roms-tools 3.2.0__py3-none-any.whl → 3.4.0__py3-none-any.whl

roms_tools/tests/test_setup/test_data/tidal_forcing.zarr/zarr.json

@@ -1,7 +1,7 @@
 {
   "attributes": {
     "title": "ROMS tidal forcing created by ROMS-Tools",
-    "roms_tools_version": "2.6.1.dev52+gd44fe5da",
+    "roms_tools_version": "3.1.3.dev32+g91d580e67.d20250929",
     "source": "TPXO",
     "model_reference_date": "2000-01-01 00:00:00"
   },
@@ -10,20 +10,21 @@
     "kind": "inline",
     "must_understand": false,
     "metadata": {
-      "v_Im": {
+      "ntides": {
         "shape": [
-          1,
-          4,
-          5
+          1
         ],
-        "data_type": "float32",
+        "data_type": {
+          "name": "null_terminated_bytes",
+          "configuration": {
+            "length_bytes": 3
+          }
+        },
         "chunk_grid": {
           "name": "regular",
           "configuration": {
             "chunk_shape": [
-              1,
-              4,
-              5
+              1
             ]
           }
         },
@@ -33,13 +34,10 @@
             "separator": "/"
           }
         },
-        "fill_value": 0.0,
+        "fill_value": "",
         "codecs": [
           {
-            "name": "bytes",
-            "configuration": {
-              "endian": "little"
-            }
+            "name": "bytes"
           },
           {
             "name": "zstd",
@@ -50,35 +48,29 @@
           }
         ],
         "attributes": {
-          "long_name": "Tidal velocity in y-direction, complex part",
-          "units": "m/s",
-          "coordinates": "omega",
-          "_FillValue": "AAAAAAAA+H8="
+          "long_name": "constituent label"
         },
         "dimension_names": [
-          "ntides",
-          "eta_v",
-          "xi_rho"
+          "ntides"
         ],
         "zarr_format": 3,
         "node_type": "array",
         "storage_transformers": []
       },
-      "ntides": {
+      "pot_Im": {
         "shape": [
-          1
+          1,
+          5,
+          5
         ],
-        "data_type": {
-          "name": "null_terminated_bytes",
-          "configuration": {
-            "length_bytes": 3
-          }
-        },
+        "data_type": "float32",
         "chunk_grid": {
           "name": "regular",
           "configuration": {
             "chunk_shape": [
-              1
+              1,
+              5,
+              5
             ]
           }
         },
@@ -88,10 +80,13 @@
             "separator": "/"
           }
         },
-        "fill_value": "",
+        "fill_value": 0.0,
         "codecs": [
           {
-            "name": "bytes"
+            "name": "bytes",
+            "configuration": {
+              "endian": "little"
+            }
           },
           {
             "name": "zstd",
@@ -102,16 +97,21 @@
           }
         ],
         "attributes": {
-          "long_name": "constituent label"
+          "long_name": "Tidal potential, complex part",
+          "units": "m",
+          "coordinates": "omega",
+          "_FillValue": "AAAAAAAA+H8="
         },
         "dimension_names": [
-          "ntides"
+          "ntides",
+          "eta_rho",
+          "xi_rho"
         ],
         "zarr_format": 3,
         "node_type": "array",
         "storage_transformers": []
       },
-      "ssh_Re": {
+      "pot_Re": {
         "shape": [
           1,
           5,
@@ -151,7 +151,7 @@
           }
         ],
         "attributes": {
-          "long_name": "Tidal elevation, real part",
+          "long_name": "Tidal potential, real part",
           "units": "m",
           "coordinates": "omega",
           "_FillValue": "AAAAAAAA+H8="
@@ -165,10 +165,10 @@
         "node_type": "array",
         "storage_transformers": []
       },
-      "pot_Im": {
+      "v_Im": {
         "shape": [
           1,
-          5,
+          4,
           5
         ],
         "data_type": "float32",
@@ -177,7 +177,7 @@
           "configuration": {
             "chunk_shape": [
               1,
-              5,
+              4,
               5
             ]
           }
@@ -205,24 +205,24 @@
           }
         ],
         "attributes": {
-          "long_name": "Tidal potential, complex part",
-          "units": "m",
+          "long_name": "Tidal velocity in y-direction, complex part",
+          "units": "m/s",
           "coordinates": "omega",
           "_FillValue": "AAAAAAAA+H8="
         },
         "dimension_names": [
           "ntides",
-          "eta_rho",
+          "eta_v",
           "xi_rho"
         ],
         "zarr_format": 3,
         "node_type": "array",
         "storage_transformers": []
       },
-      "ssh_Im": {
+      "v_Re": {
         "shape": [
           1,
-          5,
+          4,
           5
         ],
         "data_type": "float32",
@@ -231,7 +231,7 @@
           "configuration": {
             "chunk_shape": [
               1,
-              5,
+              4,
               5
             ]
           }
@@ -259,24 +259,24 @@
           }
         ],
         "attributes": {
-          "long_name": "Tidal elevation, complex part",
-          "units": "m",
+          "long_name": "Tidal velocity in y-direction, real part",
+          "units": "m/s",
           "coordinates": "omega",
           "_FillValue": "AAAAAAAA+H8="
         },
         "dimension_names": [
           "ntides",
-          "eta_rho",
+          "eta_v",
           "xi_rho"
         ],
         "zarr_format": 3,
         "node_type": "array",
         "storage_transformers": []
       },
-      "v_Re": {
+      "ssh_Re": {
         "shape": [
           1,
-          4,
+          5,
           5
         ],
         "data_type": "float32",
@@ -285,7 +285,7 @@
           "configuration": {
             "chunk_shape": [
               1,
-              4,
+              5,
               5
             ]
           }
@@ -313,14 +313,14 @@
           }
         ],
         "attributes": {
-          "long_name": "Tidal velocity in y-direction, real part",
-          "units": "m/s",
+          "long_name": "Tidal elevation, real part",
+          "units": "m",
           "coordinates": "omega",
           "_FillValue": "AAAAAAAA+H8="
         },
         "dimension_names": [
           "ntides",
-          "eta_v",
+          "eta_rho",
           "xi_rho"
         ],
         "zarr_format": 3,
@@ -428,11 +428,11 @@
         "node_type": "array",
         "storage_transformers": []
       },
-      "u_Im": {
+      "ssh_Im": {
         "shape": [
           1,
           5,
-          4
+          5
         ],
         "data_type": "float32",
         "chunk_grid": {
@@ -441,7 +441,7 @@
             "chunk_shape": [
               1,
               5,
-              4
+              5
             ]
           }
         },
@@ -468,25 +468,25 @@
           }
         ],
         "attributes": {
-          "long_name": "Tidal velocity in x-direction, complex part",
-          "units": "m/s",
+          "long_name": "Tidal elevation, complex part",
+          "units": "m",
           "coordinates": "omega",
           "_FillValue": "AAAAAAAA+H8="
         },
         "dimension_names": [
           "ntides",
           "eta_rho",
-          "xi_u"
+          "xi_rho"
         ],
         "zarr_format": 3,
         "node_type": "array",
         "storage_transformers": []
       },
-      "pot_Re": {
+      "u_Im": {
         "shape": [
           1,
           5,
-          5
+          4
         ],
         "data_type": "float32",
         "chunk_grid": {
@@ -495,7 +495,7 @@
             "chunk_shape": [
               1,
               5,
-              5
+              4
             ]
           }
         },
@@ -522,15 +522,15 @@
           }
         ],
         "attributes": {
-          "long_name": "Tidal potential, real part",
-          "units": "m",
+          "long_name": "Tidal velocity in x-direction, complex part",
+          "units": "m/s",
           "coordinates": "omega",
           "_FillValue": "AAAAAAAA+H8="
         },
         "dimension_names": [
           "ntides",
           "eta_rho",
-          "xi_rho"
+          "xi_u"
         ],
         "zarr_format": 3,
         "node_type": "array",

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):
@@ -236,6 +256,20 @@ def test_plot(grid_that_straddles_180_degree_meridian):
     grid_that_straddles_180_degree_meridian.plot(with_dim_names=True)
 
 
+def test_plot_wide_grid():
+    # This grid should be handled via different cartopy projection
+    grid = Grid(
+        nx=10,
+        ny=10,
+        size_x=15000,
+        size_y=15000,
+        center_lon=-161,
+        center_lat=14.4,
+        rot=-3,
+    )
+    grid.plot()
+
+
 @pytest.mark.skipif(xesmf is None, reason="xesmf required")
 def test_plot_along_lat_lon(grid_that_straddles_180_degree_meridian):
     grid_that_straddles_180_degree_meridian.plot(lat=61)
@@ -330,6 +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):
@@ -365,6 +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):
@@ -397,6 +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):
@@ -427,6 +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):
@@ -727,6 +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
 
 

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
@@ -10,8 +9,8 @@ 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.datasets import (
+from roms_tools.datasets.download import download_test_data
+from roms_tools.datasets.lat_lon_datasets import (
     CESMBGCDataset,
     UnifiedBGCDataset,
 )
@@ -46,9 +45,7 @@ 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",
     ],
@@ -66,6 +63,7 @@ def test_initial_conditions_creation_with_nondefault_glorys_dataset(
         "climatology": False,
     }
     assert hasattr(ic.ds, "adjust_depth_for_sea_surface_height")
+    assert ic.ds.attrs["adjust_depth_for_sea_surface_height"] == "False"
     assert isinstance(ic.ds, xr.Dataset)
     assert ic.ds.coords["ocean_time"].attrs["units"] == "seconds"
     expected_vars = {"temp", "salt", "u", "v", "zeta", "ubar", "vbar"}
@@ -171,7 +169,6 @@ 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",
     ],
@@ -303,90 +300,6 @@ 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",
     [
@@ -498,7 +411,6 @@ 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",
     ],
@@ -546,7 +458,6 @@ 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",
     ],
@@ -574,7 +485,6 @@ 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",
     ],
@@ -607,7 +517,6 @@ 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",
     ],