v2.0 b5.post1

Merge pull request #10 from BarbourLab/dev

pyproject.toml

@@ -3,27 +3,27 @@ requires = ["pip>=21.3", "setuptools>=65.6.3"]
 
 [project]
 name = "lussac"
-version = "2.0.0b5"
+version = "2.0.0b5.post1"
 authors = [
 	{name="Aurélien Wyngaard", email="[email protected]"}
 ]
 description = "Python package for automatic post-processing and merging of multiple spike-sorting analyses."
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
-	"networkx>=3.0",
-	"numpy>=1.23",
-	"pandas>=1.4.4",
-	"scikit-learn>=1.1.0",
-	"scipy>=1.9",
-	"plotly>=5.8.2",
+	"networkx >= 3.0",
+	"numpy >= 1.23",
+	"pandas >= 1.4.4",
+	"scikit-learn >= 1.1.0",
+	"scipy >= 1.9",
+	"plotly >= 5.8.2",
 	"kaleido",
-	"jsmin>=3.0",
-	"numba>=0.56.2",
-	"tqdm>=4.64.0",
-	"requests>=2.28.0",
-	"overrides>=7.3.1",
-	"spikeinterface>=0.99.1"
+	"jsmin >= 3.0",
+	"numba >= 0.56.2",
+	"tqdm >= 4.64.0",
+	"requests >= 2.28.0",
+	"overrides >= 7.3.1",
+	"spikeinterface >= 0.100.0, < 0.101.0"
 ]
 
 [project.scripts]
@@ -45,7 +45,7 @@ dev = [
 [project.urls]
 homepage = "https://github.com/BarbourLab/lussac"
 repository = "https://github.com/BarbourLab/lussac"
-documentation = "http://lussac.readthedocs.io/"
+documentation = "https://lussac.readthedocs.io/"
 changelog = "https://github.com/BarbourLab/lussac/releases"
 
 [tool.coverage.run]

src/lussac/core/module.py

@@ -113,7 +113,7 @@ def extract_waveforms(self, sorting: si.BaseSorting, sub_folder: str | None = No
 		recording = self.recording
 		if filter is not None:
 			assert len(filter) == 2, "The filter must be a list of 2 elements [min_cutoff, max_cutoff] (in Hz)."
-			recording = spre.gaussian_bandpass_filter(recording, *filter, margin_sd=2)
+			recording = spre.gaussian_filter(recording, *filter, margin_sd=2)
 
 		sorting = sorting.to_numpy_sorting()  # Convert sorting for faster extraction.
 		return si.extract_waveforms(recording, sorting, folder_path, allow_unfiltered=True, **params)
@@ -289,7 +289,7 @@ def get_units_attribute(self, attribute: str, params: dict) -> dict:
 		sorting = self.sorting
 		if 'filter' in params:
 			assert len(params['filter']) == 2, "The filter must be a list of 2 elements [min_cutoff, max_cutoff] (in Hz)."
-			recording = spre.gaussian_bandpass_filter(recording, *params['filter'], margin_sd=2)
+			recording = spre.gaussian_filter(recording, *params['filter'], margin_sd=2)
 
 		wvf_extractor = self.extract_waveforms(sub_folder=attribute, **params['wvf_extraction']) if 'wvf_extraction' in params \
 						else si.WaveformExtractor(recording, sorting, allow_unfiltered=True)

src/lussac/modules/merge_sortings.py

@@ -5,7 +5,6 @@
 from overrides import override
 import networkx as nx
 import numpy as np
-import scipy.stats
 from lussac.core import MultiSortingsModule
 import lussac.utils as utils
 import spikeinterface.core as si