Respond to Joe review

Author: chrishalcrow

src/spikeinterface/qualitymetrics/tests/conftest.py

@@ -5,10 +5,11 @@
     create_sorting_analyzer,
 )
 
-job_kwargs = dict(n_jobs=-1, progress_bar=True, chunk_duration="1s")
+job_kwargs = dict(n_jobs=2, progress_bar=True, chunk_duration="1s")
 
 
-def _small_sorting_analyzer():
+@pytest.fixture(scope="module")
+def small_sorting_analyzer():
     recording, sorting = generate_ground_truth_recording(
         durations=[2.0],
         num_units=10,
@@ -35,12 +36,7 @@ def _small_sorting_analyzer():
 
 
 @pytest.fixture(scope="module")
-def small_sorting_analyzer():
-    return _small_sorting_analyzer()
-
-
-def _sorting_analyzer_simple():
-
+def sorting_analyzer_simple():
     # we need high firing rate for amplitude_cutoff
     recording, sorting = generate_ground_truth_recording(
         durations=[
@@ -73,16 +69,3 @@ def _sorting_analyzer_simple():
     sorting_analyzer.compute("spike_amplitudes", **job_kwargs)
 
     return sorting_analyzer
-
-
-@pytest.fixture(scope="module")
-def sorting_analyzer_simple():
-    sorting_analyzer = get_sorting_analyzer(seed=2205)
-    return sorting_analyzer
-
-    return sorting_analyzer
-
-
-@pytest.fixture(scope="module")
-def sorting_analyzer_simple():
-    return _sorting_analyzer_simple()

src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py

@@ -536,40 +536,3 @@ def test_calculate_sd_ratio(sorting_analyzer_simple):
     assert np.all(list(sd_ratio.keys()) == sorting_analyzer_simple.unit_ids)
     # @aurelien can you check this, this is not working anymore
     # assert np.allclose(list(sd_ratio.values()), 1, atol=0.25, rtol=0)
-
-
-if __name__ == "__main__":
-
-    test_unit_structure_in_output(small_sorting_analyzer)
-    test_unit_id_order_independence(small_sorting_analyzer)
-
-    test_synchrony_counts_no_sync()
-    test_synchrony_counts_one_sync()
-    test_synchrony_counts_one_quad_sync()
-    test_synchrony_counts_not_all_units()
-
-    test_mahalanobis_metrics()
-    test_lda_metrics()
-    test_nearest_neighbors_metrics()
-    test_silhouette_score_metrics()
-    test_simplified_silhouette_score_metrics()
-
-    test_calculate_firing_rate_num_spikes(sorting_analyzer_simple)
-    test_calculate_snrs(sorting_analyzer)
-    test_calculate_amplitude_cutoff(sorting_analyzer)
-    test_calculate_presence_ratio(sorting_analyzer)
-    test_calculate_amplitude_median(sorting_analyzer)
-    test_calculate_sliding_rp_violations(sorting_analyzer)
-    test_calculate_drift_metrics(sorting_analyzer)
-    test_synchrony_metrics(sorting_analyzer)
-    test_synchrony_metrics_unit_id_subset(sorting_analyzer)
-    test_synchrony_metrics_no_unit_ids(sorting_analyzer)
-    test_calculate_firing_range(sorting_analyzer)
-    test_calculate_amplitude_cv_metrics(sorting_analyzer)
-    test_calculate_sd_ratio(sorting_analyzer)
-
-    sorting_analyzer_violations = _sorting_analyzer_violations()
-    # print(sorting_analyzer_violations)
-    test_calculate_isi_violations(sorting_analyzer_violations)
-    test_calculate_sliding_rp_violations(sorting_analyzer_violations)
-    test_calculate_rp_violations(sorting_analyzer_violations)

src/spikeinterface/qualitymetrics/tests/test_pca_metrics.py

@@ -22,8 +22,3 @@ def test_calculate_pc_metrics(small_sorting_analyzer):
             assert not np.all(np.isnan(res2[metric_name].values))
 
         assert np.array_equal(res1[metric_name].values, res2[metric_name].values)
-
-
-if __name__ == "__main__":
-
-    test_calculate_pc_metrics(small_sorting_analyzer)

src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py

@@ -245,9 +245,3 @@ def test_empty_units(sorting_analyzer_simple):
 #         for metric_name in metrics.columns:
 #             # NaNs are skipped
 #             assert np.allclose(metrics[metric_name].dropna(), metrics_par[metric_name].dropna())
-
-if __name__ == "__main__":
-
-    test_compute_quality_metrics(sorting_analyzer_simple)
-    test_compute_quality_metrics_recordingless(sorting_analyzer_simple)
-    test_empty_units(sorting_analyzer_simple)