Dev

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface_pipelines"
-version = "0.0.4"
+version = "0.0.5"
 description = "Collection of standardized analysis pipelines based on SpikeInterfacee."
 readme = "README.md"
 authors = [

src/spikeinterface_pipelines/postprocessing/params.py

@@ -94,10 +94,12 @@ class QMParams(BaseModel):
     nn_noise_overlap: NNIsolation = Field(default=NNIsolation(), description="Nearest neighbor noise overlap.")
 
 
-# TODO - fill in metric_names defauklt value with all the metric names
 class QualityMetrics(BaseModel):
     qm_params: QMParams = Field(default=QMParams(), description="Quality metric parameters.")
-    metric_names: Optional[List[str]] = Field(default=None, description="List of metric names to compute. If None, all available metrics are computed.")
+    metric_names: List[str] = Field(
+        default=["presence_ratio", "snr", "isi_violation", "rp_violation", "sliding_rp_violation", "amplitude_cutoff", "amplitude_median"],
+        description="List of metric names to compute. If None, all available metrics are computed."
+    )
     n_jobs: int = Field(default=1, description="Number of jobs.")
 
 

src/spikeinterface_pipelines/postprocessing/postprocessing.py

@@ -101,7 +101,8 @@ def postprocess(
     logger.info("[Postprocessing] \tComputing quality metrics")
     _ = sqm.compute_quality_metrics(waveform_extractor, **postprocessing_params.quality_metrics.model_dump())
 
-    # cleanup
+    # Cleanup
+    logger.info("[Postprocessing] \tCleaning up")
     shutil.rmtree(tmp_folder)
 
     return waveform_extractor