roms-tools 3.0.0__py3-none-any.whl → 3.1.1__py3-none-any.whl

roms_tools/tests/test_setup/test_datasets.py

@@ -13,6 +13,7 @@ from roms_tools.setup.datasets import (
     Dataset,
     ERA5Correction,
     GLORYSDataset,
+    RiverDataset,
     TPXODataset,
 )
 
@@ -221,7 +222,8 @@ def test_multiple_matching_times(
     global_dataset_with_multiple_times_per_day, tmp_path, use_dask
 ):
     """Test handling when multiple matching times are found when end_time is not
-    specified."""
+    specified.
+    """
     filepath = tmp_path / "test.nc"
     global_dataset_with_multiple_times_per_day.to_netcdf(filepath)
     dataset = Dataset(
@@ -270,7 +272,6 @@ def test_warnings_times(global_dataset, tmp_path, caplog, use_dask):
 
 def test_from_ds(global_dataset, global_dataset_with_noon_times, use_dask, tmp_path):
     """Test the from_ds method of the Dataset class."""
-
     start_time = datetime(2022, 1, 1)
 
     filepath = tmp_path / "test.nc"
@@ -299,16 +300,17 @@ def test_from_ds(global_dataset, global_dataset_with_noon_times, use_dask, tmp_p
     # Ensure other attributes are copied correctly
     for attr in vars(dataset):
         if attr != "ds":
-            assert getattr(new_dataset, attr) == getattr(
-                dataset, attr
-            ), f"Attribute {attr} not copied correctly."
+            assert getattr(new_dataset, attr) == getattr(dataset, attr), (
+                f"Attribute {attr} not copied correctly."
+            )
 
 
 def test_reverse_latitude_reverse_depth_choose_subdomain(
     global_dataset, tmp_path, use_dask
 ):
     """Test reversing latitude when it is not ascending, the choose_subdomain method,
-    and the convert_to_negative_depth method of the Dataset class."""
+    and the convert_to_negative_depth method of the Dataset class.
+    """
     start_time = datetime(2022, 1, 1)
 
     filepath = tmp_path / "test.nc"
@@ -367,7 +369,6 @@ def test_reverse_latitude_reverse_depth_choose_subdomain(
 
 
 def test_check_if_global_with_global_dataset(global_dataset, tmp_path, use_dask):
-
     filepath = tmp_path / "test.nc"
     global_dataset.to_netcdf(filepath)
     dataset = Dataset(filename=filepath, var_names={"var": "var"}, use_dask=use_dask)
@@ -378,7 +379,6 @@ def test_check_if_global_with_global_dataset(global_dataset, tmp_path, use_dask)
 def test_check_if_global_with_non_global_dataset(
     non_global_dataset, tmp_path, use_dask
 ):
-
     filepath = tmp_path / "test.nc"
     non_global_dataset.to_netcdf(filepath)
     dataset = Dataset(filename=filepath, var_names={"var": "var"}, use_dask=use_dask)
@@ -388,7 +388,6 @@ def test_check_if_global_with_non_global_dataset(
 
 
 def test_check_dataset(global_dataset, tmp_path, use_dask):
-
     ds = global_dataset.copy()
     ds = ds.drop_vars("var")
 
@@ -400,7 +399,6 @@ def test_check_dataset(global_dataset, tmp_path, use_dask):
     with pytest.raises(
         ValueError, match="Dataset does not contain all required variables."
     ):
-
         Dataset(
             filename=filepath,
             var_names={"var": "var"},
@@ -420,7 +418,6 @@ def test_check_dataset(global_dataset, tmp_path, use_dask):
     with pytest.raises(
         ValueError, match="Dataset does not contain all required dimensions."
     ):
-
         Dataset(
             filename=filepath,
             var_names={"var": "var"},
@@ -431,7 +428,6 @@ def test_check_dataset(global_dataset, tmp_path, use_dask):
 
 
 def test_era5_correction_choose_subdomain(use_dask):
-
     data = ERA5Correction(use_dask=use_dask)
     lats = data.ds.latitude[10:20]
     lons = data.ds.longitude[10:20]
@@ -442,7 +438,6 @@ def test_era5_correction_choose_subdomain(use_dask):
 
 
 def test_data_concatenation(use_dask):
-
     fname = download_test_data("GLORYS_NA_2012.nc")
     data = GLORYSDataset(
         filename=fname,
@@ -476,7 +471,6 @@ def test_data_concatenation(use_dask):
 
 
 def test_time_validation(use_dask):
-
     fname = download_test_data("GLORYS_NA_2012.nc")
 
     with pytest.raises(TypeError, match="start_time must be a datetime object"):
@@ -487,7 +481,6 @@ def test_time_validation(use_dask):
             use_dask=use_dask,
         )
     with pytest.raises(TypeError, match="end_time must be a datetime object"):
-
         GLORYSDataset(
             filename=fname,
             start_time=datetime(2012, 1, 1),
@@ -497,7 +490,6 @@ def test_time_validation(use_dask):
 
 
 def test_climatology_error(use_dask):
-
     fname = download_test_data("GLORYS_NA_2012.nc")
 
     with pytest.raises(
@@ -518,7 +510,6 @@ def test_climatology_error(use_dask):
         ValueError,
         match="The dataset contains integer time values, which are only supported when the climatology flag is set to True. However, your climatology flag is set to False.",
     ):
-
         CESMBGCDataset(
             filename=fname_bgc,
             start_time=datetime(2012, 1, 1),
@@ -541,7 +532,6 @@ def test_climatology_error(use_dask):
     ],
 )
 def test_horizontal_resolution(data_fixture, expected_resolution, request):
-
     data = request.getfixturevalue(data_fixture)
     assert np.isclose(data.resolution, expected_resolution)
 
@@ -563,7 +553,7 @@ class TestTPXODataset:
 
     @pytest.fixture
     def global_tpxo_dataset(self, use_dask):
-        """TPXO dataset with global coverage and 1 constituent: M2"""
+        """TPXO dataset with global coverage and 1 constituent: M2."""
         fname_grid = Path(download_test_data("global_grid_tpxo10.v2.nc"))
         fname_h = Path(download_test_data("global_h_tpxo10.v2.nc"))
 
@@ -603,7 +593,6 @@ class TestTPXODataset:
         ],
     )
     def test_initialization_and_clean_up(self, tpxo_dataset_fixture, request):
-
         tpxo_dataset = request.getfixturevalue(tpxo_dataset_fixture)
         assert tpxo_dataset.location == "h"
 
@@ -616,14 +605,12 @@ class TestTPXODataset:
         assert "latitude" in tpxo_dataset.ds.variables
 
     def test_select_fewer_constituents(self, regional_tpxo_dataset, omega):
-
         regional_tpxo_dataset.select_constituents(2, omega)
         assert (
             regional_tpxo_dataset.ds["ntides"].values.astype("U3") == ["m2", "s2"]
         ).all()
 
     def test_select_constituents_with_reordering(self, regional_tpxo_dataset, omega):
-
         regional_tpxo_dataset.select_constituents(11, omega)
 
         assert len(regional_tpxo_dataset.ds["ntides"]) == 11
@@ -634,9 +621,8 @@ class TestTPXODataset:
         )
 
     def test_select_constituents_omega_mismatch(self, regional_tpxo_dataset, omega):
-
         omega = OrderedDict(
-            list(omega.items())[:3] + [("fake", 6.495854e-05)] + list(omega.items())[3:]
+            [*list(omega.items())[:3], ("fake", 6.495854e-05), *list(omega.items())[3:]]
         )
         with pytest.raises(ValueError, match="The dataset contains tidal constituents"):
             regional_tpxo_dataset.select_constituents(11, omega)
@@ -644,3 +630,45 @@ class TestTPXODataset:
     def test_select_constituents_too_few(self, global_tpxo_dataset, omega):
         with pytest.raises(ValueError, match="The dataset contains tidal constituents"):
             global_tpxo_dataset.select_constituents(11, omega)
+
+
+class TestRiverDataset:
+    def test_deduplicate_river_names(self, tmp_path):
+        sample_dim_and_var_names = {
+            "dim_names": {"station": "station", "time": "time"},
+            "var_names": {
+                "latitude": "lat",
+                "longitude": "lon",
+                "flux": "flux",
+                "ratio": "ratio",
+                "name": "name",
+            },
+        }
+
+        data = {
+            "lat": (["station"], [10.0, 20.0, 30.0]),
+            "lon": (["station"], [100.0, 110.0, 120.0]),
+            "flux": (["time", "station"], np.random.rand(1, 3)),
+            "ratio": (["time", "station"], np.random.rand(1, 3)),
+            "name": (["station"], ["Amazon", "Nile", "Amazon"]),  # duplicate
+        }
+        coords = {"station": [0, 1, 2], "time": [0]}
+        ds = xr.Dataset(data, coords=coords)
+
+        # Write to temporary NetCDF file
+        file_path = tmp_path / "rivers.nc"
+        ds.to_netcdf(file_path)
+
+        river_dataset = RiverDataset(
+            filename=file_path,
+            start_time=datetime(2000, 1, 1),
+            end_time=datetime(2000, 1, 2),
+            dim_names=sample_dim_and_var_names["dim_names"],
+            var_names=sample_dim_and_var_names["var_names"],
+        )
+
+        names = river_dataset.ds["name"].values
+        assert "Amazon_1" in names
+        assert "Amazon_2" in names
+        assert "Nile" in names
+        assert len(set(names)) == len(names)  # all names must be unique

roms_tools/tests/test_setup/test_fill.py

@@ -38,7 +38,6 @@ def test_lateral_fill_no_nans(data_fixture, request):
 
 
 def test_lateral_fill_correct_order_of_magnitude(coarsened_cesm_bgc_data):
-
     lateral_fill = LateralFill(
         coarsened_cesm_bgc_data.ds["mask"],
         [
@@ -76,7 +75,6 @@ def test_lateral_fill_correct_order_of_magnitude(coarsened_cesm_bgc_data):
     ],
 )
 def test_lateral_fill_reproducibility(data_fixture, request):
-
     data = request.getfixturevalue(data_fixture)
     lateral_fill0 = LateralFill(
         data.ds["mask"],

roms_tools/tests/test_setup/test_grid.py

@@ -24,7 +24,6 @@ from roms_tools.setup.topography import _compute_rfactor
 
 @pytest.fixture()
 def counter_clockwise_rotated_grid():
-
     grid = Grid(
         nx=1, ny=1, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=20
     )
@@ -34,7 +33,6 @@ def counter_clockwise_rotated_grid():
 
 @pytest.fixture()
 def clockwise_rotated_grid():
-
     grid = Grid(
         nx=1, ny=1, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=-20
     )
@@ -44,7 +42,6 @@ def clockwise_rotated_grid():
 
 @pytest.fixture()
 def grid_that_straddles_dateline_with_shifted_global_etopo_data():
-
     grid = Grid(
         nx=5,
         ny=5,
@@ -64,7 +61,6 @@ def grid_that_straddles_dateline_with_shifted_global_etopo_data():
 
 @pytest.fixture()
 def grid_that_straddles_dateline_with_global_srtm15_data():
-
     grid = Grid(
         nx=5,
         ny=5,
@@ -84,7 +80,6 @@ def grid_that_straddles_dateline_with_global_srtm15_data():
 
 @pytest.fixture()
 def grid_that_straddles_180_degree_meridian_with_shifted_global_etopo_data():
-
     grid = Grid(
         nx=5,
         ny=5,
@@ -104,7 +99,6 @@ def grid_that_straddles_180_degree_meridian_with_shifted_global_etopo_data():
 
 @pytest.fixture()
 def grid_that_straddles_180_degree_meridian_with_global_srtm15_data():
-
     grid = Grid(
         nx=5,
         ny=5,
@@ -123,7 +117,6 @@ def grid_that_straddles_180_degree_meridian_with_global_srtm15_data():
 
 
 def test_grid_creation(grid):
-
     assert grid.nx == 1
     assert grid.ny == 1
     assert grid.size_x == 100
@@ -180,23 +173,20 @@ def test_coords_relation(grid_fixture, request):
     ],
 )
 def test_successful_initialization_with_topography(grid_fixture, request):
-
     grid = request.getfixturevalue(grid_fixture)
     assert grid is not None
 
 
 def test_plot():
-
     grid = Grid(
         nx=20, ny=20, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=0
     )
 
-    grid.plot(bathymetry=True)
-    grid.plot(bathymetry=False)
+    grid.plot(with_dim_names=False)
+    grid.plot(with_dim_names=True)
 
 
 def test_save(tmp_path):
-
     grid = Grid(
         nx=20, ny=20, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=0
     )
@@ -207,7 +197,6 @@ def test_save(tmp_path):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
             saved_filenames = grid.save(filepath)
             # Check if the .nc file was created
             filepath = Path(filepath).with_suffix(".nc")
@@ -285,8 +274,8 @@ def test_grid_straddle_crosses_meridian():
 )
 def test_roundtrip_netcdf(grid_fixture, tmp_path, request):
     """Test that creating a grid, saving it to file, and re-opening it is the same as
-    just creating it."""
-
+    just creating it.
+    """
     grid = request.getfixturevalue(grid_fixture)
 
     for file_str in ["test_grid", "test_grid.nc"]:
@@ -295,7 +284,6 @@ def test_roundtrip_netcdf(grid_fixture, tmp_path, request):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
             grid.save(filepath)
 
             filepath = Path(filepath)
@@ -320,8 +308,8 @@ def test_roundtrip_netcdf(grid_fixture, tmp_path, request):
 )
 def test_roundtrip_yaml(grid_fixture, tmp_path, request):
     """Test that creating a grid, saving its parameters to yaml file, and re-opening
-    yaml file creates the same grid."""
-
+    yaml file creates the same grid.
+    """
     grid = request.getfixturevalue(grid_fixture)
 
     # Create a temporary filepath using the tmp_path fixture
@@ -330,7 +318,6 @@ def test_roundtrip_yaml(grid_fixture, tmp_path, request):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         grid.to_yaml(filepath)
 
         grid_from_file = Grid.from_yaml(filepath)
@@ -352,7 +339,6 @@ def test_roundtrip_yaml(grid_fixture, tmp_path, request):
 )
 def test_roundtrip_from_file_yaml(grid_fixture, tmp_path, request):
     """Test that reading a grid from file and then saving it to yaml works."""
-
     grid = request.getfixturevalue(grid_fixture)
 
     filepath = Path(tmp_path / "test.nc")
@@ -368,7 +354,6 @@ def test_roundtrip_from_file_yaml(grid_fixture, tmp_path, request):
 
 
 def test_files_have_same_hash(tmp_path):
-
     # Initialize a Grid object using the initializer
     grid_init = Grid(
         nx=10,
@@ -403,7 +388,6 @@ def test_files_have_same_hash(tmp_path):
 
 
 def test_from_yaml_missing_version(tmp_path):
-
     yaml_content = textwrap.dedent(
         """\
     Grid:
@@ -425,7 +409,6 @@ def test_from_yaml_missing_version(tmp_path):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)
@@ -453,7 +436,6 @@ def test_from_yaml_missing_grid(tmp_path):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)
@@ -496,7 +478,6 @@ def test_from_yaml_version_mismatch(tmp_path, caplog):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)
@@ -517,7 +498,6 @@ def test_from_yaml_version_mismatch(tmp_path, caplog):
 def test_invalid_theta_s_value():
     """Test the validation of the theta_s value."""
     with pytest.raises(ValueError):
-
         Grid(
             nx=2,
             ny=2,
@@ -548,7 +528,6 @@ def test_invalid_theta_b_value():
 
 
 def test_update_vertical_coordinate():
-
     grid = Grid(
         nx=2, ny=2, size_x=500, size_y=1000, center_lon=0, center_lat=55, rot=10
     )
@@ -601,6 +580,9 @@ def test_plot_vertical_coordinate():
     grid.plot_vertical_coordinate(s=-1)
     grid.plot_vertical_coordinate(eta=0)
     grid.plot_vertical_coordinate(xi=0)
+    # Test that passing a maximum number of layer contours works
+    grid.plot_vertical_coordinate(xi=0, max_nr_layer_contours=2)
+    grid.plot_vertical_coordinate(xi=0, max_nr_layer_contours=100)
     # Test that passing a matplotlib.axes.Axes works
     fig, ax = plt.subplots(1, 1)
     grid.plot_vertical_coordinate(s=-1, ax=ax)
@@ -620,7 +602,6 @@ def test_plot_vertical_coordinate():
 
 
 def test_compatability_with_matlab_grid(tmp_path):
-
     fname = download_test_data("grid_created_with_matlab.nc")
 
     grid = Grid.from_file(fname)
@@ -651,7 +632,7 @@ def test_compatability_with_matlab_grid(tmp_path):
     actual_coords = set(grid.ds.coords.keys())
     assert actual_coords == expected_coords
 
-    grid.plot(bathymetry=True)
+    grid.plot()
 
     for file_str in ["test_grid", "test_grid.nc"]:
         # Create a temporary filepath using the tmp_path fixture
@@ -659,7 +640,6 @@ def test_compatability_with_matlab_grid(tmp_path):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
             # Test saving without partitioning
             _ = grid.save(filepath)
 
@@ -676,7 +656,6 @@ def test_compatability_with_matlab_grid(tmp_path):
 
 
 def test_from_file_with_vertical_coords(grid, tmp_path):
-
     theta_s = 6.0
     theta_b = 4.0
     hc = 300.0
@@ -699,7 +678,6 @@ def test_from_file_with_vertical_coords(grid, tmp_path):
 
 
 def test_from_file_with_conflicting_vertical_coords(grid, tmp_path):
-
     theta_s = 6.0
     theta_b = 4.0
     hc = 300.0
@@ -719,7 +697,6 @@ def test_from_file_with_conflicting_vertical_coords(grid, tmp_path):
 
 
 def test_from_file_missing_attributes(grid, tmp_path):
-
     grid_copy = copy.deepcopy(grid)
     del grid_copy.ds.attrs["theta_b"]
 
@@ -731,7 +708,6 @@ def test_from_file_missing_attributes(grid, tmp_path):
 
 
 def test_from_file_partial_parameters_raises_error(grid, tmp_path):
-
     path = tmp_path / "grid.nc"
     grid.save(path)
 
@@ -742,7 +718,6 @@ def test_from_file_partial_parameters_raises_error(grid, tmp_path):
 # Topography tests
 def test_enclosed_regions():
     """Test that there are only two connected regions, one dry and one wet."""
-
     grid = Grid(
         nx=100,
         ny=100,
@@ -801,8 +776,8 @@ def test_hmin_criterion():
 
 def test_mask_topography_boundary():
     """Test that the mask and topography along the grid boundaries (north, south, east,
-    west) are identical to the adjacent inland cells."""
-
+    west) are identical to the adjacent inland cells.
+    """
     # Create a grid with some land along the northern boundary
     grid = Grid(
         nx=10, ny=10, size_x=1000, size_y=1000, center_lon=-20, center_lat=60, rot=0

roms_tools/tests/test_setup/test_initial_conditions.py

@@ -27,7 +27,6 @@ from roms_tools.setup.datasets import CESMBGCDataset, UnifiedBGCDataset
 )
 def test_initial_conditions_creation(ic_fixture, request):
     """Test the creation of the InitialConditions object."""
-
     ic = request.getfixturevalue(ic_fixture)
 
     assert ic.ini_time == datetime(2021, 6, 29)
@@ -48,8 +47,8 @@ def test_initial_conditions_creation(ic_fixture, request):
 
 def test_initial_conditions_creation_with_duplicates(use_dask: bool) -> None:
     """Test the creation of the InitialConditions object with duplicates in source data
-    works as expected."""
-
+    works as expected.
+    """
     fname1 = Path(download_test_data("GLORYS_NA_20120101.nc"))
     fname2 = Path(download_test_data("GLORYS_NA_20121231.nc"))
 
@@ -94,7 +93,6 @@ def test_initial_conditions_creation_with_duplicates(use_dask: bool) -> None:
 )
 def test_initial_condition_creation_with_bgc(ic_fixture, request):
     """Test the creation of the BoundaryForcing object."""
-
     ic = request.getfixturevalue(ic_fixture)
 
     expected_bgc_variables = [
@@ -138,7 +136,6 @@ def test_initial_condition_creation_with_bgc(ic_fixture, request):
 
 @pytest.fixture
 def example_grid():
-
     grid = Grid(
         nx=2,
         ny=2,
@@ -180,7 +177,6 @@ def test_initial_conditions_missing_physics_path(example_grid, use_dask):
 
 # Test initialization with missing 'name' in bgc_source
 def test_initial_conditions_missing_bgc_name(example_grid, use_dask):
-
     fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
     with pytest.raises(
         ValueError, match="`bgc_source` must include a 'name' if it is provided."
@@ -196,7 +192,6 @@ def test_initial_conditions_missing_bgc_name(example_grid, use_dask):
 
 # Test initialization with missing 'path' in bgc_source
 def test_initial_conditions_missing_bgc_path(example_grid, use_dask):
-
     fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
     with pytest.raises(
         ValueError, match="`bgc_source` must include a 'path' if it is provided."
@@ -212,7 +207,6 @@ def test_initial_conditions_missing_bgc_path(example_grid, use_dask):
 
 # Test initialization with missing ini_time
 def test_initial_conditions_missing_ini_time(example_grid, use_dask):
-
     fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
     with pytest.raises(
         ValueError,
@@ -228,7 +222,6 @@ def test_initial_conditions_missing_ini_time(example_grid, use_dask):
 
 # Test default climatology value
 def test_initial_conditions_default_climatology(example_grid, use_dask):
-
     fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
 
     initial_conditions = InitialConditions(
@@ -243,7 +236,6 @@ def test_initial_conditions_default_climatology(example_grid, use_dask):
 
 
 def test_initial_conditions_default_bgc_climatology(example_grid, use_dask):
-
     fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
     fname_bgc = Path(download_test_data("CESM_regional_test_data_one_time_slice.nc"))
 
@@ -259,7 +251,6 @@ def test_initial_conditions_default_bgc_climatology(example_grid, use_dask):
 
 
 def test_info_depth(caplog, use_dask):
-
     grid = Grid(
         nx=2,
         ny=2,
@@ -277,7 +268,6 @@ def test_info_depth(caplog, use_dask):
     fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
 
     with caplog.at_level(logging.INFO):
-
         InitialConditions(
             grid=grid,
             ini_time=datetime(2021, 6, 29),
@@ -292,7 +282,6 @@ def test_info_depth(caplog, use_dask):
     caplog.clear()
 
     with caplog.at_level(logging.INFO):
-
         InitialConditions(
             grid=grid,
             ini_time=datetime(2021, 6, 29),
@@ -317,7 +306,6 @@ def test_info_depth(caplog, use_dask):
 def test_correct_depth_coords_adjusted_for_zeta(
     initial_conditions_fixture, request, use_dask
 ):
-
     initial_conditions = request.getfixturevalue(initial_conditions_fixture)
 
     # compute interface depth at rho-points and write it into .ds_depth_coords
@@ -355,7 +343,6 @@ def test_correct_depth_coords_adjusted_for_zeta(
     ],
 )
 def test_correct_depth_coords_zero_zeta(initial_conditions_fixture, request, use_dask):
-
     initial_conditions = request.getfixturevalue(initial_conditions_fixture)
 
     # compute interface depth at rho-points and write it into .ds_depth_coords
@@ -382,7 +369,6 @@ def test_correct_depth_coords_zero_zeta(initial_conditions_fixture, request, use
 
 
 def test_interpolation_from_climatology(use_dask):
-
     # CESM climatology
     fname_bgc = download_test_data("CESM_regional_coarse_test_data_climatology.nc")
     ds = xr.open_dataset(fname_bgc)
@@ -449,9 +435,9 @@ def test_computed_missing_optional_fields(
     # Use tight tolerances because 'DOC' and 'DOCr' can have values order 1e-6
 
     # 'DOCr' was missing in the source data and should have been filled with a constant default value
-    assert np.allclose(
-        ds.DOCr.std(), 0.0, rtol=1e-10, atol=1e-10
-    ), "DOCr should be constant across space and time"
+    assert np.allclose(ds.DOCr.std(), 0.0, rtol=1e-10, atol=1e-10), (
+        "DOCr should be constant across space and time"
+    )
     # 'DOC' was present in the source data and should show spatial or temporal variability
     assert ds.DOC.std() > 1e-10, "DOC should vary across space and time"
 
@@ -466,7 +452,6 @@ def test_computed_missing_optional_fields(
 )
 def test_initial_conditions_plot(initial_conditions_fixture, request):
     """Test plot method."""
-
     initial_conditions = request.getfixturevalue(initial_conditions_fixture)
 
     # horizontal slices plots
@@ -515,7 +500,6 @@ def test_initial_conditions_plot(initial_conditions_fixture, request):
 )
 def test_initial_conditions_save(initial_conditions_fixture, request, tmp_path):
     """Test save method."""
-
     initial_conditions = request.getfixturevalue(initial_conditions_fixture)
 
     for file_str in ["test_ic", "test_ic.nc"]:
@@ -524,7 +508,6 @@ def test_initial_conditions_save(initial_conditions_fixture, request, tmp_path):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
             saved_filenames = initial_conditions.save(filepath)
             # Check if the .nc file was created
             filepath = Path(filepath).with_suffix(".nc")
@@ -545,8 +528,8 @@ def test_initial_conditions_save(initial_conditions_fixture, request, tmp_path):
 )
 def test_roundtrip_yaml(initial_conditions_fixture, request, tmp_path, use_dask):
     """Test that creating an InitialConditions object, saving its parameters to yaml
-    file, and re-opening yaml file creates the same object."""
-
+    file, and re-opening yaml file creates the same object.
+    """
     initial_conditions = request.getfixturevalue(initial_conditions_fixture)
 
     # Create a temporary filepath using the tmp_path fixture
@@ -555,7 +538,6 @@ def test_roundtrip_yaml(initial_conditions_fixture, request, tmp_path, use_dask)
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         initial_conditions.to_yaml(filepath)
 
         initial_conditions_from_file = InitialConditions.from_yaml(
@@ -578,7 +560,6 @@ def test_roundtrip_yaml(initial_conditions_fixture, request, tmp_path, use_dask)
     ],
 )
 def test_files_have_same_hash(initial_conditions_fixture, request, tmp_path, use_dask):
-
     initial_conditions = request.getfixturevalue(initial_conditions_fixture)
 
     yaml_filepath = tmp_path / "test_yaml.yaml"
@@ -627,7 +608,6 @@ def test_from_yaml_missing_initial_conditions(tmp_path, use_dask):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)