Fix some warnings (#3864)

* Fix some warnings

* Update xarray/backends/api.py

Co-Authored-By: keewis <[email protected]>

* fix test

Co-authored-by: keewis <[email protected]>

Author: dcherian

xarray/backends/api.py

@@ -1253,7 +1253,7 @@ def check_dtype(var):
         if (
             not np.issubdtype(var.dtype, np.number)
             and not np.issubdtype(var.dtype, np.datetime64)
-            and not np.issubdtype(var.dtype, np.bool)
+            and not np.issubdtype(var.dtype, np.bool_)
             and not coding.strings.is_unicode_dtype(var.dtype)
             and not var.dtype == object
         ):

xarray/tests/test_accessor_dt.py

@@ -347,6 +347,7 @@ def test_field_access(data, field):
 
 
 @requires_cftime
+@pytest.mark.filterwarnings("ignore::RuntimeWarning")
 def test_cftime_strftime_access(data):
     """ compare cftime formatting against datetime formatting """
     date_format = "%Y%m%d%H"

xarray/tests/test_backends.py

@@ -1921,33 +1921,36 @@ def test_to_zarr_append_compute_false_roundtrip(self):
         ds, ds_to_append, _ = create_append_test_data()
         ds, ds_to_append = ds.chunk(), ds_to_append.chunk()
 
-        with self.create_zarr_target() as store:
-            delayed_obj = self.save(ds, store, compute=False, mode="w")
-            assert isinstance(delayed_obj, Delayed)
+        with pytest.warns(SerializationWarning):
+            with self.create_zarr_target() as store:
+                delayed_obj = self.save(ds, store, compute=False, mode="w")
+                assert isinstance(delayed_obj, Delayed)
+
+                with pytest.raises(AssertionError):
+                    with self.open(store) as actual:
+                        assert_identical(ds, actual)
+
+                delayed_obj.compute()
 
-            with pytest.raises(AssertionError):
                 with self.open(store) as actual:
                     assert_identical(ds, actual)
 
-            delayed_obj.compute()
+                delayed_obj = self.save(
+                    ds_to_append, store, compute=False, append_dim="time"
+                )
+                assert isinstance(delayed_obj, Delayed)
 
-            with self.open(store) as actual:
-                assert_identical(ds, actual)
+                with pytest.raises(AssertionError):
+                    with self.open(store) as actual:
+                        assert_identical(
+                            xr.concat([ds, ds_to_append], dim="time"), actual
+                        )
 
-            delayed_obj = self.save(
-                ds_to_append, store, compute=False, append_dim="time"
-            )
-            assert isinstance(delayed_obj, Delayed)
+                delayed_obj.compute()
 
-            with pytest.raises(AssertionError):
                 with self.open(store) as actual:
                     assert_identical(xr.concat([ds, ds_to_append], dim="time"), actual)
 
-            delayed_obj.compute()
-
-            with self.open(store) as actual:
-                assert_identical(xr.concat([ds, ds_to_append], dim="time"), actual)
-
     def test_encoding_chunksizes(self):
         # regression test for GH2278
         # see also test_encoding_chunksizes_unlimited
@@ -3519,6 +3522,7 @@ def test_uamiv_format_mfread(self):
             ["example.uamiv", "example.uamiv"],
             engine="pseudonetcdf",
             concat_dim="TSTEP",
+            combine="nested",
             backend_kwargs={"format": "uamiv"},
         )
 

xarray/tests/test_concat.py

@@ -40,8 +40,7 @@ def test_concat_compat():
     assert_equal(ds2.no_x_y, result.no_x_y.transpose())
 
     for var in ["has_x", "no_x_y"]:
-        assert "y" not in result[var]
-
+        assert "y" not in result[var].dims and "y" not in result[var].coords
     with raises_regex(ValueError, "coordinates in some datasets but not others"):
         concat([ds1, ds2], dim="q")
     with raises_regex(ValueError, "'q' is not present in all datasets"):

xarray/tests/test_dask.py

@@ -1344,6 +1344,7 @@ def test_normalize_token_with_backend(map_ds):
         map_ds.to_netcdf(tmp_file)
         read = xr.open_dataset(tmp_file)
         assert not dask.base.tokenize(map_ds) == dask.base.tokenize(read)
+        read.close()
 
 
 @pytest.mark.parametrize(

xarray/tests/test_dataarray.py

@@ -2035,7 +2035,7 @@ def test_stack_unstack(self):
                 codes=[[], []],
                 names=["x", "y"],
             )
-        pd.util.testing.assert_index_equal(a, b)
+        pd.testing.assert_index_equal(a, b)
 
         actual = orig.stack(z=["x", "y"]).unstack("z").drop_vars(["x", "y"])
         assert_identical(orig, actual)
@@ -3488,7 +3488,7 @@ def test_from_series_sparse(self):
 
     def test_to_and_from_empty_series(self):
         # GH697
-        expected = pd.Series([])
+        expected = pd.Series([], dtype=np.float64)
         da = DataArray.from_series(expected)
         assert len(da) == 0
         actual = da.to_series()

xarray/tests/test_dataset.py

@@ -6042,7 +6042,7 @@ def test_integrate(dask):
     actual = da.integrate("x")
     # coordinate that contains x should be dropped.
     expected_x = xr.DataArray(
-        np.trapz(da, da["x"], axis=0),
+        np.trapz(da.compute(), da["x"], axis=0),
         dims=["y"],
         coords={k: v for k, v in da.coords.items() if "x" not in v.dims},
     )

xarray/tests/test_duck_array_ops.py

@@ -279,6 +279,7 @@ def assert_dask_array(da, dask):
 
 
 @arm_xfail
+@pytest.mark.filterwarnings("ignore::RuntimeWarning")
 @pytest.mark.parametrize("dask", [False, True] if has_dask else [False])
 def test_datetime_mean(dask):
     # Note: only testing numpy, as dask is broken upstream

xarray/tests/test_groupby.py

@@ -447,7 +447,8 @@ def test_groupby_drops_nans():
 
     # reduction operation along a different dimension
     actual = grouped.mean("time")
-    expected = ds.mean("time").where(ds.id.notnull())
+    with pytest.warns(RuntimeWarning):  # mean of empty slice
+        expected = ds.mean("time").where(ds.id.notnull())
     assert_identical(actual, expected)
 
     # NaN in non-dimensional coordinate

xarray/tests/test_plot.py

@@ -1749,6 +1749,7 @@ def test_can_set_vmin_vmax(self):
             assert np.allclose(expected, clim)
 
     @pytest.mark.slow
+    @pytest.mark.filterwarnings("ignore")
     def test_can_set_norm(self):
         norm = mpl.colors.SymLogNorm(0.1)
         self.g.map_dataarray(xplt.imshow, "x", "y", norm=norm)