    if isinstance(value, collections.Iterable):
+    if isinstance(value, collections.abc.Iterable):
         return (to_datetime(v) for v in value)
 
     if isinstance(value, (datetime, date)):

tests/test_CFDataset.py

@@ -798,6 +798,15 @@ def test_get_var_bounds_and_values(tiny_dataset, var_name):
 def test_variable_range(tiny_dataset, var_name, expected):
     assert tiny_dataset.var_range(var_name, chunksize=2) == approx(expected)
 
+@mark.slow
+@mark.parametrize('dataset, var_name, fill_value, expected', [
+    ('prism_pr_small', 'pr', -9999., (45.703, 7346.324)),
+    ('tiny_gridded_obs_missing_data', 'tasmax', -32768., (-28.9, -18.18)),
+], indirect=['dataset'])
+def test_variable_range_with_missing_data(dataset, var_name, fill_value, expected):
+    assert dataset.variables[var_name]._FillValue == fill_value
+    assert fill_value in dataset.variables[var_name][:]
+    assert dataset.var_range(var_name, chunksize=2) == approx(expected)
 
 @mark.parametrize('tiny_dataset, expected', [
     ('gcm', {'time', 'lon', 'lat', 'nb2'}),

tests/test_date_utils.py

@@ -66,7 +66,7 @@ def test_jday_360_to_remapped_date(jday_360, month, day):
     (num2date(60, 'days since 1999-12-30', '360_day'), datetime(2000, 3, 1)),
 ])
 def test_to_datetime(arg, expected):
-    if isinstance(arg, collections.Iterable):
+    if isinstance(arg, collections.abc.Iterable):
         assert list(to_datetime(arg)) == list(expected)
     else:
         assert to_datetime(arg) == expected
@@ -95,4 +95,4 @@ def test_to_datetime_360(jday_360, month, day):
     (datetime(2012, 5, 1), "seasonal", datetime(2012, 3, 1))
     ])
 def test_truncate_to_resolution(date, resolution, expected):
-    assert(truncate_to_resolution(date, resolution)) == expected
+    assert(truncate_to_resolution(date, resolution)) == expected