test(echodata): add tests for ECS, local storage, cal_params; fix stale tests

- New test_ecs.py: 18 tests covering _normalize_ecs_text header rewriting,
  _coerce_to_path input handling, parse_ecs with mocked echopype,
  build_cal_params_from_ecs single/dual-pulse and error cases
- New TestLocalStorage in test_storage.py: 14 tests for use_local_storage
  toggle, env var fallback, get_azure_zarr_store/get_zarr_store_uri in
  local mode, save+open roundtrip, ensure_container_exists,
  upload_file_to_blob, _LocalListFS, module exports
- New cal_params forwarding tests in test_compute.py: verify
  compute_sv_from_echodata forwards cal_params/env_params to compute_Sv
  and omits None values from kwargs
- Fix test_calibrate.py: remove tests for deleted parse_ecs_file and
  parse_json_calibration; add tests for .ecs ValueError, JSON loading,
  TypeError on bad input, auto-detect failure
- Fix test_config.py: update attenuation_threshold assertion from 0.8
  to 6.0 matching current DenoiseConfig defaults (Ryan et al. 2015)
- Fix test_compute.py: replace module-level pytest.importorskip(echopype)
  with class-level @skipif so non-echopype tests are no longer skipped

Author: beatfactor

oceanstream/tests/unit/echodata/test_calibrate.py

@@ -148,51 +148,52 @@ def test_invalid_frequency_type(self):
 
 
 class TestECSCalibration:
-    """Tests for ECS (Simrad Calibration Software) format."""
+    """Tests for ECS calibration format handling.
+
+    The old ``parse_ecs_file`` / ``parse_json_calibration`` functions were
+    removed from ``calibration.py``.  ECS parsing now lives in
+    ``oceanstream.echodata.calibrate.ecs`` (tested in ``test_ecs.py``).
+    """
+
+    def test_load_calibration_ecs_raises(self, tmp_path: Path):
+        """load_calibration should raise ValueError for .ecs files.
+
+        Users are directed to ``ecs.parse_ecs()`` instead.
+        """
+        from oceanstream.echodata.calibrate.calibration import load_calibration
 
-    def test_parse_ecs_file(self, tmp_path: Path):
-        """Should parse ECS XML format."""
-        from oceanstream.echodata.calibrate.calibration import parse_ecs_file
-        
-        # Create minimal ECS file
-        ecs_content = """<?xml version="1.0" encoding="utf-8"?>
-<CalibrationResults>
-  <Calibration Frequency="38000">
-    <Gain>25.5</Gain>
-    <SaCorrection>-0.5</SaCorrection>
-  </Calibration>
-</CalibrationResults>
-"""
         ecs_file = tmp_path / "calibration.ecs"
-        ecs_file.write_text(ecs_content)
-        
-        try:
-            params = parse_ecs_file(ecs_file)
-            assert 38000 in params
-        except (NotImplementedError, AttributeError):
-            # Function may not be implemented yet
-            pass
+        ecs_file.write_text("SourceCal T1\n  Frequency = 38000\n")
 
-    def test_parse_json_calibration(self, tmp_path: Path):
-        """Should parse JSON calibration format."""
-        from oceanstream.echodata.calibrate.calibration import parse_json_calibration
-        
+        with pytest.raises(ValueError, match=r"\.ecs"):
+            load_calibration(ecs_file)
+
+    def test_load_calibration_json(self, tmp_path: Path):
+        """load_calibration should still load JSON calibration files."""
         import json
-        cal_data = {
-            "frequencies": {
-                "38000": {
-                    "gain": 25.5,
-                    "sa_correction": -0.5,
-                    "equivalent_beam_angle": -20.7,
-                }
-            }
-        }
-        
+        from oceanstream.echodata.calibrate.calibration import load_calibration
+
+        cal_data = {"38000": {"gain": 25.5, "sa_correction": -0.5}}
         json_file = tmp_path / "calibration.json"
         json_file.write_text(json.dumps(cal_data))
-        
-        try:
-            params = parse_json_calibration(json_file)
-            assert 38000 in params or "38000" in params
-        except (NotImplementedError, AttributeError):
-            pass
+
+        params = load_calibration(json_file)
+        assert isinstance(params, dict)
+        assert "38000" in params
+
+    def test_apply_calibration_bad_type_raises(self):
+        """apply_calibration should raise TypeError for non-Path/non-dict."""
+        from oceanstream.echodata.calibrate.calibration import apply_calibration
+
+        with pytest.raises(TypeError, match="must be a Path or dict"):
+            apply_calibration(MagicMock(), 42)
+
+    def test_apply_calibration_auto_detect_failure(self):
+        """apply_calibration should raise when provider can't be inferred."""
+        from oceanstream.echodata.calibrate.calibration import apply_calibration
+
+        # Dict without Saildrone-specific keys
+        generic_cal = {"38kHz": {"gain": 25.0}}
+
+        with pytest.raises(ValueError, match="Cannot infer calibration provider"):
+            apply_calibration(MagicMock(), generic_cal, provider="auto")

oceanstream/tests/unit/echodata/test_compute.py

@@ -100,6 +100,70 @@ def test_enrich_sv_with_location_exists(self):
         assert "sv_dataset" in params
         assert "campaign_dir" in params or "campaign_id" in params
 
+    def test_compute_sv_from_echodata_forwards_cal_params(self):
+        """compute_sv_from_echodata should forward cal_params to compute_Sv."""
+        mock_compute_Sv = MagicMock()
+        mock_add_depth = MagicMock()
+        mock_add_location = MagicMock()
+
+        sentinel_ds = xr.Dataset({"Sv": (["x"], [1, 2, 3])})
+        mock_compute_Sv.return_value = sentinel_ds
+        mock_add_depth.return_value = sentinel_ds
+        mock_add_location.return_value = sentinel_ds
+
+        mock_ep = MagicMock()
+        mock_ep.calibrate.compute_Sv = mock_compute_Sv
+        mock_ep.consolidate.add_depth = mock_add_depth
+        mock_ep.consolidate.add_location = mock_add_location
+
+        mock_ed = MagicMock()
+        mock_ed.sonar_model = "EK80"
+
+        cal = {"gain": [25.0]}
+        env = {"speed_of_sound": 1500}
+
+        with patch.dict("sys.modules", {"echopype": mock_ep}):
+            # Re-import so the local `import echopype as ep` picks up the mock
+            import importlib
+            import oceanstream.echodata.compute.sv as sv_mod
+            importlib.reload(sv_mod)
+
+            sv_mod.compute_sv_from_echodata(mock_ed, env_params=env, cal_params=cal)
+
+        call_kwargs = mock_compute_Sv.call_args.kwargs
+        assert call_kwargs["cal_params"] == cal
+        assert call_kwargs["env_params"] == env
+
+    def test_compute_sv_from_echodata_omits_none_cal_params(self):
+        """cal_params=None should not be passed as a kwarg."""
+        mock_compute_Sv = MagicMock()
+        mock_add_depth = MagicMock()
+        mock_add_location = MagicMock()
+
+        sentinel_ds = xr.Dataset({"Sv": (["x"], [1, 2, 3])})
+        mock_compute_Sv.return_value = sentinel_ds
+        mock_add_depth.return_value = sentinel_ds
+        mock_add_location.return_value = sentinel_ds
+
+        mock_ep = MagicMock()
+        mock_ep.calibrate.compute_Sv = mock_compute_Sv
+        mock_ep.consolidate.add_depth = mock_add_depth
+        mock_ep.consolidate.add_location = mock_add_location
+
+        mock_ed = MagicMock()
+        mock_ed.sonar_model = "EK80"
+
+        with patch.dict("sys.modules", {"echopype": mock_ep}):
+            import importlib
+            import oceanstream.echodata.compute.sv as sv_mod
+            importlib.reload(sv_mod)
+
+            sv_mod.compute_sv_from_echodata(mock_ed, cal_params=None, env_params=None)
+
+        call_kwargs = mock_compute_Sv.call_args.kwargs
+        assert "cal_params" not in call_kwargs
+        assert "env_params" not in call_kwargs
+
 
 class TestComputeMVBS:
     """Tests for MVBS computation."""
@@ -308,10 +372,19 @@ def test_zarr_roundtrip(self, tmp_path: Path):
 
 # ──────────────────────────────────────────────────────────────────────────
 # Strict xarray-2026 regression tests (no exception swallowing)
+# These require echopype + dask.array; skipped individually when missing.
 # ──────────────────────────────────────────────────────────────────────────
 
-echopype = pytest.importorskip("echopype")
-dask_array = pytest.importorskip("dask.array")
+_has_echopype = bool(pytest.importorskip.__module__)  # always True, just a placeholder
+try:
+    import echopype  # noqa: F401
+    import dask.array  # noqa: F401
+except ImportError:
+    _has_echopype = False
+
+_skip_no_echopype = pytest.mark.skipif(
+    not _has_echopype, reason="echopype + dask.array required for regression tests"
+)
 
 
 def _make_sv_dataset(
@@ -371,6 +444,7 @@ def _make_sv_dataset(
     return ds
 
 
+@_skip_no_echopype
 class TestMVBSXarray2026:
     """Strict MVBS regression tests — no broad except blocks."""
 
@@ -414,6 +488,7 @@ def test_compute_mvbs_bin_count(self):
         assert mvbs.sizes["echo_range"] in (5, 6)
 
 
+@_skip_no_echopype
 class TestNASCXarray2026:
     """Strict NASC regression tests — no broad except blocks."""
 

oceanstream/tests/unit/echodata/test_config.py

@@ -101,10 +101,13 @@ def test_impulse_defaults(self):
         assert config.impulse_num_lags == 3
 
     def test_attenuation_defaults(self):
-        """Attenuation detection defaults."""
+        """Attenuation detection defaults (Ryan et al. 2015 values)."""
         config = DenoiseConfig()
 
-        assert config.attenuation_threshold == 0.8
+        assert config.attenuation_threshold == 6.0
+        assert config.attenuation_upper_limit == 180.0
+        assert config.attenuation_lower_limit == 280.0
+        assert config.attenuation_side_pings == 15
 
     def test_custom_methods(self):
         """Config should accept custom method list."""