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

roms_tools/tests/test_datasets/test_utils.py

@@ -0,0 +1,527 @@
+import logging
+from copy import deepcopy
+from datetime import datetime, timedelta
+
+import cftime
+import numpy as np
+import pytest
+import xarray as xr
+
+from roms_tools.datasets.utils import (
+    _select_initial_time,
+    check_dataset,
+    convert_cftime_to_datetime,
+    convert_to_float64,
+    extrapolate_deepest_to_bottom,
+    get_time_type,
+    select_relevant_fields,
+    select_relevant_times,
+    validate_start_end_time,
+)
+
+
+def test_convert_to_float64():
+    # Create dataset with mixed dtypes
+    ds = xr.Dataset(
+        {
+            "temp": (("x",), np.array([1, 2, 3], dtype=np.float32)),
+            "mask_rho": (("x",), np.array([0, 1, 0], dtype=np.int16)),
+        }
+    )
+
+    out = convert_to_float64(ds)
+
+    # Non-mask variables should be converted to float64
+    assert out["temp"].dtype == np.float64
+
+    # Mask variables should keep their original dtype
+    assert out["mask_rho"].dtype == np.int16
+
+    # Values should be preserved
+    xr.testing.assert_equal(out["temp"], ds["temp"].astype("float64"))
+    xr.testing.assert_equal(out["mask_rho"], ds["mask_rho"])
+
+
+def test_extrapolate_deepest_to_bottom():
+    data = np.array(
+        [
+            [1, 2],
+            [3, 4],
+            [5, np.nan],
+            [np.nan, np.nan],
+            [np.nan, np.nan],
+        ]
+    )
+    ds = xr.Dataset({"var": (("s_rho", "x"), data)})
+
+    ds_filled = extrapolate_deepest_to_bottom(ds, "s_rho")
+
+    expected = np.array(
+        [
+            [1, 2],
+            [3, 4],
+            [5, 4],
+            [5, 4],
+            [5, 4],
+        ]
+    )
+    np.testing.assert_array_equal(ds_filled["var"].values, expected)
+
+
+# tests for  validate_start_end_time
+
+
+def test_valid_times():
+    start = datetime(2024, 1, 1, 12, 0)
+    end = start + timedelta(hours=3)
+
+    # Should not raise
+    validate_start_end_time(start, end)
+
+
+def test_none_times():
+    # None for both is allowed
+    validate_start_end_time(None, None)
+
+    # Only start_time provided
+    validate_start_end_time(datetime(2024, 1, 1), None)
+
+    # Only end_time provided
+    validate_start_end_time(None, datetime(2024, 1, 2))
+
+
+def test_equal_times():
+    t = datetime(2024, 1, 1, 12, 0)
+
+    # end_time == start_time is allowed
+    validate_start_end_time(t, t)
+
+
+def test_invalid_start_type():
+    with pytest.raises(TypeError):
+        validate_start_end_time("2024-01-01", None)
+
+
+def test_invalid_end_type():
+    with pytest.raises(TypeError):
+        validate_start_end_time(None, 123)
+
+
+def test_end_time_before_start_time():
+    start = datetime(2024, 1, 2)
+    end = datetime(2024, 1, 1)
+
+    with pytest.raises(ValueError):
+        validate_start_end_time(start, end)
+
+
+# tests for check_dataset
+
+
+def test_valid_dataset():
+    ds = xr.Dataset(
+        data_vars={
+            "temp": (("x", "y"), [[1, 2], [3, 4]]),
+            "salt": (("x", "y"), [[5, 6], [7, 8]]),
+        },
+        coords={
+            "x": [0, 1],
+            "y": [0, 1],
+        },
+    )
+
+    dim_names = {"xdim": "x", "ydim": "y"}
+    var_names = {"temperature": "temp", "salinity": "salt"}
+
+    # Should NOT raise
+    check_dataset(ds, dim_names, var_names)
+
+
+def test_missing_required_dimension():
+    ds = xr.Dataset(data_vars={"temp": (("x",), [1])}, coords={"x": [0]})
+
+    dim_names = {"xdim": "x", "ydim": "y"}
+
+    with pytest.raises(ValueError, match="missing"):
+        check_dataset(ds, dim_names=dim_names)
+
+
+def test_missing_required_variable():
+    ds = xr.Dataset(data_vars={"temp": (("x",), [1])}, coords={"x": [0]})
+
+    var_names = {"temperature": "temp", "salinity": "salt"}
+
+    with pytest.raises(ValueError, match="missing"):
+        check_dataset(ds, var_names=var_names)
+
+
+def test_optional_variables_warning(caplog):
+    ds = xr.Dataset(data_vars={"temp": (("x",), [1])}, coords={"x": [0]})
+
+    opt_var_names = {"some_opt": "opt_var"}
+
+    with caplog.at_level(logging.WARNING):
+        # Should not raise, only warn
+        check_dataset(ds, opt_var_names=opt_var_names)
+
+    assert "Optional variables missing" in caplog.text
+    assert "opt_var" in caplog.text
+
+
+def test_no_checks_pass():
+    ds = xr.Dataset(data_vars={"temp": (("x",), [1])}, coords={"x": [0]})
+
+    # Should not fail because no dim_names/var_names provided
+    check_dataset(ds)
+
+
+# tests for select_relevant_fields
+
+
+def test_select_relevant_fields_basic():
+    """Keep only required + optional variables and drop others."""
+    ds = xr.Dataset(
+        {
+            "temp": (("x",), np.arange(5)),
+            "salt": (("x",), np.arange(5) * 2),
+            "u": (("x",), np.arange(5) * 3),
+            "mask": (("x",), np.ones(5)),
+            "extra": (("x",), np.zeros(5)),
+        }
+    )
+
+    keep_vars = ["temp", "u"]  # required + optional
+
+    out = select_relevant_fields(ds, keep_vars)
+
+    assert set(out.data_vars) == {"temp", "u", "mask"}
+    assert "salt" not in out
+    assert "extra" not in out
+
+
+def test_select_relevant_fields_does_not_modify_input():
+    """Function must not mutate the original dataset."""
+    ds = xr.Dataset(
+        {
+            "temp": (("x",), np.arange(5)),
+            "salt": (("x",), np.arange(5)),
+            "mask": (("x",), np.ones(5)),
+        }
+    )
+
+    ds_copy = deepcopy(ds)
+
+    _ = select_relevant_fields(ds, ["temp"])
+
+    # ensure original dataset is unchanged
+    assert set(ds.data_vars) == set(ds_copy.data_vars)
+    assert "salt" in ds
+    assert "mask" in ds
+
+
+def test_select_relevant_fields_duplicate_keep_names():
+    """Duplicate keep names should not cause issues."""
+    ds = xr.Dataset(
+        {
+            "temp": (("x",), np.arange(5)),
+            "mask": (("x",), np.ones(5)),
+        }
+    )
+
+    keep_vars = ["temp", "temp"]  # duplicates
+
+    out = select_relevant_fields(ds, keep_vars)
+
+    assert set(out.data_vars) == {"temp", "mask"}
+
+
+# tests for select_relevant_times
+
+
+def make_time_dataset(times):
+    return xr.Dataset(
+        data_vars={"var": ("time", np.arange(len(times)))},
+        coords={"time": times},
+    )
+
+
+def test_missing_time_dimension(caplog):
+    ds = xr.Dataset({"x": ("x", [1, 2])})
+
+    with caplog.at_level(logging.WARNING):
+        out = select_relevant_times(
+            ds, "time", datetime(2024, 1, 1), datetime(2024, 1, 2)
+        )
+
+    assert "does not contain time dimension" in caplog.text
+    assert out is ds  # unchanged
+
+
+def test_climatology_must_have_12_steps():
+    times = np.arange(10).astype("datetime64[D]")
+    ds = make_time_dataset(times)
+
+    with pytest.raises(ValueError):
+        select_relevant_times(
+            ds,
+            "time",
+            "time",
+            datetime(2024, 1, 1),
+            climatology=True,
+            end_time=datetime(2024, 1, 2),
+        )
+
+
+def test_climatology_pass_through():
+    times = np.arange(12)
+    ds = make_time_dataset(times)
+
+    out = select_relevant_times(
+        ds,
+        "time",
+        "time",
+        datetime(2024, 1, 1),
+        end_time=datetime(2024, 1, 10),
+        climatology=True,
+    )
+    assert out.equals(ds)
+
+
+def test_int_time_rejected():
+    ds = xr.Dataset(
+        data_vars={"var": ("time", [1, 2, 3])},
+        coords={"time": [1, 2, 3]},
+    )
+
+    with pytest.raises(ValueError):
+        select_relevant_times(
+            ds, "time", "time", datetime(2024, 1, 1), datetime(2024, 1, 2)
+        )
+
+
+def test_cftime_conversion(monkeypatch):
+    times = xr.DataArray(
+        [cftime.DatetimeGregorian(2024, 1, i + 1) for i in range(3)], dims="time"
+    )
+    ds = xr.Dataset({"var": ("time", [1, 2, 3])}, coords={"time": times})
+
+    # Mock conversion function to ensure it is called
+    def mock_convert(t):
+        return np.array(
+            ["2024-01-01", "2024-01-02", "2024-01-03"], dtype="datetime64[ns]"
+        )
+
+    monkeypatch.setattr(
+        "roms_tools.datasets.utils.convert_cftime_to_datetime", mock_convert
+    )
+
+    out = select_relevant_times(
+        ds, "time", "time", datetime(2024, 1, 1), datetime(2024, 1, 3)
+    )
+
+    assert np.issubdtype(out["time"].dtype, np.datetime64)
+
+
+def test_time_range_selection():
+    times = np.array(
+        ["2024-01-01", "2024-01-02", "2024-01-05", "2024-01-10"], dtype="datetime64[ns]"
+    )
+    ds = make_time_dataset(times)
+
+    out = select_relevant_times(
+        ds,
+        "time",
+        "time",
+        datetime(2024, 1, 2),
+        datetime(2024, 1, 7),
+    )
+
+    # Should include:
+    # - closest before start: 2024-01-02
+    # - records inside strict range: 2024-01-05
+    # - closest after end: 2024-01-10
+    expected_times = np.array(
+        ["2024-01-02", "2024-01-05", "2024-01-10"],
+        dtype="datetime64[ns]",
+    )
+
+    assert np.array_equal(out["time"].values, expected_times)
+
+
+def test_range_selection_missing_before(caplog):
+    times = np.array(["2024-01-05", "2024-01-10"], dtype="datetime64[ns]")
+    ds = make_time_dataset(times)
+
+    with caplog.at_level(logging.WARNING):
+        out = select_relevant_times(
+            ds,
+            "time",
+            "time",
+            datetime(2024, 1, 1),
+            datetime(2024, 1, 12),
+        )
+
+    assert "No records found at or before the start_time" in caplog.text
+    # Should fallback to first record
+    assert out["time"].values[0] == np.datetime64("2024-01-05")
+
+
+def test_range_selection_missing_after(caplog):
+    times = np.array(["2024-01-01", "2024-01-02"], dtype="datetime64[ns]")
+    ds = make_time_dataset(times)
+
+    with caplog.at_level(logging.WARNING):
+        out = select_relevant_times(
+            ds,
+            "time",
+            "time",
+            datetime(2024, 1, 1),
+            datetime(2024, 1, 10),
+        )
+
+    assert "No records found at or after the end_time" in caplog.text
+    assert out["time"].values[-1] == np.datetime64("2024-01-02")
+
+
+# Tests for _select_initial_time
+
+
+def test_initial_time_exact_match():
+    times = np.array(["2024-01-01", "2024-01-02"], dtype="datetime64[ns]")
+    ds = make_time_dataset(times)
+
+    out = _select_initial_time(
+        ds,
+        "time",
+        "time",
+        datetime(2024, 1, 2),
+        climatology=False,
+        allow_flex_time=False,
+    )
+
+    assert out["time"].values == np.datetime64("2024-01-02")
+
+
+def test_initial_time_no_exact_match():
+    times = np.array(["2024-01-01", "2024-01-03"], dtype="datetime64[ns]")
+    ds = make_time_dataset(times)
+
+    with pytest.raises(ValueError):
+        _select_initial_time(
+            ds,
+            "time",
+            "time",
+            datetime(2024, 1, 2),
+            climatology=False,
+            allow_flex_time=False,
+        )
+
+
+def test_initial_flexible_time():
+    times = np.array(["2024-01-01", "2024-01-02", "2024-01-15"], dtype="datetime64[ns]")
+    ds = make_time_dataset(times)
+
+    out = _select_initial_time(
+        ds,
+        "time",
+        "time",
+        datetime(2024, 1, 1),
+        climatology=False,
+        allow_flex_time=True,
+    )
+
+    assert out["time"].values == np.datetime64("2024-01-01")
+
+
+def test_initial_flexible_time_out_of_range():
+    times = np.array(["2024-01-10", "2024-01-11"], dtype="datetime64[ns]")
+    ds = make_time_dataset(times)
+
+    with pytest.raises(ValueError):
+        _select_initial_time(
+            ds,
+            "time",
+            "time",
+            datetime(2024, 1, 1),
+            climatology=False,
+            allow_flex_time=True,
+        )
+
+
+# tests for get_time_type
+
+
+def test_get_time_type_datetime():
+    times = np.array(["2020-01-01", "2020-01-02"], dtype="datetime64[ns]")
+    da = xr.DataArray(times)
+    assert get_time_type(da) == "datetime"
+
+
+def test_get_time_type_cftime():
+    times = np.array(
+        [
+            cftime.DatetimeNoLeap(2000, 1, 1),
+            cftime.DatetimeNoLeap(2000, 1, 2),
+        ],
+        dtype=object,
+    )
+    da = xr.DataArray(times)
+    assert get_time_type(da) == "cftime"
+
+
+def test_get_time_type_integer():
+    da = xr.DataArray(np.array([1, 2, 3], dtype=int))
+    assert get_time_type(da) == "int"
+
+
+def test_get_time_type_unsupported_type():
+    da = xr.DataArray(np.array(["a", "b"], dtype=object))
+    with pytest.raises(ValueError, match="Unsupported data type"):
+        get_time_type(da)
+
+
+def test_get_time_type_invalid_input_type():
+    da = xr.DataArray("not-an-array")
+    with pytest.raises(ValueError):
+        get_time_type(da)
+
+
+# Tests for convert_cftime_to_datetime
+
+
+def test_convert_cftime_to_datetime_basic():
+    arr = np.array(
+        [
+            cftime.DatetimeNoLeap(2000, 1, 1),
+            cftime.DatetimeNoLeap(2000, 1, 2),
+        ]
+    )
+
+    converted = convert_cftime_to_datetime(arr)
+
+    assert converted.dtype == "datetime64[ns]"
+    assert converted[0] == np.datetime64("2000-01-01")
+    assert converted[1] == np.datetime64("2000-01-02")
+
+
+def test_convert_cftime_to_datetime_mixed_inputs():
+    arr = np.array(
+        [
+            cftime.DatetimeNoLeap(2000, 1, 1),
+            "2001-01-01",
+            np.datetime64("2002-01-01"),
+        ],
+        dtype=object,
+    )
+
+    converted = convert_cftime_to_datetime(arr)
+
+    assert converted[0] == np.datetime64("2000-01-01")
+    assert converted[1] == np.datetime64("2001-01-01")
+    assert converted[2] == np.datetime64("2002-01-01")
+
+
+def test_convert_cftime_to_datetime_returns_numpy_array():
+    arr = np.array([cftime.DatetimeNoLeap(1999, 12, 31)])
+    converted = convert_cftime_to_datetime(arr)
+    assert isinstance(converted, np.ndarray)

roms_tools/tests/{test_setup/test_fill.py → test_fill.py}

@@ -2,7 +2,7 @@ import numpy as np
 import pytest
 import xarray as xr
 
-from roms_tools.setup.fill import LateralFill
+from roms_tools.fill import LateralFill
 
 
 @pytest.mark.parametrize(
@@ -19,12 +19,12 @@ def test_lateral_fill_no_nans(data_fixture, request):
     data = request.getfixturevalue(data_fixture)
     lateral_fill = LateralFill(
         data.ds["mask"],
-        [data.dim_names["latitude"], data.dim_names["longitude"]],
+        (data.dim_names["latitude"], data.dim_names["longitude"]),
     )
     if "mask_vel" in data.ds.data_vars:
         lateral_fill_vel = LateralFill(
             data.ds["mask_vel"],
-            [data.dim_names["latitude"], data.dim_names["longitude"]],
+            (data.dim_names["latitude"], data.dim_names["longitude"]),
         )
 
     for var in data.var_names:
@@ -40,10 +40,10 @@ def test_lateral_fill_no_nans(data_fixture, request):
 def test_lateral_fill_correct_order_of_magnitude(coarsened_cesm_bgc_data):
     lateral_fill = LateralFill(
         coarsened_cesm_bgc_data.ds["mask"],
-        [
+        (
             coarsened_cesm_bgc_data.dim_names["latitude"],
             coarsened_cesm_bgc_data.dim_names["longitude"],
-        ],
+        ),
     )
 
     ALK = coarsened_cesm_bgc_data.ds["ALK"]
@@ -78,21 +78,21 @@ def test_lateral_fill_reproducibility(data_fixture, request):
     data = request.getfixturevalue(data_fixture)
     lateral_fill0 = LateralFill(
         data.ds["mask"],
-        [data.dim_names["latitude"], data.dim_names["longitude"]],
+        (data.dim_names["latitude"], data.dim_names["longitude"]),
     )
     if "mask_vel" in data.ds.data_vars:
         lateral_fill_vel0 = LateralFill(
             data.ds["mask_vel"],
-            [data.dim_names["latitude"], data.dim_names["longitude"]],
+            (data.dim_names["latitude"], data.dim_names["longitude"]),
         )
     lateral_fill1 = LateralFill(
         data.ds["mask"],
-        [data.dim_names["latitude"], data.dim_names["longitude"]],
+        (data.dim_names["latitude"], data.dim_names["longitude"]),
     )
     if "mask_vel" in data.ds.data_vars:
         lateral_fill_vel1 = LateralFill(
             data.ds["mask_vel"],
-            [data.dim_names["latitude"], data.dim_names["longitude"]],
+            (data.dim_names["latitude"], data.dim_names["longitude"]),
         )
 
     ds0 = data.ds.copy()
@@ -116,3 +116,66 @@ def test_lateral_fill_reproducibility(data_fixture, request):
             )
 
     assert ds0.equals(ds1)
+
+
+def test_lateralfill_raises_notimplemented_for_non2d_mask():
+    mask_3d = xr.DataArray(np.ones((3, 3, 3)), dims=("eta_rho", "xi_rho", "s_rho"))
+    with pytest.raises(
+        NotImplementedError, match="LateralFill currently supports only 2D masks"
+    ):
+        LateralFill(mask_3d, dims=("eta_rho", "xi_rho"))
+
+
+def test_lateralfill_raises_valueerror_for_list_of_dims():
+    mask = xr.DataArray(np.ones((3, 3)), dims=("eta_rho", "xi_rho"))
+    with pytest.raises(TypeError, match="must be a tuple"):
+        LateralFill(mask, dims=["eta_rho", "xi_rho"])
+
+
+def test_lateralfill_raises_valueerror_for_wrong_number_of_dims():
+    mask = xr.DataArray(np.ones((3, 3)), dims=("eta_rho", "xi_rho"))
+
+    with pytest.raises(ValueError, match="must contain exactly two"):
+        LateralFill(mask, dims=("eta_rho", "xi_rho", "extra_dim"))  # 3 dims
+
+
+def test_lateralfill_raises_valueerror_for_mask_dim_order_mismatch():
+    mask = xr.DataArray(np.ones((3, 3)), dims=("xi_rho", "eta_rho"))  # dims reversed
+    with pytest.raises(ValueError, match="dimension order is incorrect"):
+        LateralFill(mask, dims=("eta_rho", "xi_rho"))
+
+
+def test_apply_raises_if_var_missing_dims():
+    mask = xr.DataArray(np.ones((3, 3)), dims=("eta_rho", "xi_rho"))
+    lf = LateralFill(mask, dims=("eta_rho", "xi_rho"))
+    var = xr.DataArray(np.ones((3, 3)), dims=("eta_rho", "eta_u"))  # missing xi_rho
+    with pytest.raises(
+        ValueError, match="does not contain the required horizontal dimensions"
+    ):
+        lf.apply(var)
+
+
+def test_apply_raises_if_var_dim_order_mismatch():
+    mask = xr.DataArray(np.ones((3, 3)), dims=("eta_rho", "xi_rho"))
+    lf = LateralFill(mask, dims=("eta_rho", "xi_rho"))
+    var = xr.DataArray(np.ones((3, 3)), dims=("xi_rho", "eta_rho"))  # wrong order
+    with pytest.raises(ValueError, match="dimension order is incorrect"):
+        lf.apply(var)
+
+
+def test_apply_raises_if_var_has_nans_on_valid_mask():
+    # 2D mask
+    mask = xr.DataArray(np.ones((3, 3), dtype=bool), dims=("eta_rho", "xi_rho"))
+
+    lf = LateralFill(mask, dims=("eta_rho", "xi_rho"))
+
+    # Variable with a NaN at a location where mask is True
+    data = np.ones((3, 3))
+    data[1, 1] = np.nan
+    var = xr.DataArray(data, dims=("eta_rho", "xi_rho"))
+
+    # Expect ValueError
+    with pytest.raises(
+        ValueError, match="contains NaNs at grid points marked as valid"
+    ):
+        lf.apply(var)