roms-tools 2.6.1__py3-none-any.whl → 2.7.0__py3-none-any.whl

roms_tools/tests/test_setup/test_tides.py

@@ -7,12 +7,83 @@ from pathlib import Path
 from conftest import calculate_data_hash
 
 
-@pytest.fixture
-def grid_that_lies_within_bounds_of_regional_tpxo_data():
+@pytest.fixture(scope="session")
+def tidal_forcing_9v5a(use_dask):
+
     grid = Grid(
         nx=3, ny=3, size_x=1500, size_y=1500, center_lon=235, center_lat=25, rot=-20
     )
-    return grid
+    fname_grid = Path(download_test_data("regional_grid_tpxo9v5a.nc"))
+    fname_h = Path(download_test_data("regional_h_tpxo9v5a.nc"))
+    fname_u = Path(download_test_data("regional_u_tpxo9v5a.nc"))
+    fname_dict = {"grid": fname_grid, "h": fname_h, "u": fname_u}
+
+    return TidalForcing(
+        grid=grid,
+        source={"name": "TPXO", "path": fname_dict},
+        ntides=1,
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def tidal_forcing_10v2a(use_dask):
+
+    grid = Grid(
+        nx=3, ny=3, size_x=1500, size_y=1500, center_lon=235, center_lat=25, rot=-20
+    )
+    fname_grid = Path(download_test_data("regional_grid_tpxo10v2a.nc"))
+    fname_h = Path(download_test_data("regional_h_tpxo10v2a.nc"))
+    fname_u = Path(download_test_data("regional_u_tpxo10v2a.nc"))
+    fname_dict = {"grid": fname_grid, "h": fname_h, "u": fname_u}
+
+    return TidalForcing(
+        grid=grid,
+        source={"name": "TPXO", "path": fname_dict},
+        ntides=1,
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def tidal_forcing_from_global_data(use_dask):
+
+    grid = Grid(
+        nx=3, ny=3, size_x=1800, size_y=1500, center_lon=235, center_lat=25, rot=-20
+    )
+
+    fname_grid = Path(download_test_data("global_grid_tpxo10.v2.nc"))
+    fname_h = Path(download_test_data("global_h_tpxo10.v2.nc"))
+    fname_u = Path(download_test_data("global_u_tpxo10.v2.nc"))
+    fname_dict = {"grid": fname_grid, "h": fname_h, "u": fname_u}
+
+    return TidalForcing(
+        grid=grid,
+        source={"name": "TPXO", "path": fname_dict},
+        ntides=1,
+        use_dask=use_dask,
+    )
+
+
+@pytest.mark.parametrize(
+    "tidal_forcing_fixture",
+    ["tidal_forcing", "tidal_forcing_9v5a", "tidal_forcing_10v2a"],  # 10v2
+)
+def test_successful_initialization(tidal_forcing_fixture, request, use_dask):
+    tidal_forcing = request.getfixturevalue(tidal_forcing_fixture)
+
+    assert isinstance(tidal_forcing.ds, xr.Dataset)
+    assert "omega" in tidal_forcing.ds
+    assert "ssh_Re" in tidal_forcing.ds
+    assert "ssh_Im" in tidal_forcing.ds
+    assert "pot_Re" in tidal_forcing.ds
+    assert "pot_Im" in tidal_forcing.ds
+    assert "u_Re" in tidal_forcing.ds
+    assert "u_Im" in tidal_forcing.ds
+    assert "v_Re" in tidal_forcing.ds
+    assert "v_Im" in tidal_forcing.ds
+
+    assert tidal_forcing.ntides == 1
 
 
 @pytest.fixture
@@ -59,7 +130,6 @@ def grid_that_straddles_180_degree_meridian():
 @pytest.mark.parametrize(
     "grid_fixture",
     [
-        "grid_that_lies_within_bounds_of_regional_tpxo_data",
         "grid_that_is_out_of_bounds_of_regional_tpxo_data",
         "grid_that_straddles_dateline",
         "grid_that_straddles_180_degree_meridian",
@@ -67,39 +137,17 @@ def grid_that_straddles_180_degree_meridian():
 )
 def test_successful_initialization_with_global_data(grid_fixture, request, use_dask):
 
-    fname = Path(download_test_data("TPXO_global_test_data.nc"))
+    fname_grid = Path(download_test_data("global_grid_tpxo10.v2.nc"))
+    fname_h = Path(download_test_data("global_h_tpxo10.v2.nc"))
+    fname_u = Path(download_test_data("global_u_tpxo10.v2.nc"))
+    fname_dict = {"grid": fname_grid, "h": fname_h, "u": fname_u}
 
     grid = request.getfixturevalue(grid_fixture)
 
     tidal_forcing = TidalForcing(
-        grid=grid, source={"name": "TPXO", "path": fname}, ntides=2, use_dask=use_dask
-    )
-
-    assert isinstance(tidal_forcing.ds, xr.Dataset)
-    assert "omega" in tidal_forcing.ds
-    assert "ssh_Re" in tidal_forcing.ds
-    assert "ssh_Im" in tidal_forcing.ds
-    assert "pot_Re" in tidal_forcing.ds
-    assert "pot_Im" in tidal_forcing.ds
-    assert "u_Re" in tidal_forcing.ds
-    assert "u_Im" in tidal_forcing.ds
-    assert "v_Re" in tidal_forcing.ds
-    assert "v_Im" in tidal_forcing.ds
-
-    assert tidal_forcing.source == {"name": "TPXO", "path": fname}
-    assert tidal_forcing.ntides == 2
-
-
-def test_successful_initialization_with_regional_data(
-    grid_that_lies_within_bounds_of_regional_tpxo_data, use_dask
-):
-
-    fname = Path(download_test_data("TPXO_regional_test_data.nc"))
-
-    tidal_forcing = TidalForcing(
-        grid=grid_that_lies_within_bounds_of_regional_tpxo_data,
-        source={"name": "TPXO", "path": fname},
-        ntides=10,
+        grid=grid,
+        source={"name": "TPXO", "path": fname_dict},
+        ntides=1,
         use_dask=use_dask,
     )
 
@@ -114,20 +162,22 @@ def test_successful_initialization_with_regional_data(
     assert "v_Re" in tidal_forcing.ds
     assert "v_Im" in tidal_forcing.ds
 
-    assert tidal_forcing.source == {"name": "TPXO", "path": fname}
-    assert tidal_forcing.ntides == 10
+    assert tidal_forcing.ntides == 1
 
 
 def test_unsuccessful_initialization_with_regional_data_due_to_nans(
     grid_that_is_out_of_bounds_of_regional_tpxo_data, use_dask
 ):
 
-    fname = Path(download_test_data("TPXO_regional_test_data.nc"))
+    fname_grid = Path(download_test_data("regional_grid_tpxo10v2.nc"))
+    fname_h = Path(download_test_data("regional_h_tpxo10v2.nc"))
+    fname_u = Path(download_test_data("regional_u_tpxo10v2.nc"))
+    fname_dict = {"grid": fname_grid, "h": fname_h, "u": fname_u}
 
     with pytest.raises(ValueError, match="NaN values found"):
         TidalForcing(
             grid=grid_that_is_out_of_bounds_of_regional_tpxo_data,
-            source={"name": "TPXO", "path": fname},
+            source={"name": "TPXO", "path": fname_dict},
             ntides=10,
             use_dask=use_dask,
         )
@@ -141,7 +191,10 @@ def test_unsuccessful_initialization_with_regional_data_due_to_no_overlap(
     grid_fixture, request, use_dask
 ):
 
-    fname = Path(download_test_data("TPXO_regional_test_data.nc"))
+    fname_grid = Path(download_test_data("regional_grid_tpxo10v2.nc"))
+    fname_h = Path(download_test_data("regional_h_tpxo10v2.nc"))
+    fname_u = Path(download_test_data("regional_u_tpxo10v2.nc"))
+    fname_dict = {"grid": fname_grid, "h": fname_h, "u": fname_u}
 
     grid = request.getfixturevalue(grid_fixture)
 
@@ -150,7 +203,7 @@ def test_unsuccessful_initialization_with_regional_data_due_to_no_overlap(
     ):
         TidalForcing(
             grid=grid,
-            source={"name": "TPXO", "path": fname},
+            source={"name": "TPXO", "path": fname_dict},
             ntides=10,
             use_dask=use_dask,
         )
@@ -158,12 +211,15 @@ def test_unsuccessful_initialization_with_regional_data_due_to_no_overlap(
 
 def test_insufficient_number_of_consituents(grid_that_straddles_dateline, use_dask):
 
-    fname = Path(download_test_data("TPXO_global_test_data.nc"))
+    fname_grid = Path(download_test_data("global_grid_tpxo10.v2.nc"))
+    fname_h = Path(download_test_data("global_h_tpxo10.v2.nc"))
+    fname_u = Path(download_test_data("global_u_tpxo10.v2.nc"))
+    fname_dict = {"grid": fname_grid, "h": fname_h, "u": fname_u}
 
-    with pytest.raises(ValueError, match="The dataset contains fewer"):
+    with pytest.raises(ValueError, match="The dataset contains tidal"):
         TidalForcing(
             grid=grid_that_straddles_dateline,
-            source={"name": "TPXO", "path": fname},
+            source={"name": "TPXO", "path": fname_dict},
             ntides=10,
             use_dask=use_dask,
         )
@@ -194,10 +250,16 @@ def test_tidal_forcing_save(tidal_forcing, tmp_path):
             filepath.unlink()
 
 
-def test_roundtrip_yaml(tidal_forcing, tmp_path, use_dask):
+@pytest.mark.parametrize(
+    "tidal_forcing_fixture",
+    ["tidal_forcing", "tidal_forcing_from_global_data"],
+)
+def test_roundtrip_yaml(tidal_forcing_fixture, tmp_path, use_dask, request):
     """Test that creating a TidalForcing object, saving its parameters to yaml file, and
     re-opening yaml file creates the same object."""
 
+    tidal_forcing = request.getfixturevalue(tidal_forcing_fixture)
+
     # Create a temporary filepath using the tmp_path fixture
     file_str = "test_yaml"
     for filepath in [
@@ -215,15 +277,18 @@ def test_roundtrip_yaml(tidal_forcing, tmp_path, use_dask):
         filepath.unlink()
 
 
-def test_files_have_same_hash(tidal_forcing, tmp_path, use_dask):
+@pytest.mark.parametrize(
+    "tidal_forcing_fixture",
+    ["tidal_forcing", "tidal_forcing_from_global_data"],
+)
+def test_files_have_same_hash(tidal_forcing_fixture, tmp_path, use_dask, request):
+
+    tidal_forcing = request.getfixturevalue(tidal_forcing_fixture)
 
     yaml_filepath = tmp_path / "test_yaml.yaml"
     filepath1 = tmp_path / "test1.nc"
     filepath2 = tmp_path / "test2.nc"
 
-    print(yaml_filepath)
-    print(filepath1)
-    print(filepath2)
     tidal_forcing.to_yaml(yaml_filepath)
     tidal_forcing.save(filepath1)
     tidal_forcing_from_file = TidalForcing.from_yaml(yaml_filepath, use_dask=use_dask)

roms_tools/tests/test_setup/test_validation.py

@@ -16,13 +16,16 @@ def _get_fname(name):
         "grid_that_straddles_dateline",
         "tidal_forcing",
         "initial_conditions_with_bgc_from_climatology",
+        "initial_conditions_with_unified_bgc_from_climatology",
         "surface_forcing",
         "coarse_surface_forcing",
         "corrected_surface_forcing",
         "bgc_surface_forcing",
         "bgc_surface_forcing_from_climatology",
+        "bgc_surface_forcing_from_unified_climatology",
         "boundary_forcing",
         "bgc_boundary_forcing_from_climatology",
+        "bgc_boundary_forcing_from_unified_climatology",
         "river_forcing_with_bgc",
         "river_forcing_no_climatology",
     ],
@@ -55,13 +58,16 @@ def test_save_results(forcing_fixture, request):
         "grid_that_straddles_dateline",
         "tidal_forcing",
         "initial_conditions_with_bgc_from_climatology",
+        "initial_conditions_with_unified_bgc_from_climatology",
         "surface_forcing",
         "coarse_surface_forcing",
         "corrected_surface_forcing",
         "bgc_surface_forcing",
         "bgc_surface_forcing_from_climatology",
+        "bgc_surface_forcing_from_unified_climatology",
         "boundary_forcing",
         "bgc_boundary_forcing_from_climatology",
+        "bgc_boundary_forcing_from_unified_climatology",
         "river_forcing_with_bgc",
         "river_forcing_no_climatology",
     ],

roms_tools/utils.py

@@ -1,4 +1,5 @@
 import xarray as xr
+import numpy as np
 from pathlib import Path
 import re
 import glob
@@ -153,7 +154,7 @@ def _load_data(
 
         # Rechunk the dataset along the tidal constituent dimension ("ntides") after loading
         # because the original dataset does not have a chunk size of 1 along this dimension.
-        if "ntides" in dim_names:
+        if "ntides" in dim_names and "ntides" in ds.dims:
             ds = ds.chunk({dim_names["ntides"]: 1})
 
     else:
@@ -371,3 +372,116 @@ def get_dask_chunks(location, chunk_size):
         "v": {"eta_v": chunk_size, "xi_rho": chunk_size},
     }
     return chunk_mapping.get(location, {})
+
+
+def _generate_coordinate_range(min, max, resolution):
+    """Generate an array of target coordinates (e.g., latitude or longitude) within a
+    specified range, with a resolution that is rounded to the nearest value of the form
+    `1/n` (or integer).
+
+    This method generates an array of target coordinates between the provided `min` and `max`
+    values, ensuring that both `min` and `max` are included in the resulting range. The resolution
+    is rounded to the nearest fraction of the form `1/n` or an integer, based on the input.
+
+    Parameters
+    ----------
+    min : float
+        The minimum value (in degrees) of the coordinate range (inclusive).
+
+    max : float
+        The maximum value (in degrees) of the coordinate range (inclusive).
+
+    resolution : float
+        The spacing (in degrees) between each coordinate in the array. The resolution will
+        be rounded to the nearest value of the form `1/n` or an integer, depending on the size
+        of the resolution value.
+
+    Returns
+    -------
+    numpy.ndarray
+        An array of target coordinates generated from the specified range, with the resolution
+        rounded to a suitable fraction (e.g., `1/n`) or integer, depending on the input resolution.
+    """
+
+    # Find the closest fraction of the form 1/n or integer to match the resolution
+    resolution_rounded = None
+    min_diff = float("inf")  # Initialize the minimum difference as infinity
+
+    # Search for the best fraction or integer approximation to the resolution
+    for n in range(1, 1000):  # Try fractions 1/n, where n ranges from 1 to 999
+        if resolution <= 1:
+            fraction = (
+                1 / n
+            )  # For small resolutions (<= 1), consider fractions of the form 1/n
+        else:
+            fraction = n  # For larger resolutions (>1), consider integers (n)
+
+        diff = abs(
+            fraction - resolution
+        )  # Calculate the difference between the fraction and the resolution
+
+        if diff < min_diff:  # If the current fraction is a better approximation
+            min_diff = diff
+            resolution_rounded = fraction  # Update the best fraction (or integer) found
+
+    # Adjust the start and end of the range to include integer values
+    start_int = np.floor(min)  # Round the minimum value down to the nearest integer
+    end_int = np.ceil(max)  # Round the maximum value up to the nearest integer
+
+    # Generate the array of target coordinates, including both the min and max values
+    target = np.arange(start_int, end_int + resolution_rounded, resolution_rounded)
+
+    # Truncate any values that exceed max (including small floating point errors)
+    target = target[target <= end_int + 1e-10]
+
+    return target.astype(np.float32)
+
+
+def _remove_edge_nans(field, xdim, layer_depth=None):
+    """Trim NaN-only edges along a specified dimension.
+
+    Useful when a ROMS grid has been regridded to a fixed lat/lon section,
+    leaving NaN-filled edges (e.g., over land or outside the domain).
+    Removes leading/trailing slices along `xdim` where all values are NaN,
+    based on `field` or optionally `layer_depth`.
+
+    Parameters
+    ----------
+    field : xr.DataArray
+        Data to trim.
+    xdim : str
+        Dimension along which to remove NaN edges.
+    layer_depth : xr.DataArray, optional
+        Optional field to determine where NaNs occur.
+
+    Returns
+    -------
+    field : xr.DataArray
+        Trimmed data.
+    layer_depth : xr.DataArray or None
+        Trimmed `layer_depth` if provided.
+    """
+    if xdim in field.dims:
+        if layer_depth is not None:
+            nan_mask = layer_depth.isnull().sum(
+                dim=[dim for dim in layer_depth.dims if dim != xdim]
+            )
+        else:
+            nan_mask = field.isnull().sum(
+                dim=[dim for dim in field.dims if dim != xdim]
+            )
+
+        # Find the valid indices where the sum of the nans is 0
+        valid_indices = np.where(nan_mask.values == 0)[0]
+
+        if len(valid_indices) > 0:
+            first_valid = valid_indices[0]
+            last_valid = valid_indices[-1]
+
+            field = field.isel({xdim: slice(first_valid, last_valid + 1)})
+            if layer_depth is not None:
+                layer_depth = layer_depth.isel(
+                    {xdim: slice(first_valid, last_valid + 1)}
+                )
+
+    return field, layer_depth

{roms_tools-2.6.1.dist-info → roms_tools-2.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: roms-tools
-Version: 2.6.1
+Version: 2.7.0
 Summary: Tools for running and analysing UCLA-ROMS simulations
 Author-email: Nora Loose <nora.loose@gmail.com>, Thomas Nicholas <tom@cworthy.org>
 License: Apache-2
@@ -117,7 +117,6 @@ install `ROMS-Tools` along with the additional dependency via:
 pip install -e ".[dask]"
 ```
 
-
 ### Run the tests
 
 Before running the tests, you can activate the conda environment created in the previous section:
@@ -142,7 +141,6 @@ To learn how to use `ROMS-Tools`, check out the [documentation](https://roms-too
 
 We also accept contributions in the form of Pull Requests.
 
-
 ## See also
 
 - [ROMS source code](https://github.com/CESR-lab/ucla-roms)