roms-tools 1.0.1__py3-none-any.whl → 1.1.0__py3-none-any.whl

roms_tools/tests/test_boundary_forcing.py

@@ -1,6 +1,6 @@
 import pytest
 from datetime import datetime
-from roms_tools import BoundaryForcing, Grid, VerticalCoordinate
+from roms_tools import BoundaryForcing, Grid
 import numpy as np
 import tempfile
 import os
@@ -14,30 +14,24 @@ def example_grid():
     Fixture for creating a Grid object.
     """
     grid = Grid(
-        nx=2, ny=2, size_x=500, size_y=1000, center_lon=0, center_lat=55, rot=10
-    )
-
-    return grid
-
-
-@pytest.fixture
-def example_vertical_coordinate(example_grid):
-    """
-    Fixture for creating a VerticalCoordinate object.
-    """
-    vertical_coordinate = VerticalCoordinate(
-        grid=example_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
     )
 
-    return vertical_coordinate
+    return grid
 
 
 @pytest.fixture
-def boundary_forcing(example_grid, example_vertical_coordinate):
+def boundary_forcing(example_grid):
     """
     Fixture for creating a BoundaryForcing object.
     """
@@ -46,7 +40,6 @@ def boundary_forcing(example_grid, example_vertical_coordinate):
 
     return BoundaryForcing(
         grid=example_grid,
-        vertical_coordinate=example_vertical_coordinate,
         start_time=datetime(2021, 6, 29),
         end_time=datetime(2021, 6, 30),
         physics_source={"name": "GLORYS", "path": fname},
@@ -54,9 +47,7 @@ def boundary_forcing(example_grid, example_vertical_coordinate):
 
 
 @pytest.fixture
-def boundary_forcing_with_bgc_from_climatology(
-    example_grid, example_vertical_coordinate
-):
+def boundary_forcing_with_bgc_from_climatology(example_grid):
     """
     Fixture for creating a BoundaryForcing object.
     """
@@ -66,7 +57,6 @@ def boundary_forcing_with_bgc_from_climatology(
 
     return BoundaryForcing(
         grid=example_grid,
-        vertical_coordinate=example_vertical_coordinate,
         start_time=datetime(2021, 6, 29),
         end_time=datetime(2021, 6, 30),
         physics_source={"name": "GLORYS", "path": fname},

roms_tools/tests/test_grid.py

@@ -1,6 +1,7 @@
 import pytest
 import numpy as np
 import numpy.testing as npt
+import xarray as xr
 from roms_tools import Grid
 import os
 import tempfile
@@ -8,9 +9,44 @@ import importlib.metadata
 import textwrap
 
 
-def test_simple_regression():
+@pytest.fixture
+def simple_grid():
+
     grid = Grid(nx=1, ny=1, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=0)
 
+    return grid
+
+
+def test_grid_creation(simple_grid):
+
+    assert simple_grid.nx == 1
+    assert simple_grid.ny == 1
+    assert simple_grid.size_x == 100
+    assert simple_grid.size_y == 100
+    assert simple_grid.center_lon == -20
+    assert simple_grid.center_lat == 0
+    assert simple_grid.rot == 0
+    assert isinstance(simple_grid.ds, xr.Dataset)
+
+
+def test_plot_save_methods(simple_grid, tmp_path):
+
+    simple_grid.plot(bathymetry=True)
+    filepath = tmp_path / "grid.nc"
+    simple_grid.save(filepath)
+    assert filepath.exists()
+
+
+@pytest.fixture
+def simple_grid_that_straddles_dateline():
+
+    grid = Grid(nx=1, ny=1, size_x=100, size_y=100, center_lon=0, center_lat=0, rot=20)
+
+    return grid
+
+
+def test_simple_regression(simple_grid):
+
     expected_lat = np.array(
         [
             [-8.99249453e-01, -8.99249453e-01, -8.99249453e-01],
@@ -26,9 +62,158 @@ def test_simple_regression():
         ]
     )
 
+    expected_lat_u = np.array(
+        [
+            [-8.99249453e-01, -8.99249453e-01],
+            [-2.39610306e-15, -2.28602368e-15],
+            [8.99249453e-01, 8.99249453e-01],
+        ]
+    )
+
+    expected_lon_u = np.array(
+        [
+            [339.55036143, 340.44963857],
+            [339.55036143, 340.44963857],
+            [339.55036143, 340.44963857],
+        ]
+    )
+
+    expected_lat_v = np.array(
+        [[-0.44962473, -0.44962473, -0.44962473], [0.44962473, 0.44962473, 0.44962473]]
+    )
+
+    expected_lon_v = np.array(
+        [[339.10072286, 340.0, 340.89927714], [339.10072286, 340.0, 340.89927714]]
+    )
+
+    expected_lat_coarse = np.array(
+        [[-1.34887418, -1.34887418], [1.34887418, 1.34887418]]
+    )
+
+    expected_lon_coarse = np.array(
+        [[338.65108429, 341.34891571], [338.65108429, 341.34891571]]
+    )
+
+    expected_angle = np.array(
+        [
+            [0.00000000e00, 0.00000000e00, 0.00000000e00],
+            [-3.83707366e-17, -3.83707366e-17, -3.83707366e-17],
+            [0.00000000e00, 0.00000000e00, 0.00000000e00],
+        ]
+    )
+
+    expected_angle_coarse = np.array(
+        [[1.91853683e-17, 1.91853683e-17], [1.91853683e-17, 1.91853683e-17]]
+    )
+
+    # TODO: adapt tolerances according to order of magnitude of respective fields
+    npt.assert_allclose(simple_grid.ds["lat_rho"], expected_lat, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["lon_rho"], expected_lon, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["lat_u"], expected_lat_u, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["lon_u"], expected_lon_u, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["lat_v"], expected_lat_v, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["lon_v"], expected_lon_v, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["lat_coarse"], expected_lat_coarse, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["lon_coarse"], expected_lon_coarse, atol=1e-8)
+    npt.assert_allclose(simple_grid.ds["angle"], expected_angle, atol=1e-8)
+    npt.assert_allclose(
+        simple_grid.ds["angle_coarse"], expected_angle_coarse, atol=1e-8
+    )
+
+
+def test_simple_regression_dateline(simple_grid_that_straddles_dateline):
+
+    expected_lat = np.array(
+        [
+            [-1.15258151e00, -8.45014017e-01, -5.37470876e-01],
+            [-3.07559747e-01, -2.14815958e-15, 3.07559747e-01],
+            [5.37470876e-01, 8.45014017e-01, 1.15258151e00],
+        ]
+    )
+    expected_lon = np.array(
+        [
+            [3.59462527e02, 3.07583728e-01, 1.15258257e00],
+            [3.59154948e02, 7.81866146e-16, 8.45052212e-01],
+            [3.58847417e02, 3.59692416e02, 5.37473154e-01],
+        ]
+    )
+    expected_lat_u = np.array(
+        [
+            [-0.99879776, -0.69124245],
+            [-0.15377987, 0.15377987],
+            [0.69124245, 0.99879776],
+        ]
+    )
+    expected_lon_u = np.array(
+        [
+            [3.59885055e02, 7.30083149e-01],
+            [3.59577474e02, 4.22526106e-01],
+            [3.59269917e02, 1.14944713e-01],
+        ]
+    )
+    expected_lat_v = np.array(
+        [[-0.73007063, -0.42250701, -0.11495556], [0.11495556, 0.42250701, 0.73007063]]
+    )
+    expected_lon_v = np.array(
+        [
+            [3.59308737e02, 1.53791864e-01, 9.98817391e-01],
+            [3.59001183e02, 3.59846208e02, 6.91262683e-01],
+        ]
+    )
+    expected_lat_coarse = np.array(
+        [[-1.72887807, -0.80621877], [0.80621877, 1.72887807]]
+    )
+    expected_lon_coarse = np.array(
+        [[359.19378677, 1.72883383], [358.27116617, 0.80621323]]
+    )
+    expected_angle = np.array(
+        [
+            [0.34910175, 0.34910175, 0.34910175],
+            [0.34906217, 0.34906217, 0.34906217],
+            [0.34910175, 0.34910175, 0.34910175],
+        ]
+    )
+    expected_angle_coarse = np.array(
+        [[0.34912155, 0.34912155], [0.34912155, 0.34912155]]
+    )
+
     # TODO: adapt tolerances according to order of magnitude of respective fields
-    npt.assert_allclose(grid.ds["lat_rho"], expected_lat, atol=1e-8)
-    npt.assert_allclose(grid.ds["lon_rho"], expected_lon, atol=1e-8)
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lat_rho"], expected_lat, atol=1e-8
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lon_rho"], expected_lon, atol=1e-8
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lat_u"], expected_lat_u, atol=1e-8
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lon_u"], expected_lon_u, atol=1e-8
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lat_v"], expected_lat_v, atol=1e-8
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lon_v"], expected_lon_v, atol=1e-8
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lat_coarse"],
+        expected_lat_coarse,
+        atol=1e-8,
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["lon_coarse"],
+        expected_lon_coarse,
+        atol=1e-8,
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["angle"], expected_angle, atol=1e-8
+    )
+    npt.assert_allclose(
+        simple_grid_that_straddles_dateline.ds["angle_coarse"],
+        expected_angle_coarse,
+        atol=1e-8,
+    )
 
 
 def test_raise_if_domain_too_large():
@@ -85,9 +270,7 @@ def test_roundtrip_netcdf():
         center_lat=0.0,
         rot=0.0,
         topography_source="ETOPO5",
-        smooth_factor=2,
         hmin=5.0,
-        rmax=0.2,
     )
 
     # Create a temporary file
@@ -121,9 +304,7 @@ def test_roundtrip_yaml():
         center_lat=0.0,
         rot=0.0,
         topography_source="ETOPO5",
-        smooth_factor=2,
         hmin=5.0,
-        rmax=0.2,
     )
 
     # Create a temporary file
@@ -155,9 +336,7 @@ def test_from_yaml_missing_version():
       center_lat: 61
       rot: -20
       topography_source: ETOPO5
-      smooth_factor: 8
       hmin: 5.0
-      rmax: 0.2
     """
     )
     with tempfile.NamedTemporaryFile(delete=False) as tmp_file:
@@ -206,9 +385,7 @@ def test_from_yaml_version_mismatch():
       center_lat: 61
       rot: -20
       topography_source: ETOPO5
-      smooth_factor: 8
       hmin: 5.0
-      rmax: 0.2
     """
     )
 

roms_tools/tests/test_initial_conditions.py

@@ -1,6 +1,6 @@
 import pytest
 from datetime import datetime
-from roms_tools import InitialConditions, Grid, VerticalCoordinate
+from roms_tools import InitialConditions, Grid
 import xarray as xr
 import numpy as np
 import tempfile
@@ -16,30 +16,24 @@ def example_grid():
     Fixture for creating a Grid object.
     """
     grid = Grid(
-        nx=2, ny=2, size_x=500, size_y=1000, center_lon=0, center_lat=55, rot=10
-    )
-
-    return grid
-
-
-@pytest.fixture
-def example_vertical_coordinate(example_grid):
-    """
-    Fixture for creating a VerticalCoordinate object.
-    """
-    vertical_coordinate = VerticalCoordinate(
-        grid=example_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
     )
 
-    return vertical_coordinate
+    return grid
 
 
 @pytest.fixture
-def initial_conditions(example_grid, example_vertical_coordinate):
+def initial_conditions(example_grid):
     """
     Fixture for creating a dummy InitialConditions object.
     """
@@ -48,14 +42,13 @@ def initial_conditions(example_grid, example_vertical_coordinate):
 
     return InitialConditions(
         grid=example_grid,
-        vertical_coordinate=example_vertical_coordinate,
         ini_time=datetime(2021, 6, 29),
         physics_source={"path": fname, "name": "GLORYS"},
     )
 
 
 @pytest.fixture
-def initial_conditions_with_bgc(example_grid, example_vertical_coordinate):
+def initial_conditions_with_bgc(example_grid):
     """
     Fixture for creating a dummy InitialConditions object.
     """
@@ -65,7 +58,6 @@ def initial_conditions_with_bgc(example_grid, example_vertical_coordinate):
 
     return InitialConditions(
         grid=example_grid,
-        vertical_coordinate=example_vertical_coordinate,
         ini_time=datetime(2021, 6, 29),
         physics_source={"path": fname, "name": "GLORYS"},
         bgc_source={"path": fname_bgc, "name": "CESM_REGRIDDED"},
@@ -73,9 +65,7 @@ def initial_conditions_with_bgc(example_grid, example_vertical_coordinate):
 
 
 @pytest.fixture
-def initial_conditions_with_bgc_from_climatology(
-    example_grid, example_vertical_coordinate
-):
+def initial_conditions_with_bgc_from_climatology(example_grid):
     """
     Fixture for creating a dummy InitialConditions object.
     """
@@ -85,7 +75,6 @@ def initial_conditions_with_bgc_from_climatology(
 
     return InitialConditions(
         grid=example_grid,
-        vertical_coordinate=example_vertical_coordinate,
         ini_time=datetime(2021, 6, 29),
         physics_source={"path": fname, "name": "GLORYS"},
         bgc_source={
@@ -126,33 +115,27 @@ def test_initial_conditions_creation(ic_fixture, request):
 
 
 # Test initialization with missing 'name' in physics_source
-def test_initial_conditions_missing_physics_name(
-    example_grid, example_vertical_coordinate
-):
+def test_initial_conditions_missing_physics_name(example_grid):
     with pytest.raises(ValueError, match="`physics_source` must include a 'name'."):
         InitialConditions(
             grid=example_grid,
-            vertical_coordinate=example_vertical_coordinate,
             ini_time=datetime(2021, 6, 29),
             physics_source={"path": "physics_data.nc"},
         )
 
 
 # Test initialization with missing 'path' in physics_source
-def test_initial_conditions_missing_physics_path(
-    example_grid, example_vertical_coordinate
-):
+def test_initial_conditions_missing_physics_path(example_grid):
     with pytest.raises(ValueError, match="`physics_source` must include a 'path'."):
         InitialConditions(
             grid=example_grid,
-            vertical_coordinate=example_vertical_coordinate,
             ini_time=datetime(2021, 6, 29),
             physics_source={"name": "GLORYS"},
         )
 
 
 # Test initialization with missing 'name' in bgc_source
-def test_initial_conditions_missing_bgc_name(example_grid, example_vertical_coordinate):
+def test_initial_conditions_missing_bgc_name(example_grid):
 
     fname = download_test_data("GLORYS_test_data.nc")
     with pytest.raises(
@@ -160,7 +143,6 @@ def test_initial_conditions_missing_bgc_name(example_grid, example_vertical_coor
     ):
         InitialConditions(
             grid=example_grid,
-            vertical_coordinate=example_vertical_coordinate,
             ini_time=datetime(2021, 6, 29),
             physics_source={"name": "GLORYS", "path": fname},
             bgc_source={"path": "bgc_data.nc"},
@@ -168,7 +150,7 @@ def test_initial_conditions_missing_bgc_name(example_grid, example_vertical_coor
 
 
 # Test initialization with missing 'path' in bgc_source
-def test_initial_conditions_missing_bgc_path(example_grid, example_vertical_coordinate):
+def test_initial_conditions_missing_bgc_path(example_grid):
 
     fname = download_test_data("GLORYS_test_data.nc")
     with pytest.raises(
@@ -176,7 +158,6 @@ def test_initial_conditions_missing_bgc_path(example_grid, example_vertical_coor
     ):
         InitialConditions(
             grid=example_grid,
-            vertical_coordinate=example_vertical_coordinate,
             ini_time=datetime(2021, 6, 29),
             physics_source={"name": "GLORYS", "path": fname},
             bgc_source={"name": "CESM_REGRIDDED"},
@@ -184,15 +165,12 @@ def test_initial_conditions_missing_bgc_path(example_grid, example_vertical_coor
 
 
 # Test default climatology value
-def test_initial_conditions_default_climatology(
-    example_grid, example_vertical_coordinate
-):
+def test_initial_conditions_default_climatology(example_grid):
 
     fname = download_test_data("GLORYS_test_data.nc")
 
     initial_conditions = InitialConditions(
         grid=example_grid,
-        vertical_coordinate=example_vertical_coordinate,
         ini_time=datetime(2021, 6, 29),
         physics_source={"name": "GLORYS", "path": fname},
     )
@@ -201,16 +179,13 @@ def test_initial_conditions_default_climatology(
     assert initial_conditions.bgc_source is None
 
 
-def test_initial_conditions_default_bgc_climatology(
-    example_grid, example_vertical_coordinate
-):
+def test_initial_conditions_default_bgc_climatology(example_grid):
 
     fname = download_test_data("GLORYS_test_data.nc")
     fname_bgc = download_test_data("CESM_regional_test_data_one_time_slice.nc")
 
     initial_conditions = InitialConditions(
         grid=example_grid,
-        vertical_coordinate=example_vertical_coordinate,
         ini_time=datetime(2021, 6, 29),
         physics_source={"name": "GLORYS", "path": fname},
         bgc_source={"name": "CESM_REGRIDDED", "path": fname_bgc},

roms_tools/tests/test_surface_forcing.py

@@ -194,8 +194,6 @@ def test_successful_initialization_with_regional_data(grid_fixture, request):
 
     assert sfc_forcing.ds is not None
 
-    grid.coarsen()
-
     sfc_forcing = SurfaceForcing(
         grid=grid,
         use_coarse_grid=True,
@@ -250,8 +248,6 @@ def test_nan_detection_initialization_with_regional_data(grid_fixture, request):
             physics_source={"name": "ERA5", "path": fname},
         )
 
-    grid.coarsen()
-
     with pytest.raises(ValueError, match="NaN values found"):
         SurfaceForcing(
             grid=grid,
@@ -286,8 +282,6 @@ def test_no_longitude_intersection_initialization_with_regional_data(
             physics_source={"name": "ERA5", "path": fname},
         )
 
-    grid_that_straddles_180_degree_meridian.coarsen()
-
     with pytest.raises(
         ValueError, match="Selected longitude range does not intersect with dataset"
     ):
@@ -350,8 +344,6 @@ def test_successful_initialization_with_global_data(grid_fixture, request):
     assert "rain" in sfc_forcing.ds["physics"]
     assert sfc_forcing.ds["physics"].attrs["physics_source"] == "ERA5"
 
-    grid.coarsen()
-
     sfc_forcing = SurfaceForcing(
         grid=grid,
         use_coarse_grid=True,

roms_tools/tests/test_topography.py

@@ -31,12 +31,10 @@ def test_rmax_criterion():
         center_lon=30,
         center_lat=61,
         rot=20,
-        smooth_factor=4,
-        rmax=0.2,
     )
     r_eta, r_xi = _compute_rfactor(grid.ds.h)
     rmax0 = np.max([r_eta.max(), r_xi.max()])
-    npt.assert_array_less(rmax0, grid.rmax)
+    npt.assert_array_less(rmax0, 0.2)
 
 
 def test_hmin_criterion():
@@ -48,11 +46,15 @@ def test_hmin_criterion():
         center_lon=30,
         center_lat=61,
         rot=20,
-        smooth_factor=2,
-        rmax=0.2,
-        hmin=5,
+        hmin=5.0,
     )
 
+    assert grid.hmin == 5.0
+    assert np.less_equal(grid.hmin, grid.ds.h.min())
+
+    grid.update_topography_and_mask(hmin=10.0)
+
+    assert grid.hmin == 10.0
     assert np.less_equal(grid.hmin, grid.ds.h.min())