roms-tools 1.4.2__py3-none-any.whl → 1.5.0__py3-none-any.whl

roms_tools/tests/test_setup/test_data/bgc_surface_forcing.zarr/.zattrs

@@ -2,7 +2,7 @@
     "correct_radiation": "False",
     "end_time": "2020-02-01 00:00:00",
     "model_reference_date": "2000-01-01 00:00:00",
-    "roms_tools_version": "0.1.dev152+dirty",
+    "roms_tools_version": "0.1.dev138+dirty",
     "source": "CESM_REGRIDDED",
     "start_time": "2020-02-01 00:00:00",
     "title": "ROMS surface forcing file created by ROMS-Tools",

roms_tools/tests/test_setup/test_data/bgc_surface_forcing.zarr/.zmetadata

@@ -4,7 +4,7 @@
             "correct_radiation": "False",
             "end_time": "2020-02-01 00:00:00",
             "model_reference_date": "2000-01-01 00:00:00",
-            "roms_tools_version": "0.1.dev152+dirty",
+            "roms_tools_version": "0.1.dev138+dirty",
             "source": "CESM_REGRIDDED",
             "start_time": "2020-02-01 00:00:00",
             "title": "ROMS surface forcing file created by ROMS-Tools",

roms_tools/tests/test_setup/test_data/bgc_surface_forcing_from_climatology.zarr/.zattrs

@@ -3,7 +3,7 @@
     "correct_radiation": "False",
     "end_time": "2020-02-01 00:00:00",
     "model_reference_date": "2000-01-01 00:00:00",
-    "roms_tools_version": "0.1.dev152+dirty",
+    "roms_tools_version": "0.1.dev138+dirty",
     "source": "CESM_REGRIDDED",
     "start_time": "2020-02-01 00:00:00",
     "title": "ROMS surface forcing file created by ROMS-Tools",

roms_tools/tests/test_setup/test_data/bgc_surface_forcing_from_climatology.zarr/.zmetadata

@@ -5,7 +5,7 @@
             "correct_radiation": "False",
             "end_time": "2020-02-01 00:00:00",
             "model_reference_date": "2000-01-01 00:00:00",
-            "roms_tools_version": "0.1.dev152+dirty",
+            "roms_tools_version": "0.1.dev138+dirty",
             "source": "CESM_REGRIDDED",
             "start_time": "2020-02-01 00:00:00",
             "title": "ROMS surface forcing file created by ROMS-Tools",

roms_tools/tests/test_setup/test_data/boundary_forcing.zarr/.zattrs

@@ -2,7 +2,7 @@
     "end_time": "2021-06-30 00:00:00",
     "hc": 250.0,
     "model_reference_date": "2000-01-01 00:00:00",
-    "roms_tools_version": "0.1.dev152+dirty",
+    "roms_tools_version": "0.1.dev157+dirty",
     "source": "GLORYS",
     "start_time": "2021-06-29 00:00:00",
     "theta_b": 2.0,

roms_tools/tests/test_setup/test_data/boundary_forcing.zarr/.zmetadata

@@ -4,7 +4,7 @@
             "end_time": "2021-06-30 00:00:00",
             "hc": 250.0,
             "model_reference_date": "2000-01-01 00:00:00",
-            "roms_tools_version": "0.1.dev152+dirty",
+            "roms_tools_version": "0.1.dev157+dirty",
             "source": "GLORYS",
             "start_time": "2021-06-29 00:00:00",
             "theta_b": 2.0,

roms_tools/tests/test_setup/test_data/initial_conditions_with_bgc_from_climatology.zarr/.zattrs

@@ -3,7 +3,7 @@
     "hc": 250.0,
     "ini_time": "2021-06-29 00:00:00",
     "model_reference_date": "2000-01-01 00:00:00",
-    "roms_tools_version": "0.1.dev152+dirty",
+    "roms_tools_version": "0.1.dev157+dirty",
     "source": "GLORYS",
     "theta_b": 2.0,
     "theta_s": 5.0,

roms_tools/tests/test_setup/test_data/initial_conditions_with_bgc_from_climatology.zarr/.zmetadata

@@ -5,7 +5,7 @@
             "hc": 250.0,
             "ini_time": "2021-06-29 00:00:00",
             "model_reference_date": "2000-01-01 00:00:00",
-            "roms_tools_version": "0.1.dev152+dirty",
+            "roms_tools_version": "0.1.dev157+dirty",
             "source": "GLORYS",
             "theta_b": 2.0,
             "theta_s": 5.0,

roms_tools/tests/test_setup/test_fill.py

@@ -23,14 +23,15 @@ def era5_data(request, use_dask):
         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")
+    # the following GLORYS data has a wide enough domain
+    # to have different masks for tracers vs. velocities
+    fname = download_test_data("GLORYS_test_data.nc")
 
     data = GLORYSDataset(
         filename=fname,
@@ -38,7 +39,9 @@ def glorys_data(request, use_dask):
         end_time=datetime(2013, 1, 1),
         use_dask=use_dask,
     )
-    data.post_process()
+
+    ds = data.ds.isel(depth=[0, 10, 30])
+    object.__setattr__(data, "ds", ds)
 
     # extrapolate deepest value to bottom so all levels can use the same surface mask
     for var in data.var_names:
@@ -58,7 +61,6 @@ def tpxo_data(request, use_dask):
         filename=fname,
         use_dask=use_dask,
     )
-    data.post_process()
 
     return data
 
@@ -74,7 +76,6 @@ def cesm_bgc_data(request, use_dask):
         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:
@@ -105,15 +106,25 @@ def cesm_surface_bgc_data(request, use_dask):
     "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):
+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"]],
     )
+    if "mask_vel" in data.ds.data_vars:
+        lateral_fill_vel = LateralFill(
+            data.ds["mask_vel"],
+            [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))
+        if var in ["u", "v"]:
+            filled = lateral_fill_vel.apply(
+                data.ds[data.var_names[var]].astype(np.float64)
+            )
+        else:
+            filled = lateral_fill.apply(data.ds[data.var_names[var]].astype(np.float64))
         assert not filled.isnull().any()
 
 
@@ -150,28 +161,46 @@ def test_lateral_fill_correct_order_of_magnitude(cesm_bgc_data):
         "glorys_data",
     ],
 )
-def test_lateral_fill_reproducibility(data_fixture, request, use_dask):
+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"]],
     )
+    if "mask_vel" in data.ds.data_vars:
+        lateral_fill_vel0 = LateralFill(
+            data.ds["mask_vel"],
+            [data.dim_names["latitude"], data.dim_names["longitude"]],
+        )
     lateral_fill1 = LateralFill(
         data.ds["mask"],
         [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"]],
+        )
 
     ds0 = data.ds.copy()
     ds1 = data.ds.copy()
 
     for var in data.var_names:
+        if var in ["u", "v"]:
+            ds0[data.var_names[var]] = lateral_fill_vel0.apply(
+                ds0[data.var_names[var]].astype(np.float64)
+            )
+            ds1[data.var_names[var]] = lateral_fill_vel1.apply(
+                ds1[data.var_names[var]].astype(np.float64)
+            )
 
-        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)
-        )
+        else:
+            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_regrid.py

@@ -0,0 +1,59 @@
+import pytest
+import numpy as np
+import xarray as xr
+from roms_tools.setup.regrid import VerticalRegrid
+
+
+def vertical_regridder(depth_values, layer_depth_rho_values):
+    class DataContainer:
+        """Mock class for holding data and dimension names."""
+
+        def __init__(self, ds):
+            self.ds = ds
+            self.dim_names = {"depth": "depth"}
+
+    class Grid:
+        """Mock class representing the grid object with layer depth information."""
+
+        def __init__(self, ds):
+            self.ds = ds
+
+    # Creating minimal mock data for testing
+    # Depth levels in meters
+
+    # Create mock datasets for DataContainer and Grid
+    data_ds = xr.Dataset({"depth": (["depth"], depth_values)})
+    target_depth = xr.DataArray(data=layer_depth_rho_values, dims=["s_rho"])
+    # Instantiate DataContainer and Grid objects with mock datasets
+    mock_data = DataContainer(data_ds)
+
+    return VerticalRegrid(mock_data, target_depth)
+
+
+@pytest.mark.parametrize(
+    "depth_values, layer_depth_rho_values, temp_data",
+    [
+        ([5, 50, 100, 150], [130, 100, 70, 30, 10], [30, 25, 10, 2]),
+        ([5, 50, 100, 150], [130, 100, 70, 30, 2], [30, 25, 10, 2]),
+        ([5, 50, 100, 150], [200, 100, 70, 30, 10], [30, 25, 10, 2]),
+        ([5, 50, 100, 150], [200, 100, 70, 30, 1], [30, 25, 10, 2]),
+    ],
+)
+def test_vertical_regrid(request, depth_values, layer_depth_rho_values, temp_data):
+
+    vertical_regrid = vertical_regridder(
+        depth_values=depth_values, layer_depth_rho_values=layer_depth_rho_values
+    )
+    data = xr.Dataset({"temp_data": (["depth"], temp_data)})
+
+    # without filling in NaNs
+    regridded = vertical_regrid.apply(data.temp_data, fill_nans=False)
+    expected = np.interp(
+        layer_depth_rho_values, depth_values, temp_data, left=np.nan, right=np.nan
+    )
+    assert np.allclose(expected, regridded.data, equal_nan=True)
+
+    # with filling in NaNs
+    regridded = vertical_regrid.apply(data.temp_data, fill_nans=True)
+    expected = np.interp(layer_depth_rho_values, depth_values, temp_data)
+    assert np.allclose(expected, regridded.data, equal_nan=True)

roms_tools/tests/test_setup/test_surface_forcing.py

@@ -1,5 +1,6 @@
 import pytest
 from datetime import datetime
+import xarray as xr
 from roms_tools import Grid, SurfaceForcing
 from roms_tools.setup.download import download_test_data
 import textwrap
@@ -487,6 +488,23 @@ def test_surface_forcing_creation(
     sfc_forcing.plot("pco2_air", time=0)
 
 
+@pytest.mark.parametrize(
+    "sfc_forcing_fixture",
+    [
+        "bgc_surface_forcing",
+        "bgc_surface_forcing_from_climatology",
+    ],
+)
+def test_surface_forcing_pco2_replication(sfc_forcing_fixture, request):
+    """Test whether pco2_air and pco2_air_alt is the same after processing."""
+
+    sfc_forcing = request.getfixturevalue(sfc_forcing_fixture)
+
+    xr.testing.assert_allclose(
+        sfc_forcing.ds.pco2_air, sfc_forcing.ds.pco2_air_alt, rtol=1.0e-5
+    )
+
+
 @pytest.mark.parametrize(
     "sfc_forcing_fixture",
     [

{roms_tools-1.4.2.dist-info → roms_tools-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 1.4.2
+Version: 1.5.0
 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
@@ -47,7 +47,7 @@ A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla
 
 <mark>**DISCLAIMER**: This project is **ALPHA** and will be **EXPERIMENTAL** at least throughout Fall 2024. We do not recommend to use this software before this ALPHA development and test phase is completed.</mark>
 
-## Installation instructions
+## Installation
 
 ### Installation from pip