Add regression test for GH-4508 (deprecated metric names in legacy WE folders)

pyproject.toml

@@ -122,6 +122,7 @@ metrics = [
 ]
 
 test_core = [
+    "pandas<3",
     "pytest<8.4.0",
     "psutil",
 

src/spikeinterface/core/tests/test_waveforms_extractor_backwards_compatibility.py

@@ -1,11 +1,14 @@
 import pytest
 from pathlib import Path
 
+import json
 import shutil
 
 import numpy as np
+import pandas as pd
 
 from spikeinterface.core import generate_ground_truth_recording, SortingAnalyzer
+from spikeinterface.core.core_tools import SIJsonEncoder
 
 from spikeinterface.core.waveforms_extractor_backwards_compatibility import MockWaveformExtractor
 from spikeinterface.core.waveforms_extractor_backwards_compatibility import extract_waveforms as mock_extract_waveforms
@@ -104,6 +107,146 @@ def test_read_old_waveforms_extractor_binary():
             print(type(data))
 
 
+def _create_legacy_we_folder(recording, sorting, folder):
+    """Build a minimal legacy WaveformExtractor binary folder on disk.
+
+    Creates just enough structure for ``_read_old_waveforms_extractor_binary``
+    to load: the top-level ``params.json``, ``recording_info/``, and a
+    serialised sorting object.  No waveform data is written – only the
+    skeleton that extension sub-folders hang off of.
+    """
+    from spikeinterface.core.recording_tools import get_rec_attributes
+
+    folder.mkdir(parents=True, exist_ok=True)
+
+    # params.json
+    params = {
+        "ms_before": 1.0,
+        "ms_after": 2.0,
+        "return_scaled": True,
+        "dtype": "float32",
+    }
+    with open(folder / "params.json", "w") as f:
+        json.dump(params, f)
+
+    # recording_info/
+    rec_info_folder = folder / "recording_info"
+    rec_info_folder.mkdir()
+    rec_attributes = get_rec_attributes(recording)
+    rec_attributes["probegroup"] = None
+    with open(rec_info_folder / "recording_attributes.json", "w") as f:
+        json.dump(rec_attributes, f, cls=SIJsonEncoder)
+
+    # No need to serialize the sorting on disk – the test passes it
+    # directly via the ``sorting`` argument of ``load_waveforms_backwards``.
+
+    return folder
+
+
+def _add_legacy_quality_metrics(folder, unit_ids):
+    """Add a ``quality_metrics/`` sub-folder with deprecated 0.100-era params."""
+    ext_folder = folder / "quality_metrics"
+    ext_folder.mkdir()
+
+    deprecated_params = {
+        "metric_names": [
+            "num_spikes",
+            "firing_rate",
+            "snr",
+            "isolation_distance",
+            "l_ratio",
+        ],
+        "qm_params": {
+            "num_spikes": {},
+            "firing_rate": {},
+            "snr": {"peak_sign": "neg", "peak_mode": "extremum"},
+            "isolation_distance": {},
+            "l_ratio": {},
+            "amplitude_cutoff": {"peak_sign": "neg"},
+            "amplitude_median": {"peak_sign": "neg"},
+        },
+        "peak_sign": "neg",
+        "seed": None,
+        "skip_pc_metrics": False,
+    }
+    with open(ext_folder / "params.json", "w") as f:
+        json.dump(deprecated_params, f)
+
+    metrics_df = pd.DataFrame(index=unit_ids, columns=["num_spikes", "firing_rate", "snr"])
+    metrics_df["num_spikes"] = 100
+    metrics_df["firing_rate"] = 5.0
+    metrics_df["snr"] = 10.0
+    metrics_df.to_csv(ext_folder / "metrics.csv")
+
+
+def _add_legacy_template_metrics(folder, unit_ids):
+    """Add a ``template_metrics/`` sub-folder with deprecated 0.100-era params."""
+    ext_folder = folder / "template_metrics"
+    ext_folder.mkdir()
+
+    deprecated_params = {
+        "metric_names": [
+            "peak_to_valley",
+            "peak_trough_ratio",
+            "half_width",
+        ],
+        "metrics_kwargs": {
+            "upsampling_factor": 10,
+            "window_slope_ms": 0.7,
+        },
+    }
+    with open(ext_folder / "params.json", "w") as f:
+        json.dump(deprecated_params, f)
+
+    metrics_df = pd.DataFrame(index=unit_ids, columns=["peak_to_valley", "peak_trough_ratio", "half_width"])
+    metrics_df["peak_to_valley"] = 0.5
+    metrics_df["peak_trough_ratio"] = 2.0
+    metrics_df["half_width"] = 0.3
+    metrics_df.to_csv(ext_folder / "metrics.csv")
+
+
+def test_load_legacy_we_with_deprecated_metrics(create_cache_folder, tmp_path):
+    """Regression test for GH-4508.
+
+    A legacy WaveformExtractor folder whose ``quality_metrics/params.json``
+    or ``template_metrics/params.json`` contains deprecated metric names
+    (e.g. ``l_ratio``, ``peak_to_valley``) must load without raising a
+    ``ValueError``.  The backward-compatibility handler must migrate the
+    deprecated names before validation runs.
+    """
+    recording, sorting = get_dataset()
+
+    we_folder = tmp_path / "legacy_we_deprecated_metrics"
+    _create_legacy_we_folder(recording, sorting, we_folder)
+    _add_legacy_quality_metrics(we_folder, sorting.unit_ids)
+    _add_legacy_template_metrics(we_folder, sorting.unit_ids)
+
+    # This would raise ValueError on main before the fix
+    sorting_analyzer = load_waveforms_backwards(we_folder, sorting=sorting, output="SortingAnalyzer")
+    assert isinstance(sorting_analyzer, SortingAnalyzer)
+
+    # quality_metrics: deprecated names should be migrated
+    qm = sorting_analyzer.get_extension("quality_metrics")
+    assert qm is not None
+    qm_names = qm.params["metric_names"]
+    # The compat handler should have removed the deprecated names
+    assert "l_ratio" not in qm_names
+    assert "isolation_distance" not in qm_names
+    # qm_params should have been renamed to metric_params
+    assert "qm_params" not in qm.params
+    assert "metric_params" in qm.params
+
+    # template_metrics: deprecated names should be migrated
+    tm = sorting_analyzer.get_extension("template_metrics")
+    assert tm is not None
+    tm_names = tm.params["metric_names"]
+    assert "peak_to_valley" not in tm_names
+    assert "peak_trough_ratio" not in tm_names
+    # metrics_kwargs should have been renamed to metric_params
+    assert "metrics_kwargs" not in tm.params
+    assert "metric_params" in tm.params
+
+
 # @pytest.mark.skip("This test is run locally")
 # def test_read_old_waveforms_extractor_zarr():
 #     import pandas as pd