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Merged
alejoe91 merged 26 commits into from
Jul 3, 2026
Merged

Prepare release 0.103.0 #117

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9b73d82
build: update all repo commits
alejoe91 Jun 30, 2026
f7d4b9c
test: separate nwb/si test data and pin versions
alejoe91 Jun 30, 2026
fae3890
fix: nwb export print
alejoe91 Jun 30, 2026
6d92fa3
build: add sortingview to requirements
alejoe91 Jun 30, 2026
55eb32d
docs: update docs, params schema, and params
alejoe91 Jun 30, 2026
01b44af
build: update postprocessing version
alejoe91 Jun 30, 2026
4057006
doc: add lupin and relarted params
alejoe91 Jun 30, 2026
be03df3
test: use lupin in si test
alejoe91 Jun 30, 2026
87d46e1
build: update postprocessing
alejoe91 Jun 30, 2026
796b112
fix: update params metrics files
alejoe91 Jun 30, 2026
a4f8349
fix: rmeove template metrics sparsity
alejoe91 Jun 30, 2026
8c5609f
fix: rmeove template metrics sparsity 2
alejoe91 Jun 30, 2026
819d6f6
build: update postprocessing
alejoe91 Jun 30, 2026
bc22d65
fix: spykingcircus2 and curation params
alejoe91 Jul 1, 2026
8e0acb7
test: add check_pipeline_results script
alejoe91 Jul 1, 2026
5f2c89d
fix: num nwb sessions in si test should be 3
alejoe91 Jul 1, 2026
120b187
test: improve checker
alejoe91 Jul 2, 2026
c932f67
fix: requirements and data paths in checks
alejoe91 Jul 2, 2026
edcfe63
fix: curation.json propagation and add checker on curation
alejoe91 Jul 2, 2026
fbe775c
test: install spikeinterface[full]
alejoe91 Jul 2, 2026
8103516
test: add checker for schema and sorter params
alejoe91 Jul 2, 2026
aee3157
fix: install hdmf-zarr in custom test
alejoe91 Jul 2, 2026
e6783f6
build: update Kilosort to v4.1.7
alejoe91 Jul 2, 2026
3cf11ed
test: add concurrency check
alejoe91 Jul 2, 2026
74c6387
build: si 0.104.8, aind-nwb-utils, prepare figpack dependencies
alejoe91 Jul 3, 2026
9b58fa6
docs: fix releases and add 1.3.0 to readme
alejoe91 Jul 3, 2026
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62 changes: 51 additions & 11 deletions .github/workflows/params_test_custom.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,13 +24,11 @@
"margin_ms": 100.0
},
"highpass_filter": {
"freq_min": 300.0,
"margin_ms": 5.0
"freq_min": 300.0
},
"bandpass_filter": {
"freq_min": 300.0,
"freq_max": 6000.0,
"margin_ms": 5.0
"freq_max": 6000.0
},
"detect_and_remove_bad_channels": {
"method": "coherence+psd",
Expand Down Expand Up @@ -107,9 +105,50 @@
"chunk_duration": "1s",
"progress_bar": false
},
"query": "isi_violations_ratio < 0.5 and presence_ratio > 0.8 and amplitude_cutoff < 0.1",
"noise_neural_classifier": "SpikeInterface/UnitRefine_noise_neural_classifier",
"sua_mua_classifier": "SpikeInterface/UnitRefine_sua_mua_classifier"
"qc_thresholds": {
"rp_contamination": {"less": 0.5},
"presence_ratio": {"greater": 0.8},
"amplitude_cutoff": {"less": 0.1}
},
"unitrefine": {
"noise_neural_classifier": "SpikeInterface/UnitRefine_noise_neural_classifier",
"sua_mua_classifier": "SpikeInterface/UnitRefine_sua_mua_classifier"
},
"bombcell": {
"noise": {
"num_positive_peaks": {"greater": null, "less": 2},
"num_negative_peaks": {"greater": null, "less": 1},
"peak_to_trough_duration": {"greater": 0.0001, "less": 0.00115},
"waveform_baseline_flatness": {"greater": null, "less": 0.5},
"peak_after_to_trough_ratio": {"greater": null, "less": 0.8},
"exp_decay": {"greater": 0.01, "less": 0.1}
},
"mua": {
"amplitude_median": {"greater": 30, "less": null, "abs": true},
"snr": {"greater": 5, "less": null},
"amplitude_cutoff": {"greater": null, "less": 0.2},
"num_spikes": {"greater": 300, "less": null},
"rp_contamination": {"greater": null, "less": 0.1},
"presence_ratio": {"greater": 0.7, "less": null},
"drift_ptp": {"greater": null, "less": 100}
},
"non-somatic": {
"peak_before_to_trough_ratio": {"greater": null, "less": 3},
"peak_before_width": {"greater": 0.00015, "less": null},
"trough_width": {"greater": 0.0002, "less": null},
"peak_before_to_peak_after_ratio": {"greater": null, "less": 3},
"main_peak_to_trough_ratio": {"greater": null, "less": 0.8}
}
},
"noise_strategy": "bombcell+unitrefine",
"slay": {
"template_similarity": {"templates_diff": 0.35},
"slay": {
"k1": 0.25,
"k2": 1,
"slay_threshold": 0.4
}
}
},
"visualization": {
"job_kwargs": {
Expand Down Expand Up @@ -173,7 +212,7 @@
},
"sorter": {
"general": {"ms_before": 0.5, "ms_after": 1.5, "radius_um": 100.0},
"filtering": {"freq_min": 150, "freq_max": 7000, "ftype": "bessel", "filter_order": 2, "margin_ms": 20},
"filtering": {"freq_min": 150, "freq_max": 7000, "ftype": "bessel", "filter_order": 2},
"whitening": {"mode": "local", "regularize": false},
"detection": {
"method": "matched_filtering",
Expand All @@ -182,17 +221,18 @@
},
"selection": {
"method": "uniform",
"method_kwargs": {"n_peaks_per_channel": 5000, "min_n_peaks": 100000, "select_per_channel": false},
"method_kwargs": {"n_peaks_per_channel": 5000, "min_n_peaks": 100000, "select_per_channel": false}
},
"apply_motion_correction": true,
"motion_correction": {"preset": "dredge_fast"},
"merging": {"max_distance_um": 50},
"clustering": {"method": "iterative-hdbscan", "method_kwargs": {}},
"cleaning": {"min_snr": 5, "max_jitter_ms": 0.1, "sparsify_threshold": null},
"cleaning": {"min_snr": 5, "max_jitter_ms": 0.2, "sparsify_threshold": 1, "mean_sd_ratio_threshold": 3},
"min_firing_rate": 0.1,
"matching": {"method": "circus-omp", "method_kwargs": {}, "pipeline_kwargs": {}},
"apply_preprocessing": false,
"apply_whitening": true,
"cache_preprocessing": {"mode": "memory", "memory_limit": 0.5, "delete_cache": true},
"cache_preprocessing": {"mode": "no-cache"},
"chunk_preprocessing": {"memory_limit": null},
"multi_units_only": false,
"job_kwargs": {},
Expand Down
99 changes: 68 additions & 31 deletions .github/workflows/params_test_default.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,13 +24,11 @@
"margin_ms": 100.0
},
"highpass_filter": {
"freq_min": 300.0,
"margin_ms": 5.0
"freq_min": 300.0
},
"bandpass_filter": {
"freq_min": 300.0,
"freq_max": 6000.0,
"margin_ms": 5.0
"freq_max": 6000.0
},
"detect_and_remove_bad_channels": {
"method": "coherence+psd",
Expand Down Expand Up @@ -121,7 +119,6 @@
},
"template_metrics": {
"upsampling_factor": 10,
"sparsity": null,
"include_multi_channel_metrics": true
},
"principal_components": {
Expand All @@ -141,11 +138,12 @@
"amplitude_cutoff",
"amplitude_median",
"amplitude_cv",
"noise_cutoff",
"synchrony",
"firing_range",
"drift",
"isolation_distance",
"l_ratio",
"sd_ratio",
"mahalanobis",
"d_prime",
"nearest_neighbor",
"silhouette"
Expand All @@ -155,7 +153,7 @@
"bin_duration_s": 60
},
"snr": {
"peak_sign": "neg",
"peak_sign": "both",
"peak_mode": "extremum"
},
"isi_violation": {
Expand Down Expand Up @@ -188,6 +186,17 @@
"min_num_bins": 10,
"amplitude_extension": "spike_amplitudes"
},
"noise_cutoff": {
"high_quantile": 0.25,
"low_quantile": 0.1,
"n_bins": 100
},
"sd_ratio": {
"censored_period_ms": 4.0,
"correct_for_drift": true,
"correct_for_template_itself": true,
"peak_sign": "neg"
},
"firing_range": {
"bin_size_s": 5,
"percentiles": [5,95]
Expand All @@ -197,21 +206,7 @@
},
"nearest_neighbor": {
"max_spikes": 10000,
"n_neighbors": 4
},
"nn_isolation": {
"max_spikes": 10000,
"min_spikes": 10,
"n_neighbors": 4,
"n_components": 10,
"radius_um": 100
},
"nn_noise_overlap": {
"max_spikes": 10000,
"min_spikes": 10,
"n_neighbors": 4,
"n_components": 10,
"radius_um": 100
"n_neighbors": 5
},
"silhouette": {
"method": ["simplified"]
Expand All @@ -225,9 +220,50 @@
"chunk_duration": "1s",
"progress_bar": false
},
"query": "isi_violations_ratio < 0.5 and presence_ratio > 0.8 and amplitude_cutoff < 0.1",
"noise_neural_classifier": "SpikeInterface/UnitRefine_noise_neural_classifier",
"sua_mua_classifier": "SpikeInterface/UnitRefine_sua_mua_classifier"
"qc_thresholds": {
"rp_contamination": {"less": 0.5},
"presence_ratio": {"greater": 0.8},
"amplitude_cutoff": {"less": 0.1}
},
"unitrefine": {
"noise_neural_classifier": "SpikeInterface/UnitRefine_noise_neural_classifier",
"sua_mua_classifier": "SpikeInterface/UnitRefine_sua_mua_classifier"
},
"bombcell": {
"noise": {
"num_positive_peaks": {"greater": null, "less": 2},
"num_negative_peaks": {"greater": null, "less": 1},
"peak_to_trough_duration": {"greater": 0.0001, "less": 0.00115},
"waveform_baseline_flatness": {"greater": null, "less": 0.5},
"peak_after_to_trough_ratio": {"greater": null, "less": 0.8},
"exp_decay": {"greater": 0.01, "less": 0.1}
},
"mua": {
"amplitude_median": {"greater": 30, "less": null, "abs": true},
"snr": {"greater": 5, "less": null},
"amplitude_cutoff": {"greater": null, "less": 0.2},
"num_spikes": {"greater": 300, "less": null},
"rp_contamination": {"greater": null, "less": 0.1},
"presence_ratio": {"greater": 0.7, "less": null},
"drift_ptp": {"greater": null, "less": 100}
},
"non-somatic": {
"peak_before_to_trough_ratio": {"greater": null, "less": 3},
"peak_before_width": {"greater": 0.00015, "less": null},
"trough_width": {"greater": 0.0002, "less": null},
"peak_before_to_peak_after_ratio": {"greater": null, "less": 3},
"main_peak_to_trough_ratio": {"greater": null, "less": 0.8}
}
},
"noise_strategy": "bombcell+unitrefine",
"slay": {
"template_similarity": {"templates_diff": 0.35},
"slay": {
"k1": 0.25,
"k2": 1,
"slay_threshold": 0.4
}
}
},
"visualization": {
"job_kwargs": {
Expand Down Expand Up @@ -263,7 +299,7 @@
}
},
"nwb": {
"backend": "zarr",
"backend": "hdf5",
"ecephys": {
"stub": false,
"stub_seconds": 10,
Expand Down Expand Up @@ -291,7 +327,7 @@
},
"sorter": {
"general": {"ms_before": 0.5, "ms_after": 1.5, "radius_um": 100.0},
"filtering": {"freq_min": 150, "freq_max": 7000, "ftype": "bessel", "filter_order": 2, "margin_ms": 20},
"filtering": {"freq_min": 150, "freq_max": 7000, "ftype": "bessel", "filter_order": 2},
"whitening": {"mode": "local", "regularize": false},
"detection": {
"method": "matched_filtering",
Expand All @@ -300,17 +336,18 @@
},
"selection": {
"method": "uniform",
"method_kwargs": {"n_peaks_per_channel": 5000, "min_n_peaks": 100000, "select_per_channel": false},
"method_kwargs": {"n_peaks_per_channel": 5000, "min_n_peaks": 100000, "select_per_channel": false}
},
"apply_motion_correction": true,
"motion_correction": {"preset": "dredge_fast"},
"merging": {"max_distance_um": 50},
"clustering": {"method": "iterative-hdbscan", "method_kwargs": {}},
"cleaning": {"min_snr": 5, "max_jitter_ms": 0.1, "sparsify_threshold": null},
"cleaning": {"min_snr": 5, "max_jitter_ms": 0.2, "sparsify_threshold": 1, "mean_sd_ratio_threshold": 3},
"min_firing_rate": 0.1,
"matching": {"method": "circus-omp", "method_kwargs": {}, "pipeline_kwargs": {}},
"apply_preprocessing": false,
"apply_whitening": true,
"cache_preprocessing": {"mode": "memory", "memory_limit": 0.5, "delete_cache": true},
"cache_preprocessing": {"mode": "no-cache"},
"chunk_preprocessing": {"memory_limit": null},
"multi_units_only": false,
"job_kwargs": {},
Expand Down
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