roms-tools 0.1.0__py3-none-any.whl → 0.20__py3-none-any.whl

roms_tools/tests/test_vertical_coordinate.py

@@ -0,0 +1,337 @@
+import pytest
+import numpy as np
+import tempfile
+import os
+from roms_tools import Grid, VerticalCoordinate
+import textwrap
+
+
+@pytest.fixture
+def example_grid():
+    """
+    Fixture for creating a Grid object.
+    """
+    grid = Grid(
+        nx=2, ny=2, size_x=500, size_y=1000, center_lon=0, center_lat=55, rot=10
+    )
+
+    return grid
+
+
+def test_invalid_theta_s_value(example_grid):
+    """
+    Test the validation of the theta_s value.
+    """
+    with pytest.raises(ValueError):
+
+        VerticalCoordinate(
+            grid=example_grid,
+            N=3,
+            theta_s=11.0,  # Invalid value, should be 0 < theta_s <= 10
+            theta_b=2.0,
+            hc=250.0,
+        )
+
+
+def test_invalid_theta_b_value(example_grid):
+    """
+    Test the validation of the theta_b value.
+    """
+    with pytest.raises(ValueError):
+
+        VerticalCoordinate(
+            grid=example_grid,
+            N=3,
+            theta_s=5.0,
+            theta_b=5.0,  # Invalid value, should be 0 < theta_b <= 4
+            hc=250.0,
+        )
+
+
+@pytest.fixture
+def vertical_coordinate(example_grid):
+
+    return VerticalCoordinate(
+        grid=example_grid, N=3, theta_s=5.0, theta_b=2.0, hc=250.0
+    )
+
+
+def test_vertical_coordinate_data_consistency(vertical_coordinate, tmp_path):
+    """
+    Test that the data within the VerticalCoordinate object remains consistent.
+    """
+
+    # Define the expected data
+    expected_sc_r = np.array([-0.8333333, -0.5, -0.16666667], dtype=np.float32)
+    expected_Cs_r = np.array([-0.6641397, -0.15129805, -0.01156188], dtype=np.float32)
+    expected_layer_depth_rho = np.array(
+        [
+            [
+                [17.235603, 9.938617, 3.2495391],
+                [17.235603, 9.938617, 3.2495391],
+                [24.206884, 13.7451725, 4.4592304],
+                [24.206884, 13.7451725, 4.4592304],
+            ],
+            [
+                [17.235603, 9.938617, 3.2495391],
+                [17.235603, 9.938617, 3.2495391],
+                [24.206884, 13.7451725, 4.4592304],
+                [24.206884, 13.7451725, 4.4592304],
+            ],
+            [
+                [25.667452, 14.528268, 4.7055993],
+                [25.667452, 14.528268, 4.7055993],
+                [35.966946, 19.916193, 6.377065],
+                [35.966946, 19.916193, 6.377065],
+            ],
+            [
+                [25.667452, 14.528268, 4.7055993],
+                [25.667452, 14.528268, 4.7055993],
+                [35.966946, 19.916193, 6.377065],
+                [35.966946, 19.916193, 6.377065],
+            ],
+        ],
+        dtype=np.float32,
+    )
+    expected_layer_depth_u = np.array(
+        [
+            [
+                [17.235603, 9.938617, 3.2495391],
+                [20.721243, 11.841895, 3.854385],
+                [24.206884, 13.7451725, 4.4592304],
+            ],
+            [
+                [17.235603, 9.938617, 3.2495391],
+                [20.721243, 11.841895, 3.854385],
+                [24.206884, 13.7451725, 4.4592304],
+            ],
+            [
+                [25.667452, 14.528268, 4.7055993],
+                [30.817198, 17.22223, 5.5413322],
+                [35.966946, 19.916193, 6.377065],
+            ],
+            [
+                [25.667452, 14.528268, 4.7055993],
+                [30.817198, 17.22223, 5.5413322],
+                [35.966946, 19.916193, 6.377065],
+            ],
+        ],
+        dtype=np.float32,
+    )
+    expected_layer_depth_v = np.array(
+        [
+            [
+                [17.235603, 9.938617, 3.2495391],
+                [17.235603, 9.938617, 3.2495391],
+                [24.206884, 13.7451725, 4.4592304],
+                [24.206884, 13.7451725, 4.4592304],
+            ],
+            [
+                [21.451529, 12.233442, 3.977569],
+                [21.451529, 12.233442, 3.977569],
+                [30.086914, 16.830683, 5.418148],
+                [30.086914, 16.830683, 5.418148],
+            ],
+            [
+                [25.667452, 14.528268, 4.7055993],
+                [25.667452, 14.528268, 4.7055993],
+                [35.966946, 19.916193, 6.377065],
+                [35.966946, 19.916193, 6.377065],
+            ],
+        ],
+        dtype=np.float32,
+    )
+    expected_interface_depth_rho = np.array(
+        [
+            [
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+            ],
+            [
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+            ],
+            [
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+            ],
+            [
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+            ],
+        ],
+        dtype=np.float32,
+    )
+    expected_interface_depth_u = np.array(
+        [
+            [
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [25.350803, 16.13514, 7.78195, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+            ],
+            [
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [25.350803, 16.13514, 7.78195, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+            ],
+            [
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [38.022217, 23.705446, 11.239724, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+            ],
+            [
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [38.022217, 23.705446, 11.239724, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+            ],
+        ],
+        dtype=np.float32,
+    )
+    expected_interface_depth_v = np.array(
+        [
+            [
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [21.013529, 13.487298, 6.5489607, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+                [29.688076, 18.78298, 9.014939, -0.0],
+            ],
+            [
+                [26.26544, 16.684502, 8.034093, -0.0],
+                [26.26544, 16.684502, 8.034093, -0.0],
+                [37.10758, 23.156084, 10.987581, -0.0],
+                [37.10758, 23.156084, 10.987581, -0.0],
+            ],
+            [
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [31.51735, 19.881702, 9.519225, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+                [44.52708, 27.529188, 12.960222, -0.0],
+            ],
+        ],
+        dtype=np.float32,
+    )
+    # Check the values in the dataset
+    assert np.allclose(vertical_coordinate.ds["sc_r"].values, expected_sc_r)
+    assert np.allclose(vertical_coordinate.ds["Cs_r"].values, expected_Cs_r)
+    assert np.allclose(
+        vertical_coordinate.ds["layer_depth_rho"].values, expected_layer_depth_rho
+    )
+    assert np.allclose(
+        vertical_coordinate.ds["layer_depth_u"].values, expected_layer_depth_u
+    )
+    assert np.allclose(
+        vertical_coordinate.ds["layer_depth_v"].values, expected_layer_depth_v
+    )
+    assert np.allclose(
+        vertical_coordinate.ds["interface_depth_rho"].values,
+        expected_interface_depth_rho,
+    )
+    assert np.allclose(
+        vertical_coordinate.ds["interface_depth_u"].values, expected_interface_depth_u
+    )
+    assert np.allclose(
+        vertical_coordinate.ds["interface_depth_v"].values, expected_interface_depth_v
+    )
+
+
+def test_plot(vertical_coordinate):
+    vertical_coordinate.plot("layer_depth_u", s=0)
+    vertical_coordinate.plot("layer_depth_rho", s=-1)
+    vertical_coordinate.plot("interface_depth_v", s=-1)
+    vertical_coordinate.plot("layer_depth_rho", eta=0)
+    vertical_coordinate.plot("layer_depth_u", eta=0)
+    vertical_coordinate.plot("layer_depth_v", eta=0)
+    vertical_coordinate.plot("interface_depth_rho", eta=0)
+    vertical_coordinate.plot("interface_depth_u", eta=0)
+    vertical_coordinate.plot("interface_depth_v", eta=0)
+    vertical_coordinate.plot("layer_depth_rho", xi=0)
+    vertical_coordinate.plot("layer_depth_u", xi=0)
+    vertical_coordinate.plot("layer_depth_v", xi=0)
+    vertical_coordinate.plot("interface_depth_rho", xi=0)
+    vertical_coordinate.plot("interface_depth_u", xi=0)
+    vertical_coordinate.plot("interface_depth_v", xi=0)
+
+
+def test_save(vertical_coordinate, tmp_path):
+    filepath = tmp_path / "vertical_coordinate.nc"
+    vertical_coordinate.save(filepath)
+    assert filepath.exists()
+
+
+def test_roundtrip(vertical_coordinate):
+    """Test that creating a vertical_coordinate, saving it to file, and re-opening it is the same as just creating it."""
+
+    # Create a temporary file
+    with tempfile.NamedTemporaryFile(delete=False) as tmpfile:
+        filepath = tmpfile.name
+
+    try:
+        vertical_coordinate.save(filepath)
+
+        vertical_coordinate_from_file = VerticalCoordinate.from_file(filepath)
+
+        assert vertical_coordinate.ds == vertical_coordinate_from_file.ds
+
+    finally:
+        os.remove(filepath)
+
+
+def test_roundtrip_yaml(vertical_coordinate):
+    """Test that creating a VerticalCoordinate object, saving its parameters to yaml file, and re-opening yaml file creates the same object."""
+
+    # Create a temporary file
+    with tempfile.NamedTemporaryFile(delete=False) as tmpfile:
+        filepath = tmpfile.name
+
+    try:
+        vertical_coordinate.to_yaml(filepath)
+
+        vertical_coordinate_from_file = VerticalCoordinate.from_yaml(filepath)
+
+        assert vertical_coordinate == vertical_coordinate_from_file
+
+    finally:
+        os.remove(filepath)
+
+
+def test_from_yaml_missing_vertical_coordinate():
+    yaml_content = textwrap.dedent(
+        """\
+    ---
+    roms_tools_version: 0.0.0
+    ---
+    Grid:
+      nx: 100
+      ny: 100
+      size_x: 1800
+      size_y: 2400
+      center_lon: -10
+      center_lat: 61
+      rot: -20
+      topography_source: ETOPO5
+      smooth_factor: 8
+      hmin: 5.0
+      rmax: 0.2
+    """
+    )
+
+    with tempfile.NamedTemporaryFile(delete=False) as tmp_file:
+        yaml_filepath = tmp_file.name
+        tmp_file.write(yaml_content.encode())
+
+    try:
+        with pytest.raises(
+            ValueError,
+            match="No VerticalCoordinate configuration found in the YAML file.",
+        ):
+            VerticalCoordinate.from_yaml(yaml_filepath)
+    finally:
+        os.remove(yaml_filepath)

{roms_tools-0.1.0.dist-info → roms_tools-0.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 0.1.0
+Version: 0.20
 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: numba
 
 # ROMS-Tools
 
+[![codecov](https://codecov.io/gh/CWorthy-ocean/roms-tools/graph/badge.svg?token=5S1oNu39xE)](https://codecov.io/gh/CWorthy-ocean/roms-tools)
 [![Documentation Status](https://readthedocs.org/projects/roms-tools/badge/?version=latest)](https://roms-tools.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/roms-tools.svg)](https://badge.fury.io/py/roms-tools)
 
@@ -59,7 +60,7 @@ pip install -e .
 
 ### Run the tests
 
-Before running the tests you can install and activate the following conda environment:
+Before running the tests, you can install and activate the following conda environment:
 
 ```bash
 cd roms-tools

roms_tools-0.20.dist-info/RECORD

@@ -0,0 +1,28 @@
+ci/environment.yml,sha256=s_PPgQryNiNnGGVoheZIkwTaoDZ-CfHXRxSTOvF-ZBs,407
+roms_tools/__init__.py,sha256=lMa-9IeCSs1DNSKI00lbuDRUvtWUFWaS_x2nuOwkw88,727
+roms_tools/_version.py,sha256=dNPL38J2xFc6i31ZQ9xa3jAkzFdhMiwrWFuxzB3SCSI,71
+roms_tools/setup/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+roms_tools/setup/atmospheric_forcing.py,sha256=Gfg-rP8H9MSUGmlK7MdkpFJ9knkai7x7__EVF3f2Jjo,32200
+roms_tools/setup/boundary_forcing.py,sha256=0jxuCmx30wdcKSfXyuZ5V4hUFBuqOqMpUPRd8A46a9I,26961
+roms_tools/setup/datasets.py,sha256=1CfS9ZHKTw-Dfw5AoLpE12S5G5GU5NXK9JEwZ1wIGGo,15788
+roms_tools/setup/fill.py,sha256=45Ro5oN-n-n_qKZq3qTHn27ZKpTKWhr_9AWw6gUJ-9I,13291
+roms_tools/setup/grid.py,sha256=V3vVOrkmlHM4CfhIGGlGTCw2OvZ62MGnrUHJepDylsA,30848
+roms_tools/setup/initial_conditions.py,sha256=hKKMkOgXMqIWVmbnTVzrTW7YRKZq8FACT9QrTRt2dCE,19704
+roms_tools/setup/plot.py,sha256=vpOoAHE5HvnmeAPyhr-GijGLLlqkEple5hfr_f3Nfn8,6331
+roms_tools/setup/tides.py,sha256=vyZCZArbdoYotFEAUIUJJ5BQzAlybBF87qkTShqOjP4,25731
+roms_tools/setup/topography.py,sha256=x5XfmUmDPxQ6QY0QikmxGiAE4kiDsFtEdKccW9emw2M,8557
+roms_tools/setup/utils.py,sha256=QVfk-PnXDTnfJct3W5g7FLuxu3QLRSbuYiEPO_Sxw6I,6155
+roms_tools/setup/vertical_coordinate.py,sha256=IqZN3vDW4DyeaQSr-Di5O8qH2cLJE__XKmf4lROgF8s,16122
+roms_tools/tests/test_atmospheric_forcing.py,sha256=Ls2R_r_zJ75_nIEGX9sIPWAqrXNTyxImtteNe0oleP8,49011
+roms_tools/tests/test_boundary_forcing.py,sha256=m5Zr_8VMX0XbPhqykovxZeGtUVQ3pn7u9nHokalf9us,11053
+roms_tools/tests/test_datasets.py,sha256=FD3LznVlsdyAGe3pDv937yZYbDyjrs1ry8o0Vz1RCzQ,9793
+roms_tools/tests/test_grid.py,sha256=Dhci5NXOQsASM9mdNCmqyxVXcSasjjlNvcYxKZoah6E,5587
+roms_tools/tests/test_initial_conditions.py,sha256=v_FYD93i-u9fluegJSHZL8_9DszWKkbcX8eg7q_uo3U,9276
+roms_tools/tests/test_tides.py,sha256=arousN9-scdEeEmAa7GCSDVnXbchf2yFamRPsVpR4RA,11104
+roms_tools/tests/test_topography.py,sha256=Nwzor5ciOZfV7Y7fDazE1JH1qxotmJilOpZUcHxAypI,1945
+roms_tools/tests/test_vertical_coordinate.py,sha256=GshM5l1e9bl4RT0HATQJg9YJ9asGK4beqIKbZxr9j7U,10843
+roms_tools-0.20.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+roms_tools-0.20.dist-info/METADATA,sha256=lWrhiD6ypwLgsdIZE0gXkIJ3-7bv9NYXM5HeZIjIbsU,2709
+roms_tools-0.20.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+roms_tools-0.20.dist-info/top_level.txt,sha256=aAf4T4nYQSkay5iKJ9kmTjlDgd4ETdp9OSlB4sJdt8Y,19
+roms_tools-0.20.dist-info/RECORD,,

{roms_tools-0.1.0.dist-info → roms_tools-0.20.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.3.0)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

roms_tools/tests/test_setup.py

@@ -1,181 +0,0 @@
-import pytest
-import numpy as np
-import numpy.testing as npt
-from scipy.ndimage import label
-from roms_tools import Grid
-from roms_tools.setup.topography import _compute_rfactor
-from roms_tools.setup.tides import TPXO
-import os
-import tempfile
-
-
-class TestCreateGrid:
-    def test_simple_regression(self):
-        grid = Grid(
-            nx=1, ny=1, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=0
-        )
-
-        expected_lat = np.array(
-            [
-                [-8.99249453e-01, -8.99249453e-01, -8.99249453e-01],
-                [0.0, 0.0, 0.0],
-                [8.99249453e-01, 8.99249453e-01, 8.99249453e-01],
-            ]
-        )
-        expected_lon = np.array(
-            [
-                [339.10072286, 340.0, 340.89927714],
-                [339.10072286, 340.0, 340.89927714],
-                [339.10072286, 340.0, 340.89927714],
-            ]
-        )
-
-        # TODO: adapt tolerances according to order of magnitude of respective fields
-        npt.assert_allclose(grid.ds["lat_rho"], expected_lat, atol=1e-8)
-        npt.assert_allclose(grid.ds["lon_rho"], expected_lon, atol=1e-8)
-
-    def test_raise_if_domain_too_large(self):
-        with pytest.raises(ValueError, match="Domain size has to be smaller"):
-            Grid(nx=3, ny=3, size_x=30000, size_y=30000, center_lon=0, center_lat=51.5)
-
-        # test grid with reasonable domain size
-        grid = Grid(
-            nx=3,
-            ny=3,
-            size_x=1800,
-            size_y=2400,
-            center_lon=-21,
-            center_lat=61,
-            rot=20,
-        )
-        assert isinstance(grid, Grid)
-
-    def test_grid_straddle_crosses_meridian(self):
-        grid = Grid(
-            nx=3,
-            ny=3,
-            size_x=100,
-            size_y=100,
-            center_lon=0,
-            center_lat=61,
-            rot=20,
-        )
-        assert grid.straddle
-
-        grid = Grid(
-            nx=3,
-            ny=3,
-            size_x=100,
-            size_y=100,
-            center_lon=180,
-            center_lat=61,
-            rot=20,
-        )
-        assert not grid.straddle
-
-
-class TestGridFromFile:
-    def test_roundtrip(self):
-        """Test that creating a grid, saving it to file, and re-opening it is the same as just creating it."""
-
-        # Initialize a Grid object using the initializer
-        grid_init = Grid(
-            nx=10,
-            ny=15,
-            size_x=100.0,
-            size_y=150.0,
-            center_lon=0.0,
-            center_lat=0.0,
-            rot=0.0,
-            topography_source="etopo5",
-            smooth_factor=2,
-            hmin=5.0,
-            rmax=0.2,
-        )
-
-        # Create a temporary file
-        with tempfile.NamedTemporaryFile(delete=False) as tmpfile:
-            filepath = tmpfile.name
-
-        try:
-            # Save the grid to a file
-            grid_init.save(filepath)
-
-            # Load the grid from the file
-            grid_from_file = Grid.from_file(filepath)
-
-            # Assert that the initial grid and the loaded grid are equivalent (including the 'ds' attribute)
-            assert grid_init == grid_from_file
-
-        finally:
-            os.remove(filepath)
-
-
-class TestTopography:
-    def test_enclosed_regions(self):
-        """Test that there are only two connected regions, one dry and one wet."""
-
-        grid = Grid(
-            nx=100,
-            ny=100,
-            size_x=1800,
-            size_y=2400,
-            center_lon=30,
-            center_lat=61,
-            rot=20,
-        )
-
-        reg, nreg = label(grid.ds.mask_rho)
-        npt.assert_equal(nreg, 2)
-
-    def test_rmax_criterion(self):
-        grid = Grid(
-            nx=100,
-            ny=100,
-            size_x=1800,
-            size_y=2400,
-            center_lon=30,
-            center_lat=61,
-            rot=20,
-            smooth_factor=4,
-            rmax=0.2,
-        )
-        r_eta, r_xi = _compute_rfactor(grid.ds.h)
-        rmax0 = np.max([r_eta.max(), r_xi.max()])
-        npt.assert_array_less(rmax0, grid.rmax)
-
-    def test_hmin_criterion(self):
-        grid = Grid(
-            nx=100,
-            ny=100,
-            size_x=1800,
-            size_y=2400,
-            center_lon=30,
-            center_lat=61,
-            rot=20,
-            smooth_factor=2,
-            rmax=0.2,
-            hmin=5,
-        )
-
-        assert np.less_equal(grid.hmin, grid.ds.h.min())
-
-
-class TestTPXO:
-    def test_load_data_file_not_found(self):
-        # Test loading data from a non-existing file
-        with pytest.raises(FileNotFoundError):
-            TPXO.load_data("non_existing_file.nc")
-
-    def test_load_data_checksum_mismatch(self):
-        # Create a temporary file for testing
-        filename = "test_tidal_data.nc"
-        with open(filename, "wb") as file:
-            # Write some data to the file
-            file.write(b"test data")
-        # Test loading data with incorrect checksum
-        with open(filename, "wb") as file:
-            with pytest.raises(ValueError):
-                TPXO.load_data(filename)
-        # Remove temporary file
-        os.remove(filename)

roms_tools-0.1.0.dist-info/RECORD

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