roms-tools 3.3.0__py3-none-any.whl → 3.5.0__py3-none-any.whl

roms_tools/tests/test_setup/test_data/initial_conditions_from_roms.zarr/zeta/zarr.json

@@ -0,0 +1,54 @@
+{
+  "shape": [
+    1,
+    7,
+    7
+  ],
+  "data_type": "float32",
+  "chunk_grid": {
+    "name": "regular",
+    "configuration": {
+      "chunk_shape": [
+        1,
+        7,
+        7
+      ]
+    }
+  },
+  "chunk_key_encoding": {
+    "name": "default",
+    "configuration": {
+      "separator": "/"
+    }
+  },
+  "fill_value": 0.0,
+  "codecs": [
+    {
+      "name": "bytes",
+      "configuration": {
+        "endian": "little"
+      }
+    },
+    {
+      "name": "zstd",
+      "configuration": {
+        "level": 0,
+        "checksum": false
+      }
+    }
+  ],
+  "attributes": {
+    "long_name": "sea surface height",
+    "units": "m",
+    "coordinates": "abs_time",
+    "_FillValue": "AAAAAAAA+H8="
+  },
+  "dimension_names": [
+    "ocean_time",
+    "eta_rho",
+    "xi_rho"
+  ],
+  "zarr_format": 3,
+  "node_type": "array",
+  "storage_transformers": []
+}

roms_tools/tests/test_setup/test_data/initial_conditions_from_roms.zarr/zooC/zarr.json

@@ -0,0 +1,57 @@
+{
+  "shape": [
+    1,
+    3,
+    7,
+    7
+  ],
+  "data_type": "float32",
+  "chunk_grid": {
+    "name": "regular",
+    "configuration": {
+      "chunk_shape": [
+        1,
+        3,
+        7,
+        7
+      ]
+    }
+  },
+  "chunk_key_encoding": {
+    "name": "default",
+    "configuration": {
+      "separator": "/"
+    }
+  },
+  "fill_value": 0.0,
+  "codecs": [
+    {
+      "name": "bytes",
+      "configuration": {
+        "endian": "little"
+      }
+    },
+    {
+      "name": "zstd",
+      "configuration": {
+        "level": 0,
+        "checksum": false
+      }
+    }
+  ],
+  "attributes": {
+    "long_name": "zooplankton carbon",
+    "units": "mmol/m^3",
+    "coordinates": "abs_time",
+    "_FillValue": "AAAAAAAA+H8="
+  },
+  "dimension_names": [
+    "ocean_time",
+    "s_rho",
+    "eta_rho",
+    "xi_rho"
+  ],
+  "zarr_format": 3,
+  "node_type": "array",
+  "storage_transformers": []
+}

roms_tools/tests/test_setup/test_grid.py

@@ -18,7 +18,7 @@ from roms_tools.constants import (
     UPPER_BOUND_THETA_B,
     UPPER_BOUND_THETA_S,
 )
-from roms_tools.download import download_test_data
+from roms_tools.datasets.download import download_test_data
 from roms_tools.setup.topography import _compute_rfactor
 
 try:
@@ -121,6 +121,25 @@ def grid_that_straddles_180_degree_meridian_with_global_srtm15_data():
     return grid
 
 
+@pytest.fixture()
+def grid_with_emod_data():
+    grid = Grid(
+        nx=2,
+        ny=2,
+        size_x=32,
+        size_y=19.2,
+        center_lon=-21.68,
+        center_lat=64.325,
+        rot=0,
+        topography_source={
+            "name": "EMOD",
+            "path": download_test_data("EMODnet_C2_coarse100.nc"),
+        },
+    )
+
+    return grid
+
+
 @pytest.fixture()
 def grid_with_gshhs_coastlines():
     iceland_fjord_kwargs = {
@@ -203,6 +222,7 @@ def test_coords_relation(grid_fixture, request):
         "grid_that_straddles_dateline_with_global_srtm15_data",
         "grid_that_straddles_180_degree_meridian_with_global_srtm15_data",
         "grid_with_gshhs_coastlines",
+        "grid_with_emod_data",
     ],
 )
 def test_successful_initialization_with_topography(grid_fixture, request):
@@ -344,6 +364,7 @@ def test_grid_straddle_crosses_meridian():
         "grid_that_straddles_dateline_with_shifted_global_etopo_data",
         "grid_that_straddles_dateline_with_global_srtm15_data",
         "grid_with_gshhs_coastlines",
+        "grid_with_emod_data",
     ],
 )
 def test_roundtrip_netcdf(grid_fixture, tmp_path, request):
@@ -379,6 +400,7 @@ def test_roundtrip_netcdf(grid_fixture, tmp_path, request):
         "grid_that_straddles_dateline_with_shifted_global_etopo_data",
         "grid_that_straddles_dateline_with_global_srtm15_data",
         "grid_with_gshhs_coastlines",
+        "grid_with_emod_data",
     ],
 )
 def test_roundtrip_yaml(grid_fixture, tmp_path, request):
@@ -411,6 +433,7 @@ def test_roundtrip_yaml(grid_fixture, tmp_path, request):
         "grid_that_straddles_dateline_with_shifted_global_etopo_data",
         "grid_that_straddles_dateline_with_global_srtm15_data",
         "grid_with_gshhs_coastlines",
+        "grid_with_emod_data",
     ],
 )
 def test_roundtrip_from_file_yaml(grid_fixture, tmp_path, request):
@@ -441,6 +464,7 @@ def test_roundtrip_from_file_yaml(grid_fixture, tmp_path, request):
         "grid_that_straddles_dateline_with_shifted_global_etopo_data",
         "grid_that_straddles_dateline_with_global_srtm15_data",
         "grid_with_gshhs_coastlines",
+        "grid_with_emod_data",
     ],
 )
 def test_files_have_same_hash(grid_fixture, tmp_path, request):
@@ -741,6 +765,23 @@ def test_hmin_criterion_and_update_topography():
     assert np.less_equal(grid.hmin, grid.ds.h.min())
 
 
+def test_update_topography_raises_if_grid_loaded_from_file_has_no_source_info():
+    fname = download_test_data("grid_created_with_matlab.nc")
+    grid = Grid.from_file(fname)
+
+    with pytest.raises(
+        ValueError,
+        match="Topography source information is not available",
+    ):
+        grid.update_topography(hmin=15)
+
+    with pytest.raises(
+        ValueError,
+        match="Minimal ocean depth is not available",
+    ):
+        grid.update_topography(topography_source={"name": "ETOPO5"})
+
+
 # Mask tests
 
 
@@ -826,6 +867,30 @@ def test_mask_topography_boundary():
     )
 
 
+def test_grid_copy_with_ds_does_not_mutate_original(grid):
+    """
+    copy_with_ds should return a new Grid instance with the same metadata
+    but a different backing Dataset, leaving the original Grid unchanged.
+    """
+    orig_ds = grid.ds
+    new_ds = orig_ds.isel(xi_rho=slice(0, 2), eta_rho=slice(0, 2))
+
+    new_grid = grid.copy_with_ds(new_ds)
+
+    # New object
+    assert new_grid is not grid
+
+    # Dataset replaced on copy
+    assert new_grid.ds is new_ds
+
+    # Original grid untouched
+    assert grid.ds is orig_ds
+
+    # Metadata preserved (adjust as needed for your Grid attributes)
+    for attr in ["nx", "ny", "size_x", "size_y", "center_lon", "center_lat", "rot"]:
+        assert getattr(new_grid, attr) == getattr(grid, attr)
+
+
 # More Grid.from_file() tests
 
 

roms_tools/tests/test_setup/test_initial_conditions.py

@@ -1,4 +1,3 @@
-import logging
 import textwrap
 from datetime import datetime
 from pathlib import Path
@@ -10,17 +9,26 @@ import xarray as xr
 
 from conftest import calculate_data_hash
 from roms_tools import Grid, InitialConditions
-from roms_tools.download import download_test_data
-from roms_tools.setup.lat_lon_datasets import (
+from roms_tools.datasets.download import download_test_data
+from roms_tools.datasets.lat_lon_datasets import (
     CESMBGCDataset,
     UnifiedBGCDataset,
 )
+from roms_tools.setup.initial_conditions import _set_required_vars
 from roms_tools.tests.test_setup.utils import download_regional_and_bigger
 
 try:
     import copernicusmarine  # type: ignore
 except ImportError:
     copernicusmarine = None
+try:
+    import xesmf  # type: ignore
+except ImportError:
+    xesmf = None
+
+skip_xesmf = pytest.mark.skipif(
+    xesmf is None, reason="xesmf required for ROMS regridding"
+)
 
 
 @pytest.fixture
@@ -46,11 +54,10 @@ def example_grid():
     "ic_fixture",
     [
         "initial_conditions",
-        "initial_conditions_adjusted_for_zeta",
         "initial_conditions_with_bgc",
-        "initial_conditions_with_bgc_adjusted_for_zeta",
         "initial_conditions_with_bgc_from_climatology",
         "initial_conditions_with_unified_bgc_from_climatology",
+        pytest.param("initial_conditions_from_roms_without_bgc", marks=skip_xesmf),
     ],
 )
 def test_initial_conditions_creation_with_nondefault_glorys_dataset(
@@ -58,13 +65,6 @@ def test_initial_conditions_creation_with_nondefault_glorys_dataset(
 ):
     """Test the creation of the InitialConditions object."""
     ic = request.getfixturevalue(ic_fixture)
-
-    assert ic.ini_time == datetime(2021, 6, 29)
-    assert ic.source == {
-        "name": "GLORYS",
-        "path": Path(download_test_data("GLORYS_coarse_test_data.nc")),
-        "climatology": False,
-    }
     assert hasattr(ic.ds, "adjust_depth_for_sea_surface_height")
     assert isinstance(ic.ds, xr.Dataset)
     assert ic.ds.coords["ocean_time"].attrs["units"] == "seconds"
@@ -171,15 +171,14 @@ def test_initial_conditions_creation_with_duplicates(use_dask: bool) -> None:
     "ic_fixture",
     [
         "initial_conditions_with_bgc",
-        "initial_conditions_with_bgc_adjusted_for_zeta",
         "initial_conditions_with_bgc_from_climatology",
         "initial_conditions_with_unified_bgc_from_climatology",
+        pytest.param("initial_conditions_from_roms", marks=skip_xesmf),
     ],
 )
 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 = [
         "PO4",
         "NO3",
@@ -219,6 +218,88 @@ def test_initial_condition_creation_with_bgc(ic_fixture, request):
         assert var in ic.ds
 
 
+@pytest.mark.skipif(xesmf is None, reason="xesmf required")
+def test_initial_conditions_raises_on_regridded_nans(use_dask):
+    """Raise ValueError if regridded ROMS fields contain NaNs due to grid mismatch."""
+    parent_grid = Grid(
+        center_lon=-120, center_lat=30, nx=8, ny=13, size_x=3000, size_y=4000, rot=32
+    )
+    restart_file = Path(download_test_data("eastpac25km_rst.19980106000000.nc"))
+    # create grid that is not entirely contained in the parent grid
+    grid_params = {
+        "nx": 5,
+        "ny": 5,
+        "center_lon": -128,
+        "center_lat": 9,
+        "size_x": 100,
+        "size_y": 100,
+    }
+    grid = Grid(**grid_params)
+
+    with pytest.raises(ValueError, match="NaN values found in regridded field."):
+        InitialConditions(
+            grid=grid,
+            ini_time=datetime(1998, 1, 6),
+            source={"name": "ROMS", "grid": parent_grid, "path": restart_file},
+            use_dask=use_dask,
+            bgc_source={
+                "name": "ROMS",
+                "grid": parent_grid,
+                "path": restart_file,
+            },
+        )
+
+
+@pytest.mark.skipif(xesmf is None, reason="xesmf required")
+def test_initial_conditions_unchanged_when_parent_and_child_grids_match(use_dask):
+    grid_params = {
+        "nx": 8,
+        "ny": 13,
+        "center_lon": -120,
+        "center_lat": 30,
+        "size_x": 3000,
+        "size_y": 4000,
+        "rot": 32,
+    }
+    parent_grid = Grid(**grid_params)
+    grid = Grid(**grid_params)
+
+    restart_file = Path(download_test_data("eastpac25km_rst.19980106000000.nc"))
+    ds = xr.open_dataset(restart_file)
+
+    ic = InitialConditions(
+        grid=grid,
+        ini_time=datetime(1998, 1, 6),
+        source={"name": "ROMS", "grid": parent_grid, "path": restart_file},
+        use_dask=use_dask,
+    )
+
+    mask = grid.ds.mask_rho
+
+    # For scalar fields (temp, salt, zeta), values should be preserved exactly
+    # when parent and child grids are identical.
+    #
+    # NOTE:
+    # Velocity variables (u, v) are excluded here because their initialization
+    # involves multiple non-exact operations:
+    #   - interpolation from staggered (u/v) points to rho-points,
+    #   - rotation between grid-relative and earth-relative coordinates,
+    #   - interpolation back to staggered grids.
+    #
+    # These steps are not mathematically invertible and introduce small
+    # numerical differences throughout the domain (not only at boundaries),
+    # so bitwise or near-bitwise agreement cannot be expected.
+    for var_name in ["temp", "salt", "zeta"]:
+        restart_values = ds[var_name].isel(time=1).where(mask).values
+        ic_values = ic.ds[var_name].squeeze().where(mask).values
+
+        assert np.allclose(
+            ic_values,
+            restart_values,
+            equal_nan=True,
+        ), f"{var_name} values changed during initialization"
+
+
 # Test initialization with missing 'name' in source
 def test_initial_conditions_missing_physics_name(example_grid, use_dask):
     with pytest.raises(ValueError, match="`source` must include a 'name'"):
@@ -262,8 +343,8 @@ def test_initial_conditions_missing_bgc_path(example_grid, use_dask):
 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,
-        match="`ini_time` must be a valid datetime object and cannot be None.",
+        TypeError,
+        match="`ini_time` must be a datetime object",
     ):
         InitialConditions(
             grid=example_grid,
@@ -303,90 +384,6 @@ def test_initial_conditions_default_bgc_climatology(example_grid, use_dask):
     assert initial_conditions.bgc_source["climatology"] is False
 
 
-def test_info_depth(caplog, use_dask):
-    grid = Grid(
-        nx=2,
-        ny=2,
-        size_x=500,
-        size_y=1000,
-        center_lon=0,
-        center_lat=55,
-        rot=10,
-        N=3,  # number of vertical levels
-        theta_s=5.0,  # surface control parameter
-        theta_b=2.0,  # bottom control parameter
-        hc=250.0,  # critical depth
-    )
-
-    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),
-            source={"path": fname, "name": "GLORYS"},
-            adjust_depth_for_sea_surface_height=True,
-            use_dask=use_dask,
-        )
-    # Verify the warning message in the log
-    assert "Sea surface height will be used to adjust depth coordinates." in caplog.text
-
-    # Clear the log before the next test
-    caplog.clear()
-
-    with caplog.at_level(logging.INFO):
-        InitialConditions(
-            grid=grid,
-            ini_time=datetime(2021, 6, 29),
-            source={"path": fname, "name": "GLORYS"},
-            adjust_depth_for_sea_surface_height=False,
-            use_dask=use_dask,
-        )
-    # Verify the warning message in the log
-    assert (
-        "Sea surface height will NOT be used to adjust depth coordinates."
-        in caplog.text
-    )
-
-
-@pytest.mark.parametrize(
-    "initial_conditions_fixture",
-    [
-        "initial_conditions_adjusted_for_zeta",
-        "initial_conditions_with_bgc_adjusted_for_zeta",
-    ],
-)
-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
-    zeta = initial_conditions.ds.zeta
-    initial_conditions._get_depth_coordinates(
-        zeta, location="rho", depth_type="interface"
-    )
-    # Test that lowermost interface coincides with topography
-    assert np.allclose(
-        initial_conditions.ds_depth_coords["interface_depth_rho"]
-        .isel(s_w=0)
-        .squeeze()
-        .values,  # Extract raw NumPy array
-        initial_conditions.grid.ds.h.values,
-        atol=1e-6,  # Adjust tolerance as needed
-    )
-
-    # Test that uppermost interface coincides with sea surface height
-    assert np.allclose(
-        initial_conditions.ds_depth_coords["interface_depth_rho"]
-        .isel(s_w=-1)
-        .squeeze()
-        .values,
-        -zeta.values,
-        atol=1e-6,
-    )
-
-
 @pytest.mark.parametrize(
     "initial_conditions_fixture",
     [
@@ -498,9 +495,9 @@ def test_computed_missing_optional_fields(
 @pytest.mark.parametrize(
     "initial_conditions_fixture",
     [
-        "initial_conditions_with_bgc_adjusted_for_zeta",
         "initial_conditions_with_bgc_from_climatology",
         "initial_conditions_with_unified_bgc_from_climatology",
+        pytest.param("initial_conditions_from_roms", marks=skip_xesmf),
     ],
 )
 def test_initial_conditions_plot(initial_conditions_fixture, request):
@@ -546,9 +543,9 @@ def test_initial_conditions_plot(initial_conditions_fixture, request):
     "initial_conditions_fixture",
     [
         "initial_conditions",
-        "initial_conditions_adjusted_for_zeta",
         "initial_conditions_with_bgc_from_climatology",
         "initial_conditions_with_unified_bgc_from_climatology",
+        pytest.param("initial_conditions_from_roms", marks=skip_xesmf),
     ],
 )
 def test_initial_conditions_save(initial_conditions_fixture, request, tmp_path):
@@ -574,9 +571,9 @@ def test_initial_conditions_save(initial_conditions_fixture, request, tmp_path):
     "initial_conditions_fixture",
     [
         "initial_conditions",
-        "initial_conditions_adjusted_for_zeta",
         "initial_conditions_with_bgc_from_climatology",
         "initial_conditions_with_unified_bgc_from_climatology",
+        pytest.param("initial_conditions_from_roms", marks=skip_xesmf),
     ],
 )
 def test_roundtrip_yaml(initial_conditions_fixture, request, tmp_path, use_dask):
@@ -607,9 +604,10 @@ def test_roundtrip_yaml(initial_conditions_fixture, request, tmp_path, use_dask)
     "initial_conditions_fixture",
     [
         "initial_conditions",
-        "initial_conditions_adjusted_for_zeta",
         "initial_conditions_with_bgc_from_climatology",
         "initial_conditions_with_unified_bgc_from_climatology",
+        pytest.param("initial_conditions_from_roms_without_bgc", marks=skip_xesmf),
+        pytest.param("initial_conditions_from_roms", marks=skip_xesmf),
     ],
 )
 def test_files_have_same_hash(initial_conditions_fixture, request, tmp_path, use_dask):
@@ -676,3 +674,31 @@ def test_from_yaml_missing_initial_conditions(tmp_path, use_dask):
 
         yaml_filepath = Path(yaml_filepath)
         yaml_filepath.unlink()
+
+
+# Test _set_required_vars
+
+
+def test_default_var_type():
+    vars_map = _set_required_vars()
+    # Default is "physics"
+    expected_keys = {"zeta", "temp", "salt", "u", "v"}
+    assert set(vars_map.keys()) == expected_keys
+    # Values should match keys
+    for key, val in vars_map.items():
+        assert key == val
+
+
+def test_bgc_var_type():
+    vars_map = _set_required_vars("bgc")
+    # Check a few expected keys exist
+    expected_keys = {"PO4", "NO3", "SiO3", "NH4", "Fe", "DIC", "spChl", "zooC"}
+    assert expected_keys.issubset(vars_map.keys())
+    # Values should match keys
+    for key, val in vars_map.items():
+        assert key == val
+
+
+def test_invalid_var_type():
+    with pytest.raises(ValueError, match="Unsupported var_type"):
+        _set_required_vars("invalid_type")

roms_tools/tests/test_setup/test_nesting.py

@@ -14,7 +14,8 @@ from roms_tools.setup.nesting import (
     modify_child_mask,
     modify_child_topography,
 )
-from roms_tools.setup.utils import get_boundary_coords, wrap_longitudes
+from roms_tools.setup.utils import get_boundary_coords
+from roms_tools.utils import wrap_longitudes
 
 
 @pytest.fixture()

roms_tools/tests/test_setup/test_surface_forcing.py

@@ -9,7 +9,7 @@ import xarray as xr
 
 from conftest import calculate_data_hash
 from roms_tools import Grid, SurfaceForcing
-from roms_tools.download import download_test_data
+from roms_tools.datasets.download import download_test_data
 from roms_tools.setup.utils import RawDataSource
 
 

roms_tools/tests/test_setup/test_tides.py

@@ -6,7 +6,7 @@ import xarray as xr
 
 from conftest import calculate_data_hash
 from roms_tools import Grid, TidalForcing
-from roms_tools.download import download_test_data
+from roms_tools.datasets.download import download_test_data
 
 
 @pytest.fixture(scope="session")