roms-tools 1.7.0__py3-none-any.whl → 2.1.0__py3-none-any.whl

roms_tools/tests/test_setup/test_river_forcing.py

@@ -61,7 +61,11 @@ def compare_dictionaries(dict1, dict2):
 
 @pytest.mark.parametrize(
     "river_forcing_fixture",
-    ["river_forcing", "river_forcing_for_grid_that_straddles_dateline"],
+    [
+        "river_forcing",
+        "river_forcing_for_grid_that_straddles_dateline",
+        "river_forcing_with_bgc",
+    ],
 )
 def test_successful_initialization_with_climatological_dai_data(
     river_forcing_fixture, request
@@ -121,7 +125,11 @@ def test_reproducibility_indices(river_forcing, river_forcing_no_climatology):
 
 @pytest.mark.parametrize(
     "river_forcing_fixture",
-    ["river_forcing_climatology", "river_forcing_no_climatology"],
+    [
+        "river_forcing_climatology",
+        "river_forcing_no_climatology",
+        "river_forcing_with_bgc",
+    ],
 )
 def test_constant_tracers(river_forcing_fixture, request):
     river_forcing = request.getfixturevalue(river_forcing_fixture)
@@ -132,11 +140,18 @@ def test_constant_tracers(river_forcing_fixture, request):
     np.testing.assert_allclose(
         river_forcing.ds.river_tracer.isel(ntracers=1).values, 1.0, atol=0
     )
+    np.testing.assert_allclose(
+        river_forcing.ds.river_tracer.isel(ntracers=slice(2, None)).values, 0.0, atol=0
+    )
 
 
 @pytest.mark.parametrize(
     "river_forcing_fixture",
-    ["river_forcing_climatology", "river_forcing_no_climatology"],
+    [
+        "river_forcing_climatology",
+        "river_forcing_no_climatology",
+        "river_forcing_with_bgc",
+    ],
 )
 def test_river_locations_are_along_coast(river_forcing_fixture, request):
     river_forcing = request.getfixturevalue(river_forcing_fixture)
@@ -228,16 +243,18 @@ def test_update_river_flux_variable_without_conflicts(river_forcing, tmp_path):
     assert isinstance(another_river_forcing.ds, xr.Dataset)
 
 
-def test_river_forcing_plot(river_forcing):
+def test_river_forcing_plot(river_forcing_with_bgc):
     """Test plot method."""
 
-    river_forcing.plot_locations()
-    river_forcing.plot("river_volume")
-    river_forcing.plot("river_temperature")
-    river_forcing.plot("river_salinity")
+    river_forcing_with_bgc.plot_locations()
+    river_forcing_with_bgc.plot("river_volume")
+    river_forcing_with_bgc.plot("river_temp")
+    river_forcing_with_bgc.plot("river_salt")
+    river_forcing_with_bgc.plot("river_ALK")
+    river_forcing_with_bgc.plot("river_PO4")
 
 
-def test_river_forcing_save(river_forcing, tmp_path):
+def test_river_forcing_save(river_forcing_with_bgc, tmp_path):
     """Test save method."""
 
     for file_str, grid_file_str in zip(
@@ -250,7 +267,7 @@ def test_river_forcing_save(river_forcing, tmp_path):
         ):  # test for Path object and str
 
             # Test saving without partitioning
-            saved_filenames = river_forcing.save(filepath, grid_filepath)
+            saved_filenames = river_forcing_with_bgc.save(filepath, grid_filepath)
             # Check if the .nc file was created
             filepath = Path(filepath).with_suffix(".nc")
             grid_filepath = Path(grid_filepath).with_suffix(".nc")
@@ -262,7 +279,7 @@ def test_river_forcing_save(river_forcing, tmp_path):
             grid_filepath.unlink()
 
             # Test saving with partitioning
-            saved_filenames = river_forcing.save(
+            saved_filenames = river_forcing_with_bgc.save(
                 filepath, grid_filepath, np_eta=3, np_xi=3
             )
 
@@ -277,10 +294,20 @@ def test_river_forcing_save(river_forcing, tmp_path):
                 expected_filepath.unlink()
 
 
-def test_roundtrip_yaml(river_forcing, tmp_path):
+@pytest.mark.parametrize(
+    "river_forcing_fixture",
+    [
+        "river_forcing_climatology",
+        "river_forcing_no_climatology",
+        "river_forcing_with_bgc",
+    ],
+)
+def test_roundtrip_yaml(river_forcing_fixture, request, tmp_path):
     """Test that creating an RiverForcing object, saving its parameters to yaml file,
     and re-opening yaml file creates the same object."""
 
+    river_forcing = request.getfixturevalue(river_forcing_fixture)
+
     # Create a temporary filepath using the tmp_path fixture
     file_str = "test_yaml"
     for filepath in [
@@ -298,7 +325,17 @@ def test_roundtrip_yaml(river_forcing, tmp_path):
         filepath.unlink()
 
 
-def test_files_have_same_hash(river_forcing, tmp_path):
+@pytest.mark.parametrize(
+    "river_forcing_fixture",
+    [
+        "river_forcing_climatology",
+        "river_forcing_no_climatology",
+        "river_forcing_with_bgc",
+    ],
+)
+def test_files_have_same_hash(river_forcing_fixture, request, tmp_path):
+
+    river_forcing = request.getfixturevalue(river_forcing_fixture)
 
     yaml_filepath = tmp_path / "test_yaml.yaml"
     filepath1 = tmp_path / "test1.nc"
@@ -323,7 +360,7 @@ def test_files_have_same_hash(river_forcing, tmp_path):
     grid_filepath2.unlink()
 
 
-def test_from_yaml_missing_initial_conditions(tmp_path):
+def test_from_yaml_missing_river_forcing(tmp_path):
     yaml_content = textwrap.dedent(
         """\
     ---
@@ -337,7 +374,8 @@ def test_from_yaml_missing_initial_conditions(tmp_path):
       center_lon: -10
       center_lat: 61
       rot: -20
-      topography_source: ETOPO5
+      topography_source:
+        name: ETOPO5
       hmin: 5.0
     """
     )

roms_tools/tests/test_setup/test_surface_forcing.py

@@ -153,27 +153,6 @@ def grid_that_lies_west_of_dateline_more_than_five_degrees_away():
     return grid
 
 
-@pytest.fixture
-def grid_that_straddles_180_degree_meridian():
-    """Fixture for creating a domain that straddles 180 degree meridian.
-
-    This is a good test grid for the global ERA5 data, which comes on an [-180, 180]
-    longitude grid.
-    """
-
-    grid = Grid(
-        nx=5,
-        ny=5,
-        size_x=1800,
-        size_y=2400,
-        center_lon=180,
-        center_lat=61,
-        rot=20,
-    )
-
-    return grid
-
-
 @pytest.mark.parametrize(
     "grid_fixture",
     [
@@ -206,6 +185,7 @@ def test_successful_initialization_with_regional_data(grid_fixture, request, use
             start_time=start_time,
             end_time=end_time,
             source={"name": "ERA5", "path": fname},
+            correct_radiation=True,
             use_dask=use_dask,
         )
 
@@ -747,7 +727,8 @@ def test_from_yaml_missing_surface_forcing(tmp_path, use_dask):
       center_lon: -10
       center_lat: 61
       rot: -20
-      topography_source: ETOPO5
+      topography_source:
+        name: ETOPO5
       hmin: 5.0
     """
     )

roms_tools/tests/test_setup/test_tides.py

@@ -266,7 +266,8 @@ def test_from_yaml_missing_tidal_forcing(tmp_path, use_dask):
       center_lon: -10
       center_lat: 61
       rot: -20
-      topography_source: ETOPO5
+      topography_source:
+        name: ETOPO5
       hmin: 5.0
     """
     )

roms_tools/tests/test_setup/test_topography.py

@@ -1,5 +1,7 @@
+import pytest
 from roms_tools import Grid
 from roms_tools.setup.topography import _compute_rfactor
+from roms_tools.setup.download import download_test_data
 import numpy as np
 import numpy.testing as npt
 from scipy.ndimage import label
@@ -52,7 +54,13 @@ def test_hmin_criterion():
     assert grid.hmin == 5.0
     assert np.less_equal(grid.hmin, grid.ds.h.min())
 
-    grid.update_topography_and_mask(hmin=10.0)
+    grid.update_topography(hmin=10.0)
+
+    assert grid.hmin == 10.0
+    assert np.less_equal(grid.hmin, grid.ds.h.min())
+
+    # this should not do anything
+    grid.update_topography()
 
     assert grid.hmin == 10.0
     assert np.less_equal(grid.hmin, grid.ds.h.min())
@@ -94,3 +102,100 @@ def test_mask_topography_boundary():
     np.testing.assert_array_equal(
         grid.ds.mask_rho.isel(xi_rho=-1).data, grid.ds.mask_rho.isel(xi_rho=-2).data
     )
+
+
+@pytest.fixture()
+def grid_that_straddles_dateline_with_shifted_global_etopo_data():
+
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=0,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "ETOPO5",
+            "path": download_test_data("etopo5_coarsened_and_shifted.nc"),
+        },
+    )
+
+    return grid
+
+
+@pytest.fixture()
+def grid_that_straddles_dateline_with_global_srtm15_data():
+
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=0,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "SRTM15",
+            "path": download_test_data("srtm15_coarsened.nc"),
+        },
+    )
+
+    return grid
+
+
+@pytest.fixture()
+def grid_that_straddles_180_degree_meridian_with_shifted_global_etopo_data():
+
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=180,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "ETOPO5",
+            "path": download_test_data("etopo5_coarsened_and_shifted.nc"),
+        },
+    )
+
+    return grid
+
+
+@pytest.fixture()
+def grid_that_straddles_180_degree_meridian_with_global_srtm15_data():
+
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=180,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "SRTM15",
+            "path": download_test_data("srtm15_coarsened.nc"),
+        },
+    )
+
+    return grid
+
+
+@pytest.mark.parametrize(
+    "grid_fixture",
+    [
+        "grid_that_straddles_dateline",
+        "grid_that_straddles_180_degree_meridian",
+        "grid_that_straddles_dateline_with_shifted_global_etopo_data",
+        "grid_that_straddles_180_degree_meridian_with_shifted_global_etopo_data",
+        "grid_that_straddles_dateline_with_global_srtm15_data",
+        "grid_that_straddles_180_degree_meridian_with_global_srtm15_data",
+    ],
+)
+def test_successful_initialization(grid_fixture, request):
+
+    grid = request.getfixturevalue(grid_fixture)
+    assert grid is not None

roms_tools/tests/test_setup/test_validation.py

@@ -23,7 +23,7 @@ def _get_fname(name):
         "bgc_surface_forcing_from_climatology",
         "boundary_forcing",
         "bgc_boundary_forcing_from_climatology",
-        "river_forcing",
+        "river_forcing_with_bgc",
         "river_forcing_no_climatology",
     ],
 )
@@ -62,7 +62,7 @@ def test_save_results(forcing_fixture, request):
         "bgc_surface_forcing_from_climatology",
         "boundary_forcing",
         "bgc_boundary_forcing_from_climatology",
-        "river_forcing",
+        "river_forcing_with_bgc",
         "river_forcing_no_climatology",
     ],
 )

{roms_tools-1.7.0.dist-info → roms_tools-2.1.0.dist-info}/LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2024 [C-Worthy]
+   Copyright 2024 [C]-Worthy LLC.
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

{roms_tools-1.7.0.dist-info → roms_tools-2.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 1.7.0
+Version: 2.1.0
 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
@@ -31,6 +31,7 @@ Requires-Dist: netcdf4
 Requires-Dist: PyYAML
 Requires-Dist: pyamg
 Requires-Dist: bottleneck
+Requires-Dist: regionmask
 Provides-Extra: dask
 Requires-Dist: dask[diagnostics]; extra == "dask"
 
@@ -42,12 +43,16 @@ Requires-Dist: dask[diagnostics]; extra == "dask"
 ![Run Tests](https://github.com/CWorthy-ocean/roms-tools/actions/workflows/tests.yaml/badge.svg)
 ![Supported Python Versions](https://img.shields.io/pypi/pyversions/roms-tools)
 
+> [!Warning]
+> **This project is still in an early phase of development.**
+>
+> The [python API](https://roms-tools.readthedocs.io/en/latest/api.html) is not yet stable.
+> Therefore whilst you are welcome to try out using the package, we cannot yet guarantee backwards compatibility.
+> We expect to reach a more stable version in Q1 2025.
 
 ## Overview
 
-A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla-roms) simulation.
-
-<mark>**DISCLAIMER**: This project is **ALPHA** and will be **EXPERIMENTAL** at least throughout 2024. We do not recommend to use this software before this ALPHA development and test phase is completed.</mark>
+A suite of Python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla-roms) simulation.
 
 ## Installation