Feature/issue 233 group dependabot updates

.github/dependabot.yml

@@ -9,6 +9,10 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
+    groups:
+      pip-dependencies:
+        patterns:
+          - "*"
     # Raise pull requests for version updates
     # to pip against the `develop` branch
     target-branch: "develop"
@@ -17,6 +21,10 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "monthly"
+    groups:
+      gha-dependencies:
+        patterns:
+          - "*"
     # Raise pull requests for version updates
     # to pip against the `develop` branch
     target-branch: "develop"

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.16.0
     hooks:
       - id: pyupgrade
         args: [ "--py39-plus" ]
@@ -24,7 +24,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.4.6'
+    rev: 'v0.4.9'
     hooks:
       - id: ruff
         args: [ "--fix" ]

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - [Issue #229](https://github.com/nasa/ncompare/issues/229): Added Journal of Open Source Software (JOSS) info to README and CITATION docs.
 ### Changed
+- [Issue #233](https://github.com/nasa/ncompare/issues/233): Group dependabot updates into fewer PRs.
 ### Deprecated
 ### Removed
 ### Fixed

ncompare/core.py

@@ -636,7 +636,7 @@ def _get_groups(nc_filepath: Union[str, Path]) -> list:
 def _get_dims(nc_filepath: Union[str, Path]) -> list:
     def __get_dim_list(decode_times=True):
         with xr.open_dataset(nc_filepath, decode_times=decode_times) as dataset:
-            return list(dataset.dims.items())
+            return list(dataset.sizes.items())
 
     try:
         dims_list = __get_dim_list()

ncompare/utils.py

@@ -29,36 +29,16 @@
 
 
 def ensure_valid_path_exists(should_be_path: Union[str, Path]) -> Path:
-    """Convert input to a pathlib.Path and check that the resulting filepath exists."""
-    fails_to_exist_msg = "Expected file does not exist: "
-    wrong_type_msg = "Unexpected type for something that should be convertable to a Path: "
-
-    if isinstance(should_be_path, str):
-        # Convert to a Path object
-        path_obj = Path(should_be_path)
-        if path_obj.exists():
-            return path_obj
-        raise FileNotFoundError(fails_to_exist_msg + str(should_be_path))
-
-    if isinstance(should_be_path, Path):
-        if should_be_path.exists():
-            return should_be_path
-        raise FileNotFoundError(fails_to_exist_msg + str(should_be_path))
-
-    raise TypeError(wrong_type_msg + str(type(should_be_path)))
+    """Coerce input to a pathlib.Path and check that the resulting filepath exists."""
+    path_obj = _coerce_str_or_path_to_path(should_be_path)
+    if path_obj.exists():
+        return path_obj
+    raise FileNotFoundError("Expected file does not exist: " + str(should_be_path))
 
 
 def ensure_valid_path_with_suffix(should_be_path: Union[str, Path], suffix: str) -> Path:
     """Coerce input to a pathlib.Path with given suffix."""
-    wrong_type_msg = "Unexpected type for something that should be convertable to a Path: "
-
-    if isinstance(should_be_path, str):
-        path_obj = Path(should_be_path)
-    elif isinstance(should_be_path, Path):
-        path_obj = should_be_path
-    else:
-        raise TypeError(wrong_type_msg + str(type(should_be_path)))
-
+    path_obj = _coerce_str_or_path_to_path(should_be_path)
     return path_obj.with_suffix(suffix)
 
 
@@ -72,3 +52,13 @@ def coerce_to_str(some_object: Union[str, int, tuple]):
         return str(some_object)
 
     raise TypeError(f"Unable to coerce value to str. Unexpected type <{type(some_object)}>.")
+
+
+def _coerce_str_or_path_to_path(should_be_path: Union[Path, str]) -> Path:
+    wrong_type_msg = "Unexpected type for something that should be convertable to a Path: "
+    if isinstance(should_be_path, str):
+        return Path(should_be_path)
+    elif isinstance(should_be_path, Path):
+        return should_be_path
+    else:
+        raise TypeError(wrong_type_msg + str(type(should_be_path)))

tests/conftest.py

@@ -74,6 +74,34 @@ def ds_3dims_2vars_4coords(temp_data_dir) -> Path:
     return filepath
 
 
+@pytest.fixture(scope="session")
+def ds_1dim_1var_1coord(temp_data_dir) -> Path:
+    ds = Dataset(
+        data_vars=dict(z1=(["y"], np.array([5, 6]))),
+        coords=dict(
+            y=range(2),
+        ),
+    )
+    filepath = temp_data_dir / "test_1dim_1var_1coord.nc"
+    ds.to_netcdf(path=filepath)
+
+    return filepath
+
+
+@pytest.fixture(scope="session")
+def ds_1dim_1var_allnan_1coord(temp_data_dir) -> Path:
+    ds = Dataset(
+        data_vars=dict(z1=(["y"], np.array([np.nan, np.nan]))),
+        coords=dict(
+            y=range(2),
+        ),
+    )
+    filepath = temp_data_dir / "test_1dim_1var_allnan_1coord.nc"
+    ds.to_netcdf(path=filepath)
+
+    return filepath
+
+
 @pytest.fixture(scope="session")
 def ds_4dims_3vars_5coords(temp_data_dir):
     ds = Dataset(

tests/test_complete_file_output.py

@@ -94,13 +94,4 @@ def test_full_run_to_xlsx_output(temp_data_dir):
     difference = df1[df1 != df2]
     rows_with_differences = [(idx, row) for idx, row in difference.notnull().iterrows() if any(row)]
 
-    if len(rows_with_differences) != 0:
-        print(
-            f"Test will fail because of differences in <{len(rows_with_differences)}> rows. "
-            f"Differences identified (Row index ----> row contents):"
-        )
-        for idx, row in rows_with_differences:
-            diff = difference.loc[idx]
-            print(f"  {idx} ----> {diff}")
-
     assert len(rows_with_differences) == 0

tests/test_core.py

@@ -72,10 +72,14 @@ def test_matching_random_values(
     ds_3dims_2vars_4coords,
     ds_4dims_3vars_5coords,
     ds_3dims_3vars_4coords_1group,
+    ds_1dim_1var_1coord,
+    ds_1dim_1var_allnan_1coord,
     outputter_to_console,
 ):
     variable_array_1 = xr.open_dataset(ds_3dims_2vars_4coords).variables['z1']
     variable_array_2 = xr.open_dataset(ds_4dims_3vars_5coords).variables['z1']
+    variable_array_3 = xr.open_dataset(ds_1dim_1var_1coord).variables['z1']
+    variable_array_allnan = xr.open_dataset(ds_1dim_1var_allnan_1coord).variables['z1']
 
     assert (
         _match_random_value(
@@ -93,6 +97,32 @@ def test_matching_random_values(
         )
         is False
     )
+    assert (
+        _match_random_value(
+            outputter_to_console,
+            variable_array_3,
+            variable_array_3,
+        )
+        is True
+    )
+    # NaN to non-NaN is NOT considered a match
+    assert (
+        _match_random_value(
+            outputter_to_console,
+            variable_array_3,
+            variable_array_allnan,
+        )
+        is None
+    )
+    # NaN to NaN is considered a match
+    assert (
+        _match_random_value(
+            outputter_to_console,
+            variable_array_allnan,
+            variable_array_allnan,
+        )
+        is True
+    )
 
 
 def test_print_values_runs_with_no_error(ds_3dims_3vars_4coords_1group, outputter_to_console):
@@ -137,10 +167,7 @@ def test_comparison_group_no_error_for_duplicate_dataset(
             if "Variables within specified group <Group1>:" in line:
                 found_expected = True
 
-    if found_expected:
-        assert True
-    else:
-        assert False
+    assert found_expected
 
 
 def test_comparison_var_no_error_for_duplicate_dataset(
@@ -160,10 +187,7 @@ def test_comparison_var_no_error_for_duplicate_dataset(
             if "Sample values within specified variable <var1>:" in line:
                 found_expected = True
 
-    if found_expected:
-        assert True
-    else:
-        assert False
+    assert found_expected
 
 
 def test_get_vars_with_group(ds_3dims_3vars_4coords_1group):

tests/test_utils.py

@@ -50,9 +50,19 @@ def test_make_valid_path_from_Path_in_repo():
     assert isinstance(returnval, Path)
 
 
+def test_error_from_wrong_path_type():
+    with pytest.raises(TypeError):
+        ensure_valid_path_exists((0, 1))
+
+
 def test_coerce_int_to_str():
     assert coerce_to_str(5) == "5"
 
 
 def test_coerce_tuple_to_str():
     assert coerce_to_str(('step', 123)) == "('step', 123)"
+
+
+def test_error_from_not_able_to_coerce_to_str():
+    with pytest.raises(TypeError):
+        coerce_to_str(list[5, 6, 7])