Merge

pyproject.toml

@@ -91,7 +91,7 @@ full = [
     "networkx",
     "distinctipy",
     "matplotlib",
-    "cuda-python; sys_platform != 'darwin'",
+    "cuda-python; platform_system != 'Darwin'",
     "numba",
 ]
 
@@ -151,9 +151,9 @@ docs = [
     # for notebooks in the gallery
     "MEArec",   # Use as an example
     "datalad==0.16.2",  # Download mearec data, not sure if needed as is installed with conda as well because of git-annex
-    "pandas", # Don't know where this is needed
-    "hdbscan>=0.8.33",   # For sorters, probably spikingcircus
-    "numba", # For sorters, probably spikingcircus
+    "pandas", # in the modules gallery comparison tutorial
+    "hdbscan>=0.8.33",   # For sorters spykingcircus2 + tridesclous
+    "numba", # For many postprocessing functions
     # for release we need pypi, so this needs to be commented
     "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",  # We always build from the latest version
     "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",  # We always build from the latest version

src/spikeinterface/qualitymetrics/misc_metrics.py

@@ -242,7 +242,7 @@ def compute_isi_violations(waveform_extractor, isi_threshold_ms=1.5, min_isi_ms=
 
     It computes several metrics related to isi violations:
         * isi_violations_ratio: the relative firing rate of the hypothetical neurons that are
-                                generating the ISI violations. Described in [1]. See Notes.
+                                generating the ISI violations. Described in [Hill]_. See Notes.
         * isi_violation_count: number of ISI violations
 
     Parameters
@@ -262,7 +262,7 @@ def compute_isi_violations(waveform_extractor, isi_threshold_ms=1.5, min_isi_ms=
     Returns
     -------
     isi_violations_ratio : dict
-        The isi violation ratio described in [1].
+        The isi violation ratio described in [Hill]_.
     isi_violation_count : dict
         Number of violations.
 
@@ -343,7 +343,7 @@ def compute_refrac_period_violations(
     Returns
     -------
     rp_contamination : dict
-        The refactory period contamination described in [1].
+        The refactory period contamination described in [Llobet]_.
     rp_violations : dict
         Number of refractory period violations.
 
@@ -446,7 +446,8 @@ def compute_sliding_rp_violations(
     References
     ----------
     Based on metrics described in [IBL]_
-    This code was adapted from https://github.com/SteinmetzLab/slidingRefractory/blob/1.0.0/python/slidingRP/metrics.py
+    This code was adapted from:
+    https://github.com/SteinmetzLab/slidingRefractory/blob/1.0.0/python/slidingRP/metrics.py
     """
     duration = waveform_extractor.get_total_duration()
     sorting = waveform_extractor.sorting
@@ -609,7 +610,8 @@ def compute_amplitude_cutoffs(
     ----------
     Inspired by metric described in [Hill]_
 
-    This code was adapted from https://github.com/AllenInstitute/ecephys_spike_sorting/tree/master/ecephys_spike_sorting/modules/quality_metrics
+    This code was adapted from:
+    https://github.com/AllenInstitute/ecephys_spike_sorting/tree/master/ecephys_spike_sorting/modules/quality_metrics
 
     """
     sorting = waveform_extractor.sorting
@@ -1080,7 +1082,8 @@ def slidingRP_violations(
     return_conf_matrix : bool
         If True, the confidence matrix (n_contaminations, n_ref_periods) is returned, by default False
 
-    See: https://github.com/SteinmetzLab/slidingRefractory/blob/master/python/slidingRP/metrics.py#L166
+    Code adapted from:
+    https://github.com/SteinmetzLab/slidingRefractory/blob/master/python/slidingRP/metrics.py#L166
 
     Returns
     -------