roms-tools 1.3.0__py3-none-any.whl → 1.4.0__py3-none-any.whl

roms_tools/tests/test_setup/test_fill.py

@@ -0,0 +1,177 @@
+import pytest
+from roms_tools.setup.datasets import (
+    GLORYSDataset,
+    ERA5Dataset,
+    CESMBGCDataset,
+    CESMBGCSurfaceForcingDataset,
+    TPXODataset,
+)
+from roms_tools.setup.download import download_test_data
+from roms_tools.setup.fill import LateralFill
+from roms_tools.setup.utils import extrapolate_deepest_to_bottom
+from datetime import datetime
+import numpy as np
+import xarray as xr
+
+
+@pytest.fixture()
+def era5_data(request, use_dask):
+    fname = download_test_data("ERA5_regional_test_data.nc")
+    data = ERA5Dataset(
+        filename=fname,
+        start_time=datetime(2020, 1, 31),
+        end_time=datetime(2020, 2, 2),
+        use_dask=use_dask,
+    )
+    data.post_process()
+
+    return data
+
+
+@pytest.fixture()
+def glorys_data(request, use_dask):
+    fname = download_test_data("GLORYS_NA_2012.nc")
+
+    data = GLORYSDataset(
+        filename=fname,
+        start_time=datetime(2012, 1, 1),
+        end_time=datetime(2013, 1, 1),
+        use_dask=use_dask,
+    )
+    data.post_process()
+
+    # extrapolate deepest value to bottom so all levels can use the same surface mask
+    for var in data.var_names:
+        if var != "zeta":
+            data.ds[data.var_names[var]] = extrapolate_deepest_to_bottom(
+                data.ds[data.var_names[var]], data.dim_names["depth"]
+            )
+
+    return data
+
+
+@pytest.fixture()
+def tpxo_data(request, use_dask):
+    fname = download_test_data("TPXO_regional_test_data.nc")
+
+    data = TPXODataset(
+        filename=fname,
+        use_dask=use_dask,
+    )
+    data.post_process()
+
+    return data
+
+
+@pytest.fixture()
+def cesm_bgc_data(request, use_dask):
+    fname = download_test_data("CESM_BGC_2012.nc")
+
+    data = CESMBGCDataset(
+        filename=fname,
+        start_time=datetime(2012, 1, 1),
+        end_time=datetime(2013, 1, 1),
+        climatology=False,
+        use_dask=use_dask,
+    )
+    data.post_process()
+
+    # extrapolate deepest value to bottom so all levels can use the same surface mask
+    for var in data.var_names:
+        data.ds[data.var_names[var]] = extrapolate_deepest_to_bottom(
+            data.ds[data.var_names[var]], data.dim_names["depth"]
+        )
+
+    return data
+
+
+@pytest.fixture()
+def cesm_surface_bgc_data(request, use_dask):
+    fname = download_test_data("CESM_BGC_SURFACE_2012.nc")
+
+    data = CESMBGCSurfaceForcingDataset(
+        filename=fname,
+        start_time=datetime(2012, 1, 1),
+        end_time=datetime(2013, 1, 1),
+        climatology=False,
+        use_dask=use_dask,
+    )
+    data.post_process()
+
+    return data
+
+
+@pytest.mark.parametrize(
+    "data_fixture",
+    ["era5_data", "glorys_data", "tpxo_data", "cesm_bgc_data", "cesm_surface_bgc_data"],
+)
+def test_lateral_fill_no_nans(data_fixture, request, use_dask):
+    data = request.getfixturevalue(data_fixture)
+    lateral_fill = LateralFill(
+        data.ds["mask"],
+        [data.dim_names["latitude"], data.dim_names["longitude"]],
+    )
+
+    for var in data.var_names:
+        filled = lateral_fill.apply(data.ds[data.var_names[var]].astype(np.float64))
+        assert not filled.isnull().any()
+
+
+def test_lateral_fill_correct_order_of_magnitude(cesm_bgc_data):
+
+    lateral_fill = LateralFill(
+        cesm_bgc_data.ds["mask"],
+        [cesm_bgc_data.dim_names["latitude"], cesm_bgc_data.dim_names["longitude"]],
+    )
+
+    ALK = cesm_bgc_data.ds["ALK"]
+
+    # zero out alkalinity field in all depth levels but the uppermost
+    ALK = xr.where(cesm_bgc_data.ds.ALK.depth > 25, 0, cesm_bgc_data.ds.ALK)
+    ALK = ALK.where(cesm_bgc_data.ds.mask)
+
+    filled = lateral_fill.apply(ALK.astype(np.float64))
+
+    # check that alkalinity values in the uppermost values are of the correct order of magnitude
+    # and that no new minima and maxima are introduced
+    assert filled.isel(depth=0).min() == ALK.isel(depth=0).min()
+    assert filled.isel(depth=0).max() == ALK.isel(depth=0).max()
+
+    # check that the filled alkalinity values are zero in all deeper layers
+    assert filled.isel(depth=slice(1, None)).equals(
+        xr.zeros_like(filled.isel(depth=slice(1, None)))
+    )
+
+
+@pytest.mark.parametrize(
+    "data_fixture",
+    [
+        "era5_data",
+        "glorys_data",
+    ],
+)
+def test_lateral_fill_reproducibility(data_fixture, request, use_dask):
+
+    data = request.getfixturevalue(data_fixture)
+    lateral_fill0 = LateralFill(
+        data.ds["mask"],
+        [data.dim_names["latitude"], data.dim_names["longitude"]],
+    )
+    lateral_fill1 = LateralFill(
+        data.ds["mask"],
+        [data.dim_names["latitude"], data.dim_names["longitude"]],
+    )
+
+    ds0 = data.ds.copy()
+    ds1 = data.ds.copy()
+
+    for var in data.var_names:
+
+        ds0[data.var_names[var]] = lateral_fill0.apply(
+            ds0[data.var_names[var]].astype(np.float64)
+        )
+        ds1[data.var_names[var]] = lateral_fill1.apply(
+            ds1[data.var_names[var]].astype(np.float64)
+        )
+
+    assert ds0.equals(ds1)

roms_tools/tests/test_setup/test_initial_conditions.py

@@ -6,8 +6,8 @@ import numpy as np
 import textwrap
 from roms_tools.setup.download import download_test_data
 from roms_tools.setup.datasets import CESMBGCDataset
-from conftest import calculate_file_hash
 from pathlib import Path
+from conftest import calculate_file_hash
 
 
 @pytest.mark.parametrize(
@@ -143,7 +143,7 @@ def test_initial_conditions_default_bgc_climatology(example_grid, use_dask):
         use_dask=use_dask,
     )
 
-    assert initial_conditions.bgc_source["climatology"] is True
+    assert initial_conditions.bgc_source["climatology"] is False
 
 
 def test_interpolation_from_climatology(
@@ -159,6 +159,7 @@ def test_interpolation_from_climatology(
         start_time=datetime(2012, 1, 15),
         climatology=True,
         use_dask=use_dask,
+        apply_post_processing=False,
     )
     assert np.allclose(ds["ALK"].sel(month=1), bgc_data.ds["ALK"], equal_nan=True)
 
@@ -168,6 +169,7 @@ def test_interpolation_from_climatology(
         start_time=datetime(2012, 1, 30),
         climatology=True,
         use_dask=use_dask,
+        apply_post_processing=False,
     )
     assert np.allclose(
         0.5 * (ds["ALK"].sel(month=1) + ds["ALK"].sel(month=2)),
@@ -272,7 +274,7 @@ def test_roundtrip_yaml(initial_conditions, tmp_path, use_dask):
 
 def test_files_have_same_hash(initial_conditions, tmp_path, use_dask):
 
-    yaml_filepath = tmp_path / "test_yaml"
+    yaml_filepath = tmp_path / "test_yaml.yaml"
     filepath1 = tmp_path / "test1.nc"
     filepath2 = tmp_path / "test2.nc"
 

roms_tools/tests/test_setup/test_surface_forcing.py

@@ -3,8 +3,8 @@ from datetime import datetime
 from roms_tools import Grid, SurfaceForcing
 from roms_tools.setup.download import download_test_data
 import textwrap
-from conftest import calculate_file_hash
 from pathlib import Path
+from conftest import calculate_file_hash
 
 
 @pytest.fixture
@@ -643,7 +643,7 @@ def test_files_have_same_hash(sfc_forcing_fixture, request, tmp_path, use_dask):
 
     sfc_forcing = request.getfixturevalue(sfc_forcing_fixture)
 
-    yaml_filepath = tmp_path / "test_yaml"
+    yaml_filepath = tmp_path / "test_yaml.yaml"
     filepath1 = tmp_path / "test1.nc"
     filepath2 = tmp_path / "test2.nc"
 

roms_tools/tests/test_setup/test_tides.py

@@ -3,8 +3,8 @@ from roms_tools import Grid, TidalForcing
 import xarray as xr
 from roms_tools.setup.download import download_test_data
 import textwrap
-from conftest import calculate_file_hash
 from pathlib import Path
+from conftest import calculate_file_hash
 
 
 @pytest.fixture
@@ -232,10 +232,13 @@ def test_roundtrip_yaml(tidal_forcing, tmp_path, use_dask):
 
 def test_files_have_same_hash(tidal_forcing, tmp_path, use_dask):
 
-    yaml_filepath = tmp_path / "test_yaml"
+    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

@@ -69,4 +69,4 @@ def test_check_results(forcing_fixture, request):
 
     forcing = request.getfixturevalue(forcing_fixture)
 
-    xr.testing.assert_allclose(forcing.ds, expected_forcing_ds)
+    xr.testing.assert_allclose(forcing.ds, expected_forcing_ds, rtol=1.0e-5)

{roms_tools-1.3.0.dist-info → roms_tools-1.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 1.3.0
+Version: 1.4.0
 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
@@ -26,9 +26,10 @@ Requires-Dist: cartopy
 Requires-Dist: packaging
 Requires-Dist: scipy
 Requires-Dist: gcm-filters
-Requires-Dist: numba
 Requires-Dist: netcdf4
 Requires-Dist: PyYAML
+Requires-Dist: pyamg
+Requires-Dist: bottleneck
 Provides-Extra: dask
 Requires-Dist: dask; extra == "dask"
 
@@ -52,6 +53,13 @@ A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla
 pip install roms-tools
 ```
 
+If you want to use `ROMS-Tools` together with dask (which we recommend), you can
+install `ROMS-Tools` along with the additional dependency via:
+
+```bash
+pip install roms-tools[dask]
+```
+
 ### Installation from GitHub
 
 To obtain the latest development version, first clone the source repository:
@@ -75,7 +83,7 @@ pip install -e .
 ```
 
 If you want to use `ROMS-Tools` together with dask (which we recommend), you can
-install the additional dependency via:
+install `ROMS-Tools` along with the additional dependency via:
 
 ```bash
 pip install -e .[dask]