Contiguous store with unlim dim bug fix

doc/whats-new.rst

@@ -39,6 +39,9 @@ Enhancements
 Bug fixes
 ~~~~~~~~~
 
+- NetCDF4 output: variables with unlimited dimensions must be chunked (not
+  contiguous) on output. (:issue:`1849`)
+  By `James McCreight <https://github.com/jmccreight>`_.
 - indexing with an empty list creates an object with zero-length axis (:issue:`2882`)
   By `Mayeul d'Avezac <https://github.com/mdavezac>`_.
 - Return correct count for scalar datetime64 arrays (:issue:`2770`)

xarray/backends/netCDF4_.py

@@ -183,7 +183,8 @@ def _force_native_endianness(var):
 
 def _extract_nc4_variable_encoding(variable, raise_on_invalid=False,
                                    lsd_okay=True, h5py_okay=False,
-                                   backend='netCDF4', unlimited_dims=None):
+                                   backend='netCDF4', unlimited_dims=None,
+                                   name=None):
     if unlimited_dims is None:
         unlimited_dims = ()
 
@@ -210,6 +211,19 @@ def _extract_nc4_variable_encoding(variable, raise_on_invalid=False,
         if chunks_too_big or changed_shape:
             del encoding['chunksizes']
 
+    var_has_unlim_dim = any(dim in unlimited_dims for dim in variable.dims)
+    if var_has_unlim_dim:
+        if 'contiguous' in encoding.keys():
+            del encoding['contiguous']
+            # The above does not modify the variable (encoding) itself.
+            if name is None:
+                name = '(name not supplied)'
+            warnings.warn(
+                "The variable " + name + " contains an unlimited dimension "
+                "and has encoding['contiguous']=True. This is not possible "
+                "for netCDF4 and the variable is written to file chunked."
+            )
+
     for k in safe_to_drop:
         if k in encoding:
             del encoding[k]
@@ -444,7 +458,8 @@ def prepare_variable(self, name, variable, check_encoding=False,
 
         encoding = _extract_nc4_variable_encoding(
             variable, raise_on_invalid=check_encoding,
-            unlimited_dims=unlimited_dims)
+            unlimited_dims=unlimited_dims, name=name)
+
         if name in self.ds.variables:
             nc4_var = self.ds.variables[name]
         else:

xarray/tests/test_backends.py

@@ -3525,6 +3525,11 @@ def test_extract_nc4_variable_encoding(self):
         encoding = _extract_nc4_variable_encoding(var, raise_on_invalid=True)
         assert {'shuffle': True} == encoding
 
+        # Variables with unlim dims must be chunked on output.
+        var = xr.Variable(('x',), [1, 2, 3], {}, {'contiguous': True})
+        encoding = _extract_nc4_variable_encoding(var, unlimited_dims=('x',))
+        assert {} == encoding
+
     def test_extract_h5nc_encoding(self):
         # not supported with h5netcdf (yet)
         var = xr.Variable(('x',), [1, 2, 3], {},