[PR]: Remove deprecated features and APIs for next release (#628)

* Remove deprecated features and APIs
- Remove `horizontal_xesmf()` and  `horizontal_regrid2()`
- Remove `**kwargs` from `create_grid()` and `_deprecated_create_grid()`
- Remove `add_bounds` accepting boolean arg in `open_dataset()`, `open_mfdataset()` and `_postprocess_dataset()`
* Remove tests for deprecated code
- Remove `lxml` dependency
* Remove `_prepare_coordinate()`
* Fix `test_global_mean_grid` and `test_zonal_grid`

conda-env/ci.yml

@@ -10,7 +10,6 @@ dependencies:
     - cf_xarray >=0.7.3 # Constrained because https://github.com/xarray-contrib/cf-xarray/issues/467
     - cftime
     - dask
-    - lxml # TODO: Remove this in v0.7.0 once cdml/XML support is dropped
     - netcdf4
     - numpy >=1.23.0 # This version of numpy includes support for Python 3.11.
     - pandas

conda-env/dev.yml

@@ -10,7 +10,6 @@ dependencies:
     - cf_xarray >=0.7.3 # Constrained because https://github.com/xarray-contrib/cf-xarray/issues/467
     - cftime
     - dask
-    - lxml # TODO: Remove this in v0.7.0 once cdml/XML support is dropped
     - netcdf4
     - numpy >=1.23.0 # This version of numpy includes support for Python 3.11.
     - pandas

tests/test_dataset.py

@@ -5,7 +5,6 @@
 import numpy as np
 import pytest
 import xarray as xr
-from lxml import etree
 
 from tests.fixtures import generate_dataset
 from xcdat._logger import _setup_custom_logger
@@ -77,9 +76,6 @@ def test_skips_adding_bounds(self):
         ds = generate_dataset(decode_times=True, cf_compliant=True, has_bounds=False)
         ds.to_netcdf(self.file_path)
 
-        result = open_dataset(self.file_path, add_bounds=False)
-        assert result.identical(ds)
-
         result = open_dataset(self.file_path, add_bounds=None)
         assert result.identical(ds)
 
@@ -324,48 +320,6 @@ def test_keeps_specified_var_and_preserves_bounds(self):
 
         assert result.identical(expected)
 
-    def test_raises_deprecation_warning_when_passing_add_bounds_true(self):
-        ds_no_bounds = generate_dataset(
-            decode_times=True, cf_compliant=True, has_bounds=False
-        )
-        ds_no_bounds.to_netcdf(self.file_path)
-
-        with warnings.catch_warnings(record=True) as w:
-            result = open_dataset(self.file_path, add_bounds=True)
-
-            assert len(w) == 1
-            assert issubclass(w[0].category, DeprecationWarning)
-            assert str(w[0].message) == (
-                "`add_bounds=True` will be deprecated after v0.6.0. Please use a list "
-                "of axis strings instead (e.g., `add_bounds=['X', 'Y']`)."
-            )
-
-        expected = generate_dataset(
-            decode_times=True, cf_compliant=True, has_bounds=True
-        )
-        expected = expected.drop_vars("time_bnds")
-        del expected["time"].attrs["bounds"]
-
-        assert result.identical(expected)
-
-    def test_raises_deprecation_warning_when_passing_add_bounds_false(self):
-        ds_no_bounds = generate_dataset(
-            decode_times=True, cf_compliant=True, has_bounds=False
-        )
-        ds_no_bounds.to_netcdf(self.file_path)
-
-        with warnings.catch_warnings(record=True) as w:
-            result = open_dataset(self.file_path, add_bounds=False)
-
-            assert len(w) == 1
-            assert issubclass(w[0].category, DeprecationWarning)
-            assert str(w[0].message) == (
-                "`add_bounds=False` will be deprecated after v0.6.0. Please use "
-                "`add_bounds=None` instead."
-            )
-
-        assert result.identical(ds_no_bounds)
-
 
 class TestOpenMfDataset:
     @pytest.fixture(autouse=True)
@@ -410,80 +364,9 @@ def test_skips_adding_bounds(self):
         ds = generate_dataset(decode_times=True, cf_compliant=True, has_bounds=False)
         ds.to_netcdf(self.file_path1)
 
-        result = open_mfdataset(self.file_path1, add_bounds=False)
-        assert result.identical(ds)
-
         result = open_mfdataset(self.file_path1, add_bounds=None)
         assert result.identical(ds)
 
-    def test_raises_error_if_xml_does_not_have_root_directory_attr(self):
-        ds1 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds1.to_netcdf(self.file_path1)
-        ds2 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds2 = ds2.rename_vars({"ts": "tas"})
-        ds2.to_netcdf(self.file_path2)
-
-        # Create the XML file
-        xml_path = f"{self.dir}/datasets.xml"
-        page = etree.Element("dataset")
-        doc = etree.ElementTree(page)
-        doc.write(xml_path, xml_declaration=True, encoding="utf-16")
-
-        with pytest.raises(KeyError):
-            open_mfdataset(xml_path, decode_times=True)
-
-    def test_opens_datasets_from_xml_using_str_path(self):
-        ds1 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds1.to_netcdf(self.file_path1)
-        ds2 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds2 = ds2.rename_vars({"ts": "tas"})
-        ds2.to_netcdf(self.file_path2)
-
-        # Create the XML file
-        xml_path = f"{self.dir}/datasets.xml"
-        page = etree.Element("dataset", directory=str(self.dir))
-        doc = etree.ElementTree(page)
-        doc.write(xml_path, xml_declaration=True, encoding="utf-16")
-
-        result = open_mfdataset(xml_path, decode_times=True)
-        expected = ds1.merge(ds2)
-
-        result.identical(expected)
-
-    def test_opens_datasets_from_xml_raises_deprecation_warning(self):
-        ds1 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds1.to_netcdf(self.file_path1)
-        ds2 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds2 = ds2.rename_vars({"ts": "tas"})
-        ds2.to_netcdf(self.file_path2)
-
-        # Create the XML file
-        xml_path = f"{self.dir}/datasets.xml"
-        page = etree.Element("dataset", directory=str(self.dir))
-        doc = etree.ElementTree(page)
-        doc.write(xml_path, xml_declaration=True, encoding="utf-16")
-
-        with pytest.warns(DeprecationWarning):
-            open_mfdataset(xml_path, decode_times=True)
-
-    def test_opens_datasets_from_xml_using_pathlib_path(self):
-        ds1 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds1.to_netcdf(self.file_path1)
-        ds2 = generate_dataset(decode_times=False, cf_compliant=False, has_bounds=True)
-        ds2 = ds2.rename_vars({"ts": "tas"})
-        ds2.to_netcdf(self.file_path2)
-
-        # Create the XML file
-        xml_path = self.dir / "datasets.xml"
-        page = etree.Element("dataset", directory=str(self.dir))
-        doc = etree.ElementTree(page)
-        doc.write(xml_path, xml_declaration=True, encoding="utf-16")
-
-        result = open_mfdataset(xml_path, decode_times=True)
-        expected = ds1.merge(ds2)
-
-        result.identical(expected)
-
     def test_raises_error_if_directory_has_no_netcdf_files(self):
         with pytest.raises(ValueError):
             open_mfdataset(str(self.dir), decode_times=True)

tests/test_regrid.py

@@ -1,7 +1,6 @@
 import datetime
 import re
 import sys
-import warnings
 from unittest import mock
 
 import numpy as np
@@ -38,7 +37,8 @@ class TestXGCMRegridder:
     def setup(self):
         self.ds = fixtures.generate_lev_dataset()
 
-        self.output_grid = grid.create_grid(lev=np.linspace(10000, 2000, 2))
+        z = grid.create_axis("lev", np.linspace(10000, 2000, 2), generate_bounds=False)
+        self.output_grid = grid.create_grid(z=z)
 
     def test_multiple_z_axes(self):
         self.ds = self.ds.assign_coords({"ilev": self.ds.lev.copy().rename("ilev")})
@@ -891,73 +891,6 @@ def test_create_grid_wrong_axis_value(self):
         ):
             grid.create_grid(x=(self.lon, self.lon_bnds, self.lat))  # type: ignore[arg-type]
 
-    def test_deprecated_unexpected_coordinate(self):
-        lev = np.linspace(1000, 1, 2)
-
-        with pytest.raises(
-            ValueError,
-            match="Coordinate mass is not valid, reference `xcdat.axis.VAR_NAME_MAP` for valid options.",
-        ):
-            grid.create_grid(lev=lev, mass=np.linspace(10, 20, 2))
-
-    def test_deprecated_create_grid_lev(self):
-        lev = np.linspace(1000, 1, 2)
-        lev_bnds = np.array([[1499.5, 500.5], [500.5, -498.5]])
-
-        with warnings.catch_warnings(record=True) as w:
-            new_grid = grid.create_grid(lev=(lev, lev_bnds))
-
-            assert len(w) == 1
-            assert issubclass(w[0].category, DeprecationWarning)
-            assert (
-                str(w[0].message)
-                == "**kwargs will be deprecated, see docstring and use 'x', 'y', or 'z' arguments"
-            )
-
-        assert np.array_equal(new_grid.lev, lev)
-        assert np.array_equal(new_grid.lev_bnds, lev_bnds)
-
-    def test_deprecated_create_grid(self):
-        lat = np.array([-45, 0, 45])
-        lon = np.array([30, 60, 90, 120, 150])
-        lat_bnds = np.array([[-67.5, -22.5], [-22.5, 22.5], [22.5, 67.5]])
-        lon_bnds = np.array([[15, 45], [45, 75], [75, 105], [105, 135], [135, 165]])
-
-        new_grid = grid.create_grid(lat=lat, lon=lon)
-
-        assert np.array_equal(new_grid.lat, lat)
-        assert np.array_equal(new_grid.lat_bnds, lat_bnds)
-        assert new_grid.lat.units == "degrees_north"
-        assert np.array_equal(new_grid.lon, lon)
-        assert np.array_equal(new_grid.lon_bnds, lon_bnds)
-        assert new_grid.lon.units == "degrees_east"
-
-        da_lat = xr.DataArray(
-            name="lat",
-            data=lat,
-            dims=["lat"],
-            attrs={"units": "degrees_north", "axis": "Y"},
-        )
-        da_lon = xr.DataArray(
-            name="lon",
-            data=lon,
-            dims=["lon"],
-            attrs={"units": "degrees_east", "axis": "X"},
-        )
-        da_lat_bnds = xr.DataArray(name="lat_bnds", data=lat_bnds, dims=["lat", "bnds"])
-        da_lon_bnds = xr.DataArray(name="lon_bnds", data=lon_bnds, dims=["lon", "bnds"])
-
-        new_grid = grid.create_grid(
-            lat=(da_lat, da_lat_bnds), lon=(da_lon, da_lon_bnds)
-        )
-
-        assert np.array_equal(new_grid.lat, lat)
-        assert np.array_equal(new_grid.lat_bnds, lat_bnds)
-        assert new_grid.lat.units == "degrees_north"
-        assert np.array_equal(new_grid.lon, lon)
-        assert np.array_equal(new_grid.lon_bnds, lon_bnds)
-        assert new_grid.lon.units == "degrees_east"
-
     def test_uniform_grid(self):
         new_grid = grid.create_uniform_grid(-90, 90, 4.0, -180, 180, 5.0)
 
@@ -986,10 +919,14 @@ def test_gaussian_grid(self):
         assert uneven_grid.lon.shape == (67,)
 
     def test_global_mean_grid(self):
-        source_grid = grid.create_grid(
-            lat=np.array([-80, -40, 0, 40, 80]),
-            lon=np.array([0, 45, 90, 180, 270, 360]),
+        x = grid.create_axis(
+            "lon", np.array([0, 45, 90, 180, 270, 360]), generate_bounds=True
         )
+        y = grid.create_axis(
+            "lat", np.array([-80, -40, 0, 40, 80]), generate_bounds=True
+        )
+
+        source_grid = grid.create_grid(x=x, y=y)
 
         mean_grid = grid.create_global_mean_grid(source_grid)
 
@@ -1068,9 +1005,14 @@ def test_raises_error_for_global_mean_grid_if_an_axis_has_multiple_dimensions(se
             grid.create_global_mean_grid(source_grid_with_2_lons)
 
     def test_zonal_grid(self):
-        source_grid = grid.create_grid(
-            lat=np.array([-80, -40, 0, 40, 80]), lon=np.array([-160, -80, 80, 160])
+        x = grid.create_axis(
+            "lon", np.array([-160, -80, 80, 160]), generate_bounds=True
         )
+        y = grid.create_axis(
+            "lat", np.array([-80, -40, 0, 40, 80]), generate_bounds=True
+        )
+
+        source_grid = grid.create_grid(x=x, y=y)
 
         zonal_grid = grid.create_zonal_grid(source_grid)
 
@@ -1194,7 +1136,9 @@ def test_horizontal(self):
         assert output_data.ts.shape == (15, 4, 4)
 
     def test_vertical(self):
-        output_grid = grid.create_grid(lev=np.linspace(10000, 2000, 2))
+        z = grid.create_axis("lev", np.linspace(10000, 2000, 2), generate_bounds=False)
+
+        output_grid = grid.create_grid(z=z)
 
         output_data = self.vertical_ds.regridder.vertical(
             "so", output_grid, tool="xgcm", method="linear"
@@ -1210,7 +1154,8 @@ def test_vertical(self):
         assert output_data.so.shape == (15, 4, 4, 4)
 
     def test_vertical_multiple_z_axes(self):
-        output_grid = grid.create_grid(lev=np.linspace(10000, 2000, 2))
+        z = grid.create_axis("lev", np.linspace(10000, 2000, 2), generate_bounds=False)
+        output_grid = grid.create_grid(z=z)
 
         self.vertical_ds = self.vertical_ds.assign_coords(
             {"ilev": self.vertical_ds.lev.copy().rename("ilev")}
@@ -1312,22 +1257,6 @@ def test_vertical_tool_check(self, _get_input_grid):
         ):
             self.ac.vertical("ts", mock_data, tool="dummy", target_data=None)  # type: ignore
 
-    @pytest.mark.filterwarnings("ignore:.*invalid value.*divide.*:RuntimeWarning")
-    def test_convenience_methods(self):
-        ds = fixtures.generate_dataset(
-            decode_times=True, cf_compliant=False, has_bounds=True
-        )
-
-        out_grid = grid.create_gaussian_grid(32)
-
-        output_xesmf = ds.regridder.horizontal_xesmf("ts", out_grid, method="bilinear")
-
-        assert output_xesmf.ts.shape == (15, 32, 65)
-
-        output_regrid2 = ds.regridder.horizontal_regrid2("ts", out_grid)
-
-        assert output_regrid2.ts.shape == (15, 32, 65)
-
 
 class TestBase:
     def test_preserve_bounds(self):