From a2677f44324d1dd656478d109afd9e78a9f5f41c Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Wed, 20 Mar 2024 16:52:49 -0500
Subject: [PATCH 1/8] 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()`

---
 xcdat/dataset.py            | 102 +------------------------------
 xcdat/regridder/accessor.py | 118 ------------------------------------
 xcdat/regridder/grid.py     |  56 -----------------
 3 files changed, 2 insertions(+), 274 deletions(-)

diff --git a/xcdat/dataset.py b/xcdat/dataset.py
index f3fe3e01..a8e2092a 100644
--- a/xcdat/dataset.py
+++ b/xcdat/dataset.py
@@ -46,7 +46,7 @@
 def open_dataset(
     path: str | os.PathLike[Any] | BufferedIOBase | AbstractDataStore,
     data_var: Optional[str] = None,
-    add_bounds: List[CFAxisKey] | None | bool = ["X", "Y"],
+    add_bounds: List[CFAxisKey] | None = ["X", "Y"],
     decode_times: bool = True,
     center_times: bool = False,
     lon_orient: Optional[Tuple[float, float]] = None,
@@ -54,10 +54,6 @@ def open_dataset(
 ) -> xr.Dataset:
     """Wraps ``xarray.open_dataset()`` with post-processing options.
 
-    .. deprecated:: v0.6.0
-        ``add_bounds`` boolean arguments (True/False) are being deprecated.
-        Please use either a list (e.g., ["X", "Y"]) to specify axes or ``None``.
-
     Parameters
     ----------
     path : str, Path, file-like or DataStore
@@ -133,7 +129,7 @@ def open_dataset(
 def open_mfdataset(
     paths: str | NestedSequence[str | os.PathLike],
     data_var: Optional[str] = None,
-    add_bounds: List[CFAxisKey] | None | Literal[False] = ["X", "Y"],
+    add_bounds: List[CFAxisKey] | None = ["X", "Y"],
     decode_times: bool = True,
     center_times: bool = False,
     lon_orient: Optional[Tuple[float, float]] = None,
@@ -143,10 +139,6 @@ def open_mfdataset(
 ) -> xr.Dataset:
     """Wraps ``xarray.open_mfdataset()`` with post-processing options.
 
-    .. deprecated:: v0.6.0
-        ``add_bounds`` boolean arguments (True/False) are being deprecated.
-        Please use either a list (e.g., ["X", "Y"]) to specify axes or ``None``.
-
     Parameters
     ----------
     paths : str | NestedSequence[str | os.PathLike]
@@ -240,15 +232,6 @@ def open_mfdataset(
     in-memory copy you are manipulating in xarray is modified: the original file
     on disk is never touched.
 
-    The CDAT "Climate Data Markup Language" (CDML) is a deprecated dialect of
-    XML with a defined set of attributes. CDML is still used by current and
-    former users of CDAT. To enable CDML users to adopt xCDAT more easily in
-    their workflows, xCDAT can parse XML/CDML files for the ``directory``
-    to generate a glob or list of file paths. Refer to [4]_ for more information
-    on CDML. NOTE: This feature is deprecated in v0.6.0 and will be removed in
-    the subsequent release. CDAT (including cdms2/CDML) is in maintenance only
-    mode and marked for end-of-life by the end of 2023.
-
     References
     ----------
     .. [2] https://docs.xarray.dev/en/stable/generated/xarray.combine_nested.html
@@ -258,13 +241,6 @@ def open_mfdataset(
     if isinstance(paths, str) or isinstance(paths, pathlib.Path):
         if os.path.isdir(paths):
             paths = _parse_dir_for_nc_glob(paths)
-        elif _is_xml_filepath(paths):
-            warnings.warn(
-                "`open_mfdataset()` will no longer support CDML/XML paths after "
-                "v0.6.0 because CDAT is marked for end-of-life at the end of 2023.",
-                DeprecationWarning,
-            )
-            paths = _parse_xml_for_nc_glob(paths)
 
     preprocess = partial(_preprocess, decode_times=decode_times, callable=preprocess)
 
@@ -422,58 +398,6 @@ def decode_time(dataset: xr.Dataset) -> xr.Dataset:
     return ds
 
 
-def _is_xml_filepath(paths: str | pathlib.Path) -> bool:
-    """Checks if the ``paths`` argument is a path to an XML file.
-
-    Parameters
-    ----------
-    paths : str | pathlib.Path
-        A string or pathlib.Path represnting a file path.
-
-    Returns
-    -------
-    bool
-    """
-    if isinstance(paths, str):
-        return paths.split(".")[-1] == "xml"
-    elif isinstance(paths, pathlib.Path):
-        return paths.parts[-1].endswith("xml")
-
-
-def _parse_xml_for_nc_glob(xml_path: str | pathlib.Path) -> str | List[str]:
-    """
-    Parses an XML file for the ``directory`` attr to return a string glob or
-    list of string file paths.
-
-    Parameters
-    ----------
-    xml_path : str | pathlib.Path
-        The XML file path.
-
-    Returns
-    -------
-    str | List[str]
-        A string glob of `*.nc` paths.
-
-    """
-    # `resolve_entities=False` and `no_network=True` guards against XXE attacks.
-    # Source: https://rules.sonarsource.com/python/RSPEC-2755
-    parser = etree.XMLParser(resolve_entities=False, no_network=True)
-    tree = etree.parse(xml_path, parser)
-    root = tree.getroot()
-
-    dir_attr = root.attrib.get("directory")
-    if dir_attr is None:
-        raise KeyError(
-            f"The XML file ({xml_path}) does not have a 'directory' attribute "
-            "that points to a directory of `.nc` dataset files."
-        )
-
-    glob_path = dir_attr + "/*.nc"
-
-    return glob_path
-
-
 def _parse_dir_for_nc_glob(dir_path: str | pathlib.Path) -> str:
     """Parses a directory for a glob of `*.nc` paths.
 
@@ -611,28 +535,6 @@ def _postprocess_dataset(
     if center_times:
         ds = center_times_func(dataset)
 
-    # TODO: Boolean (`True`/`False`) will be deprecated after v0.6.0.
-    if add_bounds is True:
-        add_bounds = ["X", "Y"]
-        warnings.warn(
-            (
-                "`add_bounds=True` will be deprecated after v0.6.0. Please use a list "
-                "of axis strings instead (e.g., `add_bounds=['X', 'Y']`)."
-            ),
-            DeprecationWarning,
-            stacklevel=2,
-        )
-    elif add_bounds is False:
-        add_bounds = None
-        warnings.warn(
-            (
-                "`add_bounds=False` will be deprecated after v0.6.0. Please use "
-                "`add_bounds=None` instead."
-            ),
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
     if add_bounds is not None:
         ds = ds.bounds.add_missing_bounds(axes=add_bounds)
 
diff --git a/xcdat/regridder/accessor.py b/xcdat/regridder/accessor.py
index b8a93c35..96dae3d7 100644
--- a/xcdat/regridder/accessor.py
+++ b/xcdat/regridder/accessor.py
@@ -117,124 +117,6 @@ def _get_axis_data(
 
         return coord_var, bounds_var
 
-    # TODO Either provide generic `horizontal` and `vertical` methods or tool specific
-    def horizontal_xesmf(
-        self,
-        data_var: str,
-        output_grid: xr.Dataset,
-        **options: Any,
-    ) -> xr.Dataset:
-        """
-        Deprecated, will be removed with 0.7.0 release.
-
-        Extends the xESMF library for horizontal regridding between structured
-        rectilinear and curvilinear grids.
-
-        This method extends ``xESMF`` by automatically constructing the
-        ``xe.XESMFRegridder`` object, preserving source bounds, and generating
-        missing bounds. It regrids ``data_var`` in the dataset to
-        ``output_grid``.
-
-        Option documentation :py:func:`xcdat.regridder.xesmf.XESMFRegridder`
-
-        Parameters
-        ----------
-        data_var: str
-            Name of the variable in the `xr.Dataset` to regrid.
-        output_grid : xr.Dataset
-            Dataset containing output grid.
-        options : Dict[str, Any]
-            Dictionary with extra parameters for the regridder.
-
-        Returns
-        -------
-        xr.Dataset
-            With the ``data_var`` variable on the grid defined in ``output_grid``.
-
-        Raises
-        ------
-        ValueError
-            If tool is not supported.
-
-        Examples
-        --------
-
-        Generate output grid:
-
-        >>> output_grid = xcdat.create_gaussian_grid(32)
-
-        Regrid data to output grid using xesmf:
-
-        >>> ds.regridder.horizontal_xesmf("ts", output_grid)
-        """
-        warnings.warn(
-            "`horizontal_xesmf` will be deprecated in 0.7.x, please migrate to using "
-            "`horizontal(..., tool='xesmf')` method.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
-        regridder = HORIZONTAL_REGRID_TOOLS["xesmf"](self._ds, output_grid, **options)
-
-        return regridder.horizontal(data_var, self._ds)
-
-    # TODO Either provide generic `horizontal` and `vertical` methods or tool specific
-    def horizontal_regrid2(
-        self,
-        data_var: str,
-        output_grid: xr.Dataset,
-        **options: Any,
-    ) -> xr.Dataset:
-        """
-        Deprecated, will be removed with 0.7.0 release.
-
-        Pure python implementation of CDAT's regrid2 horizontal regridder.
-
-        Regrids ``data_var`` in dataset to ``output_grid`` using regrid2's
-        algorithm.
-
-        Options documentation :py:func:`xcdat.regridder.regrid2.Regrid2Regridder`
-
-        Parameters
-        ----------
-        data_var: str
-            Name of the variable in the `xr.Dataset` to regrid.
-        output_grid : xr.Dataset
-            Dataset containing output grid.
-        options : Dict[str, Any]
-            Dictionary with extra parameters for the regridder.
-
-        Returns
-        -------
-        xr.Dataset
-            With the ``data_var`` variable on the grid defined in ``output_grid``.
-
-        Raises
-        ------
-        ValueError
-            If tool is not supported.
-
-        Examples
-        --------
-        Generate output grid:
-
-        >>> output_grid = xcdat.create_gaussian_grid(32)
-
-        Regrid data to output grid using regrid2:
-
-        >>> ds.regridder.horizontal_regrid2("ts", output_grid)
-        """
-        warnings.warn(
-            "`horizontal_regrid2` will be deprecated in 0.7.x, please migrate to using "
-            "`horizontal(..., tool='regrid2')` method.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
-        regridder = HORIZONTAL_REGRID_TOOLS["regrid2"](self._ds, output_grid, **options)
-
-        return regridder.horizontal(data_var, self._ds)
-
     def horizontal(
         self,
         data_var: str,
diff --git a/xcdat/regridder/grid.py b/xcdat/regridder/grid.py
index b2b32564..7bcfc15b 100644
--- a/xcdat/regridder/grid.py
+++ b/xcdat/regridder/grid.py
@@ -454,14 +454,9 @@ def create_grid(
         ]
     ] = None,
     attrs: Optional[Dict[str, str]] = None,
-    **kwargs: CoordOptionalBnds,
 ) -> xr.Dataset:
     """Creates a grid dataset using the specified axes.
 
-    .. deprecated:: v0.6.0
-        ``**kwargs`` argument is being deprecated, please migrate to
-        ``x``, ``y``, or ``z`` arguments to create future grids.
-
     Parameters
     ----------
     x : Optional[Union[xr.DataArray, Tuple[xr.DataArray]]]
@@ -515,17 +510,6 @@ def create_grid(
     >>> )
     >>> grid = create_grid(z=z)
     """
-    if np.all([item is None for item in (x, y, z)]) and len(kwargs) == 0:
-        raise ValueError("Must pass at least 1 axis to create a grid.")
-    elif np.all([item is None for item in (x, y, z)]) and len(kwargs) > 0:
-        warnings.warn(
-            "**kwargs will be deprecated, see docstring and use 'x', 'y', or 'z' arguments",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
-        return _deprecated_create_grid(**kwargs)
-
     axes = {"x": x, "y": y, "z": z}
     ds = xr.Dataset(attrs={} if attrs is None else attrs.copy())
 
@@ -557,46 +541,6 @@ def create_grid(
     return ds
 
 
-def _deprecated_create_grid(**kwargs: CoordOptionalBnds) -> xr.Dataset:
-    coords = {}
-    data_vars = {}
-
-    for name, data in kwargs.items():
-        if name in VAR_NAME_MAP["X"]:
-            coord, bnds = _prepare_coordinate(name, data, **COORD_DEFAULT_ATTRS["X"])
-        elif name in VAR_NAME_MAP["Y"]:
-            coord, bnds = _prepare_coordinate(name, data, **COORD_DEFAULT_ATTRS["Y"])
-        elif name in VAR_NAME_MAP["Z"]:
-            coord, bnds = _prepare_coordinate(name, data, **COORD_DEFAULT_ATTRS["Z"])
-        else:
-            raise ValueError(
-                f"Coordinate {name} is not valid, reference "
-                "`xcdat.axis.VAR_NAME_MAP` for valid options."
-            )
-
-        coords[name] = coord
-
-        if bnds is not None:
-            bnds = bnds.copy()
-
-            if isinstance(bnds, np.ndarray):
-                bnds = xr.DataArray(
-                    name=f"{name}_bnds",
-                    data=bnds.copy(),
-                    dims=[name, "bnds"],
-                )
-
-            data_vars[bnds.name] = bnds
-
-            coord.attrs["bounds"] = bnds.name
-
-    grid = xr.Dataset(data_vars, coords=coords)
-
-    grid = grid.bounds.add_missing_bounds(axes=["X", "Y"])
-
-    return grid
-
-
 def _prepare_coordinate(name: str, data: CoordOptionalBnds, **attrs: Any):
     if isinstance(data, tuple):
         coord, bnds = data[0], data[1]

From bf34e2542c4c6f475c8e249e8c1426644285dbcb Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Wed, 20 Mar 2024 16:56:17 -0500
Subject: [PATCH 2/8] Remove tests for deprecated code - Remove `lxml`
 dependency

---
 conda-env/ci.yml      |   1 -
 conda-env/dev.yml     |   1 -
 tests/test_dataset.py | 110 ------------------------------------------
 tests/test_regrid.py  |  67 -------------------------
 xcdat/dataset.py      |  13 -----
 5 files changed, 192 deletions(-)

diff --git a/conda-env/ci.yml b/conda-env/ci.yml
index 455062e0..3df06815 100644
--- a/conda-env/ci.yml
+++ b/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
diff --git a/conda-env/dev.yml b/conda-env/dev.yml
index 83088470..bdcd3c48 100644
--- a/conda-env/dev.yml
+++ b/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
diff --git a/tests/test_dataset.py b/tests/test_dataset.py
index 74b5edcc..c83f6a81 100644
--- a/tests/test_dataset.py
+++ b/tests/test_dataset.py
@@ -324,48 +324,6 @@ 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)
@@ -416,74 +374,6 @@ def test_skips_adding_bounds(self):
         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)
diff --git a/tests/test_regrid.py b/tests/test_regrid.py
index 13de350b..9b639c41 100644
--- a/tests/test_regrid.py
+++ b/tests/test_regrid.py
@@ -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)
 
diff --git a/xcdat/dataset.py b/xcdat/dataset.py
index a8e2092a..8fcba526 100644
--- a/xcdat/dataset.py
+++ b/xcdat/dataset.py
@@ -154,15 +154,6 @@ def open_mfdataset(
           If concatenation along more than one dimension is desired, then
           ``paths`` must be a nested list-of-lists (see [2]_
           ``xarray.combine_nested`` for details).
-        * File path to an XML file with a ``directory`` attribute (e.g.,
-          ``"path/to/files"``). If ``directory`` is set to a blank string
-          (""), then the current directory is substituted ("."). This option
-          is intended to support the CDAT CDML dialect of XML files, but it
-          can work with any XML file that has the ``directory`` attribute.
-          Refer to [4]_ for more information on CDML. NOTE: This feature is
-          deprecated in v0.6.0 and will be removed in the subsequent release.
-          CDAT (including cdms2/CDML) is in maintenance only mode and marked
-          for end-of-life by the end of 2023.
     add_bounds: List[CFAxisKey] | None | bool
         List of CF axes to try to add bounds for (if missing), by default
         ["X", "Y"]. Set to None to not add any missing bounds. Please note that
@@ -481,10 +472,6 @@ def _postprocess_dataset(
 ) -> xr.Dataset:
     """Post-processes a Dataset object.
 
-    .. deprecated:: v0.6.0
-        ``add_bounds`` boolean arguments (True/False) are being deprecated.
-        Please use either a list (e.g., ["X", "Y"]) to specify axes or ``None``.
-
     Parameters
     ----------
     dataset : xr.Dataset

From 5dbf6f3ab8e775703a2251b2205c704117b2b599 Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Wed, 20 Mar 2024 17:00:05 -0500
Subject: [PATCH 3/8] Remove unused imports

---
 tests/test_dataset.py       | 1 -
 tests/test_regrid.py        | 1 -
 xcdat/dataset.py            | 2 --
 xcdat/regridder/accessor.py | 1 -
 xcdat/regridder/grid.py     | 1 -
 5 files changed, 6 deletions(-)

diff --git a/tests/test_dataset.py b/tests/test_dataset.py
index c83f6a81..612cd3c6 100644
--- a/tests/test_dataset.py
+++ b/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
diff --git a/tests/test_regrid.py b/tests/test_regrid.py
index 9b639c41..347fa6a6 100644
--- a/tests/test_regrid.py
+++ b/tests/test_regrid.py
@@ -1,7 +1,6 @@
 import datetime
 import re
 import sys
-import warnings
 from unittest import mock
 
 import numpy as np
diff --git a/xcdat/dataset.py b/xcdat/dataset.py
index 8fcba526..45774b48 100644
--- a/xcdat/dataset.py
+++ b/xcdat/dataset.py
@@ -3,7 +3,6 @@
 
 import os
 import pathlib
-import warnings
 from datetime import datetime
 from functools import partial
 from io import BufferedIOBase
@@ -13,7 +12,6 @@
 import xarray as xr
 from dateutil import parser
 from dateutil import relativedelta as rd
-from lxml import etree
 from xarray.backends.common import AbstractDataStore
 from xarray.coding.cftime_offsets import get_date_type
 from xarray.coding.times import convert_times, decode_cf_datetime
diff --git a/xcdat/regridder/accessor.py b/xcdat/regridder/accessor.py
index 96dae3d7..b4b34d95 100644
--- a/xcdat/regridder/accessor.py
+++ b/xcdat/regridder/accessor.py
@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import warnings
 from typing import Any, List, Literal, Tuple
 
 import xarray as xr
diff --git a/xcdat/regridder/grid.py b/xcdat/regridder/grid.py
index 7bcfc15b..28b1a2bf 100644
--- a/xcdat/regridder/grid.py
+++ b/xcdat/regridder/grid.py
@@ -1,4 +1,3 @@
-import warnings
 from typing import Any, Dict, List, Optional, Tuple, Union
 
 import numpy as np

From 68c58a8d2b97425ae6e285dec39c5767aa6a1610 Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Wed, 20 Mar 2024 17:04:37 -0500
Subject: [PATCH 4/8] Remove deprecated `_prepare_coordinate()` - Add
 ValueError conditional back to `create_grid()`

---
 xcdat/regridder/grid.py | 23 +++--------------------
 1 file changed, 3 insertions(+), 20 deletions(-)

diff --git a/xcdat/regridder/grid.py b/xcdat/regridder/grid.py
index 28b1a2bf..87fea019 100644
--- a/xcdat/regridder/grid.py
+++ b/xcdat/regridder/grid.py
@@ -509,6 +509,9 @@ def create_grid(
     >>> )
     >>> grid = create_grid(z=z)
     """
+    if np.all([item is None for item in (x, y, z)]):
+        raise ValueError("Must pass at least 1 axis to create a grid.")
+
     axes = {"x": x, "y": y, "z": z}
     ds = xr.Dataset(attrs={} if attrs is None else attrs.copy())
 
@@ -540,26 +543,6 @@ def create_grid(
     return ds
 
 
-def _prepare_coordinate(name: str, data: CoordOptionalBnds, **attrs: Any):
-    if isinstance(data, tuple):
-        coord, bnds = data[0], data[1]
-    else:
-        coord, bnds = data, None
-
-    # ensure we make a copy
-    coord = coord.copy()
-
-    if isinstance(coord, np.ndarray):
-        coord = xr.DataArray(
-            name=name,
-            data=coord,
-            dims=[name],
-            attrs=attrs,
-        )
-
-    return coord, bnds
-
-
 def create_axis(
     name: str,
     data: Union[List[Union[int, float]], np.ndarray],

From 232b0abec4e63561c36e46f65185f78315b2c26b Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Wed, 20 Mar 2024 17:13:44 -0500
Subject: [PATCH 5/8] Fix tests and update docstring for `create_grid()`

---
 tests/test_dataset.py   |  6 ------
 tests/test_regrid.py    | 33 +++++++++++----------------------
 xcdat/regridder/grid.py | 30 +++++++-----------------------
 3 files changed, 18 insertions(+), 51 deletions(-)

diff --git a/tests/test_dataset.py b/tests/test_dataset.py
index 612cd3c6..b3841dff 100644
--- a/tests/test_dataset.py
+++ b/tests/test_dataset.py
@@ -76,9 +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)
 
@@ -367,9 +364,6 @@ 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)
 
diff --git a/tests/test_regrid.py b/tests/test_regrid.py
index 347fa6a6..4b2c6c08 100644
--- a/tests/test_regrid.py
+++ b/tests/test_regrid.py
@@ -37,7 +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")})
@@ -919,8 +920,8 @@ def test_gaussian_grid(self):
 
     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=np.array([0, 45, 90, 180, 270, 360]),
+            y=np.array([-80, -40, 0, 40, 80]),
         )
 
         mean_grid = grid.create_global_mean_grid(source_grid)
@@ -1001,7 +1002,8 @@ def test_raises_error_for_global_mean_grid_if_an_axis_has_multiple_dimensions(se
 
     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=np.array([-160, -80, 80, 160]),
+            y=np.array([-80, -40, 0, 40, 80]),
         )
 
         zonal_grid = grid.create_zonal_grid(source_grid)
@@ -1126,7 +1128,9 @@ 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"
@@ -1142,7 +1146,8 @@ 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")}
@@ -1244,22 +1249,6 @@ 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):
diff --git a/xcdat/regridder/grid.py b/xcdat/regridder/grid.py
index 87fea019..3752b2ef 100644
--- a/xcdat/regridder/grid.py
+++ b/xcdat/regridder/grid.py
@@ -1,11 +1,10 @@
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np
 import xarray as xr
 
 from xcdat.axis import COORD_DEFAULT_ATTRS, VAR_NAME_MAP, CFAxisKey, get_dim_coords
 from xcdat.bounds import create_bounds
-from xcdat.regridder.base import CoordOptionalBnds
 
 # First 50 zeros for the bessel function
 # Taken from https://github.com/CDAT/cdms/blob/dd41a8dd3b5bac10a4bfdf6e56f6465e11efc51d/regrid2/Src/_regridmodule.c#L3390-L3402
@@ -434,35 +433,20 @@ def create_zonal_grid(grid: xr.Dataset) -> xr.Dataset:
 
 
 def create_grid(
-    x: Optional[
-        Union[
-            xr.DataArray,
-            Tuple[xr.DataArray, Optional[xr.DataArray]],
-        ]
-    ] = None,
-    y: Optional[
-        Union[
-            xr.DataArray,
-            Tuple[xr.DataArray, Optional[xr.DataArray]],
-        ]
-    ] = None,
-    z: Optional[
-        Union[
-            xr.DataArray,
-            Tuple[xr.DataArray, Optional[xr.DataArray]],
-        ]
-    ] = None,
+    x: xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None = None,
+    y: xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None = None,
+    z: xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None = None,
     attrs: Optional[Dict[str, str]] = None,
 ) -> xr.Dataset:
     """Creates a grid dataset using the specified axes.
 
     Parameters
     ----------
-    x : Optional[Union[xr.DataArray, Tuple[xr.DataArray]]]
+    x : xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None
         Data with optional bounds to use for the "X" axis, by default None.
-    y : Optional[Union[xr.DataArray, Tuple[xr.DataArray]]]
+    y : xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None
         Data with optional bounds to use for the "Y" axis, by default None.
-    z : Optional[Union[xr.DataArray, Tuple[xr.DataArray]]]
+    z : xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None
         Data with optional bounds to use for the "Z" axis, by default None.
     attrs : Optional[Dict[str, str]]
         Custom attributes to be added to the generated `xr.Dataset`.

From bf98ad2d4e882e7600a9c1c92f644f14116ebdb3 Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Wed, 20 Mar 2024 17:20:14 -0500
Subject: [PATCH 6/8] Fix `test_global_mean_grid` and `test_zonal_grid`

---
 tests/test_regrid.py | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/tests/test_regrid.py b/tests/test_regrid.py
index 4b2c6c08..193a22a6 100644
--- a/tests/test_regrid.py
+++ b/tests/test_regrid.py
@@ -919,10 +919,14 @@ def test_gaussian_grid(self):
         assert uneven_grid.lon.shape == (67,)
 
     def test_global_mean_grid(self):
-        source_grid = grid.create_grid(
-            x=np.array([0, 45, 90, 180, 270, 360]),
-            y=np.array([-80, -40, 0, 40, 80]),
+        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)
 
@@ -1001,10 +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(
-            x=np.array([-160, -80, 80, 160]),
-            y=np.array([-80, -40, 0, 40, 80]),
+        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)
 

From 424bd11ace5f55ba73917276b0ae67bc80e0f6e6 Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Thu, 21 Mar 2024 11:47:45 -0500
Subject: [PATCH 7/8] Fix type annotation for Python 3.9

---
 xcdat/regridder/grid.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/xcdat/regridder/grid.py b/xcdat/regridder/grid.py
index 3752b2ef..152b2272 100644
--- a/xcdat/regridder/grid.py
+++ b/xcdat/regridder/grid.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np

From c5cdab3f6f3213e2365544b593eae312066a4729 Mon Sep 17 00:00:00 2001
From: tomvothecoder <tomvothecoder@gmail.com>
Date: Thu, 21 Mar 2024 11:50:48 -0500
Subject: [PATCH 8/8] Update type annotation for

---
 xcdat/regridder/grid.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/xcdat/regridder/grid.py b/xcdat/regridder/grid.py
index 152b2272..28600a6f 100644
--- a/xcdat/regridder/grid.py
+++ b/xcdat/regridder/grid.py
@@ -435,21 +435,24 @@ def create_zonal_grid(grid: xr.Dataset) -> xr.Dataset:
 
 
 def create_grid(
-    x: xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None = None,
-    y: xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None = None,
-    z: xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None = None,
+    x: xr.DataArray | Tuple[xr.DataArray, xr.DataArray | None] | None = None,
+    y: xr.DataArray | Tuple[xr.DataArray, xr.DataArray | None] | None = None,
+    z: xr.DataArray | Tuple[xr.DataArray, xr.DataArray | None] | None = None,
     attrs: Optional[Dict[str, str]] = None,
 ) -> xr.Dataset:
     """Creates a grid dataset using the specified axes.
 
     Parameters
     ----------
-    x : xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None
-        Data with optional bounds to use for the "X" axis, by default None.
-    y : xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None
-        Data with optional bounds to use for the "Y" axis, by default None.
-    z : xr.DataArray | Tuple[xr.DataArray, Optional[xr.DataArray]] | None
-        Data with optional bounds to use for the "Z" axis, by default None.
+    x : xr.DataArray | Tuple[xr.DataArray, xr.DataArray | None] | None
+        An optional dataarray or tuple of a datarray with optional bounds to use
+        for the "X" axis, by default None.
+    y : xr.DataArray | Tuple[xr.DataArray, xr.DataArray | None] | None = None,
+        An optional dataarray or tuple of a datarray with optional bounds to use
+        for the "Y" axis, by default None.
+    z : xr.DataArray | Tuple[xr.DataArray, xr.DataArray | None] | None
+        An optional dataarray or tuple of a datarray with optional bounds to use
+        for the "Z" axis, by default None.
     attrs : Optional[Dict[str, str]]
         Custom attributes to be added to the generated `xr.Dataset`.