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

roms_tools/tests/test_analysis/test_cdr_ensemble.py

@@ -86,18 +86,16 @@ def test_extract_efficiency(create_member_ds: xr.Dataset) -> None:
     assert eff_rel.time.attrs.get("long_name") == "time since release start"
 
 
-def test_extract_efficiency_missing_abs_time() -> None:
-    """Test that _extract_efficiency raises an error if 'abs_time' is missing."""
+def test_extract_efficiency_missing_time() -> None:
+    """Test that _extract_efficiency raises an error if 'time' is missing."""
     times = np.array(["2000-01-01", "2000-01-02"], dtype="datetime64[ns]")
     ds = xr.Dataset(
         {"cdr_efficiency": ("time", [0.1, 0.2])},
-        coords={"time": times},  # Note: no 'abs_time' coordinate
+        coords={"abs_time": times},  # Note: no 'time' coordinate
     )
 
     ens = Ensemble.__new__(Ensemble)
-    with pytest.raises(
-        ValueError, match="Dataset must contain an 'abs_time' coordinate."
-    ):
+    with pytest.raises(ValueError, match="Dataset must contain a 'time' coordinate."):
         ens._extract_efficiency(ds)
 
 

roms_tools/tests/test_analysis/test_roms_output.py

@@ -1,6 +1,3 @@
-import logging
-import os
-from datetime import datetime
 from pathlib import Path
 
 import matplotlib.pyplot as plt
@@ -9,7 +6,7 @@ import pytest
 import xarray as xr
 
 from roms_tools import Grid, ROMSOutput
-from roms_tools.download import download_test_data
+from roms_tools.datasets.download import download_test_data
 
 try:
     import xesmf  # type: ignore
@@ -58,20 +55,6 @@ def roms_output_from_restart_file_with_straddling_grid(use_dask):
     )
 
 
-@pytest.mark.parametrize(
-    "roms_output_fixture",
-    [
-        "roms_output_from_restart_file",
-        "roms_output_from_restart_file_adjusted_for_zeta",
-        "roms_output_from_restart_file_with_straddling_grid",
-    ],
-)
-def test_load_model_output_file(roms_output_fixture, request):
-    roms_output = request.getfixturevalue(roms_output_fixture)
-
-    assert isinstance(roms_output.ds, xr.Dataset)
-
-
 @pytest.fixture
 def roms_output_from_two_restart_files(use_dask):
     fname_grid = Path(download_test_data("epac25km_grd.nc"))
@@ -83,208 +66,6 @@ def roms_output_from_two_restart_files(use_dask):
     return ROMSOutput(grid=grid, path=[file1, file2], use_dask=use_dask)
 
 
-def test_load_model_output_file_list(roms_output_from_two_restart_files):
-    assert isinstance(roms_output_from_two_restart_files.ds, xr.Dataset)
-
-
-def test_load_model_output_with_wildcard(use_dask):
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-
-    # Download at least two files, so these will be found within the pooch directory
-    Path(download_test_data("eastpac25km_rst.19980106000000.nc"))
-    Path(download_test_data("eastpac25km_rst.19980126000000.nc"))
-    directory = Path(
-        os.path.dirname(download_test_data("eastpac25km_rst.19980106000000.nc"))
-    )
-
-    output = ROMSOutput(grid=grid, path=directory / "*rst*.nc", use_dask=use_dask)
-    assert isinstance(output.ds, xr.Dataset)
-
-
-def test_invalid_path(use_dask):
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-
-    # Non-existent file
-    with pytest.raises(FileNotFoundError):
-        ROMSOutput(
-            grid=grid,
-            path=Path("/path/to/nonexistent/file.nc"),
-            use_dask=use_dask,
-        )
-
-
-def test_set_correct_model_reference_date(use_dask):
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-
-    output = ROMSOutput(
-        grid=grid,
-        path=Path(download_test_data("eastpac25km_rst.19980106000000.nc")),
-        use_dask=use_dask,
-    )
-    assert output.model_reference_date == datetime(1995, 1, 1)
-
-
-def test_model_reference_date_mismatch(use_dask):
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-
-    # Create a ROMSOutput with a specified model_reference_date
-    model_ref_date = datetime(2020, 1, 1)
-    with pytest.raises(
-        ValueError, match="Mismatch between `self.model_reference_date`"
-    ):
-        ROMSOutput(
-            grid=grid,
-            path=Path(download_test_data("eastpac25km_rst.19980106000000.nc")),
-            model_reference_date=model_ref_date,
-            use_dask=use_dask,
-        )
-
-
-def test_model_reference_date_no_metadata(use_dask, tmp_path, caplog):
-    # Helper function to handle the test logic for cases where metadata is missing or invalid
-    def test_no_metadata(faulty_ocean_time_attr, expected_exception, log_message=None):
-        ds = xr.open_dataset(fname)
-        ds["ocean_time"].attrs = faulty_ocean_time_attr
-
-        # Write modified dataset to a new file
-        fname_mod = tmp_path / "eastpac25km_rst.19980106000000_without_metadata.nc"
-        ds.to_netcdf(fname_mod)
-
-        # Test case 1: Expecting a ValueError when metadata is missing or invalid
-        with pytest.raises(
-            expected_exception,
-            match="Model reference date could not be inferred from the metadata",
-        ):
-            ROMSOutput(grid=grid, path=fname_mod, use_dask=use_dask)
-
-        # Test case 2: When a model reference date is explicitly set, verify the warning
-        with caplog.at_level(logging.WARNING):
-            ROMSOutput(
-                grid=grid,
-                path=fname_mod,
-                model_reference_date=datetime(1995, 1, 1),
-                use_dask=use_dask,
-            )
-
-            if log_message:
-                # Verify the warning message in the log
-                assert log_message in caplog.text
-
-        fname_mod.unlink()
-
-    # Load grid and test data
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-    fname = download_test_data("eastpac25km_rst.19980106000000.nc")
-
-    # Test 1: Ocean time attribute 'long_name' is missing
-    test_no_metadata({}, ValueError)
-
-    # Test 2: Ocean time attribute 'long_name' contains invalid information
-    test_no_metadata(
-        {"long_name": "some random text"},
-        ValueError,
-        "Could not infer the model reference date from the metadata.",
-    )
-
-
-def test_compute_depth_coordinates(use_dask):
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-    fname_restart1 = Path(download_test_data("eastpac25km_rst.19980106000000.nc"))
-
-    for adjust_depth_for_sea_surface_height in [True, False]:
-        output = ROMSOutput(
-            grid=grid,
-            path=fname_restart1,
-            use_dask=use_dask,
-            adjust_depth_for_sea_surface_height=adjust_depth_for_sea_surface_height,
-        )
-
-        # Before calling get_vertical_coordinates, check if the dataset doesn't already have depth coordinates
-        assert "layer_depth_rho" not in output.ds_depth_coords.data_vars
-
-        # Call the method to get vertical coordinates
-        output._get_depth_coordinates(depth_type="layer")
-
-        # Check if the depth coordinates were added
-        assert "layer_depth_rho" in output.ds_depth_coords.data_vars
-
-
-def test_missing_zeta_gets_raised(use_dask):
-    """Test that a ValueError is raised when `zeta` is missing from the dataset and
-    `adjust_depth_for_sea_surface_height` is enabled.
-    """
-    # Load the grid
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-
-    # Load the ROMS output
-    fname_restart1 = Path(download_test_data("eastpac25km_rst.19980106000000.nc"))
-    roms_output = ROMSOutput(
-        grid=grid,
-        path=fname_restart1,
-        use_dask=use_dask,
-        adjust_depth_for_sea_surface_height=True,
-    )
-
-    # Remove `zeta` from the dataset
-    object.__setattr__(
-        roms_output, "ds", roms_output.ds.drop_vars("zeta", errors="ignore")
-    )
-
-    # Expect ValueError when calling `_get_depth_coordinates`
-    with pytest.raises(
-        ValueError,
-        match="`zeta` is required in provided ROMS output when `adjust_depth_for_sea_surface_height` is enabled.",
-    ):
-        roms_output._get_depth_coordinates()
-
-
-def test_check_vertical_coordinate_mismatch(use_dask):
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-
-    fname_restart1 = Path(download_test_data("eastpac25km_rst.19980106000000.nc"))
-    output = ROMSOutput(grid=grid, path=fname_restart1, use_dask=use_dask)
-
-    # create a mock dataset with inconsistent vertical coordinate parameters
-    ds_mock = output.ds.copy()
-
-    # Modify one of the vertical coordinate attributes to cause a mismatch
-    ds_mock.attrs["theta_s"] = 999
-
-    # Check if ValueError is raised due to mismatch
-    with pytest.raises(ValueError, match="theta_s from grid"):
-        output._check_vertical_coordinate(ds_mock)
-
-    # create a mock dataset with inconsistent vertical coordinate parameters
-    ds_mock = output.ds.copy()
-
-    # Modify one of the vertical coordinate attributes to cause a mismatch
-    ds_mock.attrs["Cs_w"] = ds_mock.attrs["Cs_w"] + 0.01
-
-    # Check if ValueError is raised due to mismatch
-    with pytest.raises(ValueError, match="Cs_w from grid"):
-        output._check_vertical_coordinate(ds_mock)
-
-
-def test_that_coordinates_are_added(use_dask):
-    fname_grid = Path(download_test_data("epac25km_grd.nc"))
-    grid = Grid.from_file(fname_grid)
-
-    fname_restart1 = Path(download_test_data("eastpac25km_rst.19980106000000.nc"))
-    output = ROMSOutput(grid=grid, path=fname_restart1, use_dask=use_dask)
-
-    assert "abs_time" in output.ds.coords
-    assert "lat_rho" in output.ds.coords
-    assert "lon_rho" in output.ds.coords
-
-
 @pytest.mark.parametrize(
     "roms_output_fixture",
     [

roms_tools/tests/{test_setup → test_datasets}/test_lat_lon_datasets.py

@@ -8,8 +8,8 @@ import numpy as np
 import pytest
 import xarray as xr
 
-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 (
     GLORYS_GLOBAL_GRID_PATH,
     CESMBGCDataset,
     ERA5ARCODataset,
@@ -604,14 +604,14 @@ 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"):
+    with pytest.raises(TypeError, match="`start_time` must be a datetime object"):
         GLORYSDataset(
             filename=fname,
             start_time="dummy",
             end_time=datetime(2013, 1, 1),
             use_dask=use_dask,
         )
-    with pytest.raises(TypeError, match="end_time must be a datetime object"):
+    with pytest.raises(TypeError, match="`end_time` must be a datetime object"):
         GLORYSDataset(
             filename=fname,
             start_time=datetime(2012, 1, 1),

roms_tools/tests/{test_setup → test_datasets}/test_river_datasets.py

@@ -3,7 +3,7 @@ from datetime import datetime
 import numpy as np
 import xarray as xr
 
-from roms_tools.setup.river_datasets import RiverDataset
+from roms_tools.datasets.river_datasets import RiverDataset
 
 
 class TestRiverDataset: