Merge pull request #20 from John-Ragland/add_tests

added tests

Author: John-Ragland

.github/workflows/tests.yml

@@ -0,0 +1,27 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync --group dev
+
+      - name: Run tests
+        run: uv run pytest tests/

.gitignore

@@ -3,4 +3,5 @@ __pycache__/
 .DS_Store
 docs/_build/
 dist/
-.vscode/
+.vscode/
+uv.lock

pyproject.toml

@@ -74,3 +74,9 @@ exclude_lines = [
   "if __name__ == .__main__.:",
   "if TYPE_CHECKING:",
 ]
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.5",
+    "pytest-cov>=5.0.0",
+]

tests/conftest.py

@@ -0,0 +1,55 @@
+"""
+Shared test fixtures for pygenray tests.
+"""
+import matplotlib
+matplotlib.use('Agg')
+
+
+def pytest_addoption(parser):
+    """Register --regenerate-physics CLI flag for physics regression tests."""
+    parser.addoption(
+        '--regenerate-physics', action='store_true', default=False,
+        help='Regenerate physics regression fixture and skip comparison.',
+    )
+
+import numpy as np
+import pytest
+import xarray as xr
+
+from pygenray.ray_objects import Ray, RayFan
+
+
+def _make_ray(launch_angle: float, source_depth: float, n_bottom: int = 0,
+              n_surface: int = 0, N: int = 10, R: float = 10000.0) -> Ray:
+    """Helper: build a synthetic Ray without running the ODE solver.
+
+    The y array uses the positive-z convention expected by Ray.__init__:
+        y[0,:] = travel times
+        y[1,:] = depth (positive = deeper)
+        y[2,:] = ray parameter sin(θ)/c (positive for downward ray in ODE)
+    """
+    r = np.linspace(0.0, R, N)
+    t = r / 1500.0
+    # Depth increases linearly (simulating a shallow downward ray)
+    z_ode = np.linspace(source_depth, source_depth + R * 0.01, N)
+    p_ode = np.ones(N) * np.sin(np.radians(abs(launch_angle) + 1e-3)) / 1500.0
+    y = np.vstack([t, z_ode, p_ode])  # shape (3, N)
+    return Ray(r=r, y=y, n_bottom=n_bottom, n_surface=n_surface,
+               launch_angle=launch_angle, source_depth=source_depth)
+
+
+@pytest.fixture
+def simple_ray():
+    """Single synthetic Ray with 10 range steps."""
+    return _make_ray(launch_angle=-10.0, source_depth=100.0)
+
+
+@pytest.fixture
+def simple_rayfan():
+    """Small RayFan of 3 synthetic Rays — no ray tracing needed."""
+    rays = [
+        _make_ray(launch_angle=-5.0,  source_depth=100.0, n_bottom=0),
+        _make_ray(launch_angle=5.0,   source_depth=150.0, n_bottom=1),
+        _make_ray(launch_angle=-10.0, source_depth=200.0, n_bottom=0),
+    ]
+    return RayFan(rays)

tests/fixtures/munk_regression.npz

@@ -0,0 +1,180 @@
+"""
+Tests for pygenray.environment: munk_ssp, OceanEnvironment2D, eflat, eflatinv.
+"""
+import numpy as np
+import pytest
+import xarray as xr
+from matplotlib import pyplot as plt
+
+from pygenray.environment import (
+    OceanEnvironment2D,
+    eflat,
+    eflatinv,
+    munk_ssp,
+)
+
+
+# ---------------------------------------------------------------------------
+# munk_ssp
+# ---------------------------------------------------------------------------
+
+class TestMunkSSP:
+    def test_output_shape_matches_input(self):
+        z = np.arange(0, 5000, 10)
+        c = munk_ssp(z)
+        assert c.shape == z.shape
+
+    def test_minimum_at_sofar_depth(self):
+        sofar = 1300.0
+        z = np.arange(0, 6000, 1)
+        c = munk_ssp(z, sofar_depth=sofar)
+        # Minimum should be at the SOFAR depth
+        assert z[np.argmin(c)] == pytest.approx(sofar, abs=2.0)
+
+    def test_default_params_near_1500_at_sofar(self):
+        sofar = 1300.0
+        c_sofar = munk_ssp(np.array([sofar]))
+        assert c_sofar[0] == pytest.approx(1500.0, abs=5.0)
+
+    def test_scalar_input(self):
+        c = munk_ssp(np.array([0.0]))
+        assert c.shape == (1,)
+
+
+# ---------------------------------------------------------------------------
+# OceanEnvironment2D construction
+# ---------------------------------------------------------------------------
+
+class TestOceanEnvironment2DConstruction:
+    def test_default_init_attributes_exist(self):
+        env = OceanEnvironment2D()
+        for attr in ('sound_speed', 'bathymetry', 'dcdz', 'bottom_angle',
+                     'bottom_angle_interp'):
+            assert hasattr(env, attr), f"Missing attribute: {attr}"
+
+    def test_default_sound_speed_is_2d(self):
+        env = OceanEnvironment2D()
+        assert env.sound_speed.ndim == 2
+        assert set(env.sound_speed.dims) == {'range', 'depth'}
+
+    def test_default_flat_earth_attributes_exist(self):
+        env = OceanEnvironment2D(flat_earth_transform=True)
+        assert hasattr(env, 'sound_speed_fe')
+        assert hasattr(env, 'bathymetry_fe')
+
+    def test_flat_earth_false_no_fe_attributes(self):
+        env = OceanEnvironment2D(flat_earth_transform=False)
+        assert not hasattr(env, 'sound_speed_fe')
+        assert not hasattr(env, 'bathymetry_fe')
+
+    def test_custom_1d_sound_speed(self):
+        z = np.arange(0.0, 3000.0, 10.0)
+        c_vals = munk_ssp(z)
+        ssp = xr.DataArray(c_vals, dims=['depth'], coords={'depth': z})
+        bathy = xr.DataArray(
+            np.ones(20) * 4000.0, dims=['range'],
+            coords={'range': np.linspace(0, 50e3, 20)}
+        )
+        env = OceanEnvironment2D(sound_speed=ssp, bathymetry=bathy,
+                                 flat_earth_transform=False)
+        assert env.sound_speed.ndim == 1
+        assert 'depth' in env.sound_speed.dims
+
+    def test_custom_2d_sound_speed(self):
+        z = np.arange(0.0, 3000.0, 50.0)
+        r = np.linspace(0.0, 50e3, 20)
+        c_2d = np.outer(np.ones(len(r)), munk_ssp(z))
+        ssp = xr.DataArray(c_2d, dims=['range', 'depth'],
+                           coords={'range': r, 'depth': z})
+        env = OceanEnvironment2D(sound_speed=ssp, flat_earth_transform=False)
+        assert env.sound_speed.ndim == 2
+
+    def test_custom_bathymetry_stored(self):
+        bathy_vals = np.ones(20) * 3500.0
+        r = np.linspace(0.0, 50e3, 20)
+        bathy = xr.DataArray(bathy_vals, dims=['range'], coords={'range': r})
+        env = OceanEnvironment2D(bathymetry=bathy, flat_earth_transform=False)
+        np.testing.assert_array_equal(env.bathymetry.values, bathy_vals)
+
+    # --- invalid inputs ---
+
+    def test_sound_speed_not_dataarray_raises_type_error(self):
+        with pytest.raises(TypeError):
+            OceanEnvironment2D(sound_speed=np.ones(100))
+
+    def test_sound_speed_3d_raises_value_error(self):
+        da = xr.DataArray(
+            np.ones((5, 10, 20)),
+            dims=['range', 'depth', 'extra'],
+            coords={'range': np.arange(5), 'depth': np.arange(10),
+                    'extra': np.arange(20)}
+        )
+        with pytest.raises(ValueError):
+            OceanEnvironment2D(sound_speed=da)
+
+    def test_sound_speed_missing_depth_dim_raises_value_error(self):
+        da = xr.DataArray(np.ones(50), dims=['range'],
+                          coords={'range': np.arange(50)})
+        with pytest.raises(ValueError):
+            OceanEnvironment2D(sound_speed=da)
+
+    def test_2d_sound_speed_missing_range_dim_raises_value_error(self):
+        da = xr.DataArray(
+            np.ones((10, 20)),
+            dims=['depth', 'extra'],
+            coords={'depth': np.arange(10), 'extra': np.arange(20)}
+        )
+        with pytest.raises(ValueError):
+            OceanEnvironment2D(sound_speed=da)
+
+    def test_bathymetry_not_dataarray_raises_type_error(self):
+        with pytest.raises(TypeError):
+            OceanEnvironment2D(bathymetry=np.ones(50))
+
+    def test_bathymetry_missing_range_dim_raises_value_error(self):
+        da = xr.DataArray(np.ones(50), dims=['depth'],
+                          coords={'depth': np.arange(50)})
+        with pytest.raises(ValueError):
+            OceanEnvironment2D(bathymetry=da)
+
+
+# ---------------------------------------------------------------------------
+# eflat / eflatinv round-trip
+# ---------------------------------------------------------------------------
+
+class TestEflat:
+    LAT = 35.0
+
+    def test_depth_roundtrip(self):
+        dep = np.array([100.0, 500.0, 1000.0, 2000.0, 4000.0])
+        depf, _ = eflat(dep, self.LAT)
+        dep_rec, _ = eflatinv(depf, np.array([self.LAT]))
+        np.testing.assert_allclose(dep_rec, dep, atol=1.0,
+                                   err_msg="Depth round-trip outside 1 m tolerance")
+
+    def test_sound_speed_roundtrip(self):
+        dep = np.array([100.0, 500.0, 1000.0, 2000.0])
+        cs = np.array([1500.0, 1490.0, 1480.0, 1510.0])
+        depf, csf = eflat(dep, self.LAT, cs)
+        _, cs_rec = eflatinv(depf, np.array([self.LAT]), csf)
+        np.testing.assert_allclose(cs_rec, cs, rtol=1e-4,
+                                   err_msg="Sound speed round-trip outside 0.01% tolerance")
+
+    def test_eflat_increases_depth(self):
+        """Flat-earth transformation should increase effective depths."""
+        dep = np.array([100.0, 1000.0, 3000.0])
+        depf, _ = eflat(dep, self.LAT)
+        assert np.all(depf > dep)
+
+
+# ---------------------------------------------------------------------------
+# OceanEnvironment2D.plot smoke test
+# ---------------------------------------------------------------------------
+
+class TestOceanEnvironment2DPlot:
+    def test_plot_runs_without_error(self):
+        env = OceanEnvironment2D()
+        fig, ax = plt.subplots()
+        plt.sca(ax)
+        env.plot()
+        plt.close('all')