Merge branch 'main' into docs/630-docs-readability

.github/workflows/build_workflow.yml

@@ -107,10 +107,11 @@ jobs:
                   pytest
 
             - name: Upload Coverage Report
-              uses: codecov/codecov-action@v3
+              uses: codecov/codecov-action@v4
               with:
                   file: "tests_coverage_reports/coverage.xml"
                   fail_ci_if_error: true
+                  token: ${{ secrets.CODECOV_TOKEN }}
 
     # `build-result` is a workaround to skipped matrix jobs in `build` not being considered "successful",
     # which can block PR merges if matrix jobs are required status checks.

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)