From cf65301c82c48e72e10a77f6a7f891453b69e409 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Mon, 2 Oct 2023 15:24:30 +0200
Subject: [PATCH 01/27] Check main_ids are ints or strings

---
 src/spikeinterface/core/base.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
index 8b4f094c20..86692fa69c 100644
--- a/src/spikeinterface/core/base.py
+++ b/src/spikeinterface/core/base.py
@@ -47,6 +47,7 @@ def __init__(self, main_ids: Sequence) -> None:
         # 'main_ids' will either be channel_ids or units_ids
         # They is used for properties
         self._main_ids = np.array(main_ids)
+        assert self._main_ids.dtype.kind in "uiSU", "Main IDs can only be integers (signed/unsigned) or strings"
 
         # dict at object level
         self._annotations = {}

From 8343d3a70a6bb3cf56f3013abc77c8e534059150 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Mon, 2 Oct 2023 15:57:54 +0200
Subject: [PATCH 02/27] Fix NpySnippets

---
 src/spikeinterface/core/base.py                  | 3 ++-
 src/spikeinterface/core/baserecordingsnippets.py | 4 ++--
 src/spikeinterface/core/basesnippets.py          | 2 --
 src/spikeinterface/core/npysnippetsextractor.py  | 5 ++++-
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
index 86692fa69c..f1a51c99d1 100644
--- a/src/spikeinterface/core/base.py
+++ b/src/spikeinterface/core/base.py
@@ -47,7 +47,8 @@ def __init__(self, main_ids: Sequence) -> None:
         # 'main_ids' will either be channel_ids or units_ids
         # They is used for properties
         self._main_ids = np.array(main_ids)
-        assert self._main_ids.dtype.kind in "uiSU", "Main IDs can only be integers (signed/unsigned) or strings"
+        if len(self._main_ids) > 0:
+            assert self._main_ids.dtype.kind in "uiSU", "Main IDs can only be integers (signed/unsigned) or strings"
 
         # dict at object level
         self._annotations = {}
diff --git a/src/spikeinterface/core/baserecordingsnippets.py b/src/spikeinterface/core/baserecordingsnippets.py
index affde8a75e..d411f38d2a 100644
--- a/src/spikeinterface/core/baserecordingsnippets.py
+++ b/src/spikeinterface/core/baserecordingsnippets.py
@@ -1,4 +1,4 @@
-from typing import List
+from __future__ import annotations
 from pathlib import Path
 
 import numpy as np
@@ -19,7 +19,7 @@ class BaseRecordingSnippets(BaseExtractor):
 
     has_default_locations = False
 
-    def __init__(self, sampling_frequency: float, channel_ids: List, dtype):
+    def __init__(self, sampling_frequency: float, channel_ids: list[str, int], dtype: np.dtype):
         BaseExtractor.__init__(self, channel_ids)
         self._sampling_frequency = sampling_frequency
         self._dtype = np.dtype(dtype)
diff --git a/src/spikeinterface/core/basesnippets.py b/src/spikeinterface/core/basesnippets.py
index f35bc2b266..b4e3c11f55 100644
--- a/src/spikeinterface/core/basesnippets.py
+++ b/src/spikeinterface/core/basesnippets.py
@@ -1,10 +1,8 @@
 from typing import List, Union
-from pathlib import Path
 from .base import BaseSegment
 from .baserecordingsnippets import BaseRecordingSnippets
 import numpy as np
 from warnings import warn
-from probeinterface import Probe, ProbeGroup, write_probeinterface, read_probeinterface, select_axes
 
 # snippets segments?
 
diff --git a/src/spikeinterface/core/npysnippetsextractor.py b/src/spikeinterface/core/npysnippetsextractor.py
index 80979ce6c9..69c48356e5 100644
--- a/src/spikeinterface/core/npysnippetsextractor.py
+++ b/src/spikeinterface/core/npysnippetsextractor.py
@@ -27,6 +27,9 @@ def __init__(
         num_segments = len(file_paths)
         data = np.load(file_paths[0], mmap_mode="r")
 
+        if channel_ids is None:
+            channel_ids = np.arange(data["snippet"].shape[2])
+
         BaseSnippets.__init__(
             self,
             sampling_frequency,
@@ -84,7 +87,7 @@ def write_snippets(snippets, file_paths, dtype=None):
             arr = np.empty(n, dtype=snippets_t, order="F")
             arr["frame"] = snippets.get_frames(segment_index=i)
             arr["snippet"] = snippets.get_snippets(segment_index=i).astype(dtype, copy=False)
-
+            file_paths[i].parent.mkdir(parents=True, exist_ok=True)
             np.save(file_paths[i], arr)
 
 

From 89d1f827c445702a61eda864c9972401567a9b67 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Mon, 2 Oct 2023 16:26:25 +0200
Subject: [PATCH 03/27] Force CellExplorer unit ids as int

---
 src/spikeinterface/core/base.py                               | 4 +++-
 src/spikeinterface/extractors/cellexplorersortingextractor.py | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
index f1a51c99d1..1116aeb507 100644
--- a/src/spikeinterface/core/base.py
+++ b/src/spikeinterface/core/base.py
@@ -48,7 +48,9 @@ def __init__(self, main_ids: Sequence) -> None:
         # They is used for properties
         self._main_ids = np.array(main_ids)
         if len(self._main_ids) > 0:
-            assert self._main_ids.dtype.kind in "uiSU", "Main IDs can only be integers (signed/unsigned) or strings"
+            assert (
+                self._main_ids.dtype.kind in "uiSU"
+            ), f"Main IDs can only be integers (signed/unsigned) or strings, not {self._main_ids.dtype}"
 
         # dict at object level
         self._annotations = {}
diff --git a/src/spikeinterface/extractors/cellexplorersortingextractor.py b/src/spikeinterface/extractors/cellexplorersortingextractor.py
index 31241a4147..f72670fbcd 100644
--- a/src/spikeinterface/extractors/cellexplorersortingextractor.py
+++ b/src/spikeinterface/extractors/cellexplorersortingextractor.py
@@ -118,7 +118,7 @@ def __init__(
         spike_times = spikes_data["times"]
 
         # CellExplorer reports spike times in units seconds; SpikeExtractors uses time units of sampling frames
-        unit_ids = unit_ids[:].tolist()
+        unit_ids = unit_ids[:].astype(int).tolist()
         spiketrains_dict = {unit_id: spike_times[index] for index, unit_id in enumerate(unit_ids)}
         for unit_id in unit_ids:
             spiketrains_dict[unit_id] = (sampling_frequency * spiketrains_dict[unit_id]).round().astype(np.int64)

From d75f0588707da10a61e926e337334739a0b9a20b Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Tue, 3 Oct 2023 10:58:15 +0200
Subject: [PATCH 04/27] Update
 src/spikeinterface/extractors/cellexplorersortingextractor.py

Co-authored-by: Heberto Mayorquin <h.mayorquin@gmail.com>
---
 src/spikeinterface/extractors/cellexplorersortingextractor.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/spikeinterface/extractors/cellexplorersortingextractor.py b/src/spikeinterface/extractors/cellexplorersortingextractor.py
index f72670fbcd..0096a40a79 100644
--- a/src/spikeinterface/extractors/cellexplorersortingextractor.py
+++ b/src/spikeinterface/extractors/cellexplorersortingextractor.py
@@ -119,6 +119,7 @@ def __init__(
 
         # CellExplorer reports spike times in units seconds; SpikeExtractors uses time units of sampling frames
         unit_ids = unit_ids[:].astype(int).tolist()
+        unit_ids = [str(unit_id) for unit_id in unit_ids]
         spiketrains_dict = {unit_id: spike_times[index] for index, unit_id in enumerate(unit_ids)}
         for unit_id in unit_ids:
             spiketrains_dict[unit_id] = (sampling_frequency * spiketrains_dict[unit_id]).round().astype(np.int64)

From 86b2271df55b671b49cd5b58601df94ab0dd2109 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Wed, 4 Oct 2023 16:03:51 +0200
Subject: [PATCH 05/27] Change some default parameters for better user
 experience.

---
 src/spikeinterface/core/waveform_extractor.py          | 8 ++++----
 src/spikeinterface/postprocessing/correlograms.py      | 4 ++--
 src/spikeinterface/postprocessing/unit_localization.py | 2 +-
 src/spikeinterface/sorters/runsorter.py                | 2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/spikeinterface/core/waveform_extractor.py b/src/spikeinterface/core/waveform_extractor.py
index 6d9e5d41e3..1c6002226f 100644
--- a/src/spikeinterface/core/waveform_extractor.py
+++ b/src/spikeinterface/core/waveform_extractor.py
@@ -1458,13 +1458,13 @@ def extract_waveforms(
     folder=None,
     mode="folder",
     precompute_template=("average",),
-    ms_before=3.0,
-    ms_after=4.0,
+    ms_before=1.0,
+    ms_after=2.0,
     max_spikes_per_unit=500,
     overwrite=False,
     return_scaled=True,
     dtype=None,
-    sparse=False,
+    sparse=True,
     sparsity=None,
     num_spikes_for_sparsity=100,
     allow_unfiltered=False,
@@ -1508,7 +1508,7 @@ def extract_waveforms(
         If True and recording has gain_to_uV/offset_to_uV properties, waveforms are converted to uV.
     dtype: dtype or None
         Dtype of the output waveforms. If None, the recording dtype is maintained.
-    sparse: bool (default False)
+    sparse: bool (default True)
         If True, before extracting all waveforms the `precompute_sparsity()` function is run using
         a few spikes to get an estimate of dense templates to create a ChannelSparsity object.
         Then, the waveforms will be sparse at extraction time, which saves a lot of memory.
diff --git a/src/spikeinterface/postprocessing/correlograms.py b/src/spikeinterface/postprocessing/correlograms.py
index 6cd5238abd..6e693635eb 100644
--- a/src/spikeinterface/postprocessing/correlograms.py
+++ b/src/spikeinterface/postprocessing/correlograms.py
@@ -137,8 +137,8 @@ def compute_crosscorrelogram_from_spiketrain(spike_times1, spike_times2, window_
 def compute_correlograms(
     waveform_or_sorting_extractor,
     load_if_exists=False,
-    window_ms: float = 100.0,
-    bin_ms: float = 5.0,
+    window_ms: float = 50.0,
+    bin_ms: float = 1.0,
     method: str = "auto",
 ):
     """Compute auto and cross correlograms.
diff --git a/src/spikeinterface/postprocessing/unit_localization.py b/src/spikeinterface/postprocessing/unit_localization.py
index d2739f69dd..48ceb34a4e 100644
--- a/src/spikeinterface/postprocessing/unit_localization.py
+++ b/src/spikeinterface/postprocessing/unit_localization.py
@@ -96,7 +96,7 @@ def get_extension_function():
 
 
 def compute_unit_locations(
-    waveform_extractor, load_if_exists=False, method="center_of_mass", outputs="numpy", **method_kwargs
+    waveform_extractor, load_if_exists=False, method="monopolar_triangulation", outputs="numpy", **method_kwargs
 ):
     """
     Localize units in 2D or 3D with several methods given the template.
diff --git a/src/spikeinterface/sorters/runsorter.py b/src/spikeinterface/sorters/runsorter.py
index 9bacd8e2c9..a49a605a75 100644
--- a/src/spikeinterface/sorters/runsorter.py
+++ b/src/spikeinterface/sorters/runsorter.py
@@ -91,7 +91,7 @@ def run_sorter(
     sorter_name: str,
     recording: BaseRecording,
     output_folder: Optional[str] = None,
-    remove_existing_folder: bool = True,
+    remove_existing_folder: bool = False,
     delete_output_folder: bool = False,
     verbose: bool = False,
     raise_error: bool = True,

From d9803d43e9598810337d11d2e68414261dbc3b81 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Wed, 4 Oct 2023 17:07:05 +0200
Subject: [PATCH 06/27] oups

---
 src/spikeinterface/core/waveform_extractor.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/spikeinterface/core/waveform_extractor.py b/src/spikeinterface/core/waveform_extractor.py
index d83b3d66f1..eb027faf81 100644
--- a/src/spikeinterface/core/waveform_extractor.py
+++ b/src/spikeinterface/core/waveform_extractor.py
@@ -1726,6 +1726,7 @@ def precompute_sparsity(
             max_spikes_per_unit=num_spikes_for_sparsity,
             return_scaled=False,
             allow_unfiltered=allow_unfiltered,
+            sparse=False,
             **job_kwargs,
         )
         local_sparsity = compute_sparsity(local_we, **sparse_kwargs)

From 590cd6ba2440569469859a0e08ce321a5320e27d Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Wed, 4 Oct 2023 21:04:26 +0200
Subject: [PATCH 07/27] small fix

---
 src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py b/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
index d25f1ea97b..364fc298c6 100644
--- a/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
+++ b/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
@@ -43,6 +43,8 @@ def plot(self):
         self._do_plot()
 
     def _do_plot(self):
+        from matplotlib import pyplot as plt
+        
         fig = self.figure
 
         for ax in fig.axes:

From 204c8e90fd44d56e4b5eb6b0b7e92f09ea18db91 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Wed, 4 Oct 2023 21:08:17 +0200
Subject: [PATCH 08/27] fix waveform extactor with empty sorting and sparse

---
 src/spikeinterface/core/sparsity.py                      | 6 +++++-
 src/spikeinterface/core/tests/test_waveform_extractor.py | 3 ++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/sparsity.py b/src/spikeinterface/core/sparsity.py
index 8c5c62d568..896e3800d7 100644
--- a/src/spikeinterface/core/sparsity.py
+++ b/src/spikeinterface/core/sparsity.py
@@ -102,7 +102,11 @@ def __init__(self, mask, unit_ids, channel_ids):
 
         self.num_channels = self.channel_ids.size
         self.num_units = self.unit_ids.size
-        self.max_num_active_channels = self.mask.sum(axis=1).max()
+        if self.mask.shape[0]:
+            self.max_num_active_channels = self.mask.sum(axis=1).max()
+        else:
+            # empty sorting without units
+            self.max_num_active_channels = 0
 
     def __repr__(self):
         density = np.mean(self.mask)
diff --git a/src/spikeinterface/core/tests/test_waveform_extractor.py b/src/spikeinterface/core/tests/test_waveform_extractor.py
index 2bbf5e9b0f..00244f600b 100644
--- a/src/spikeinterface/core/tests/test_waveform_extractor.py
+++ b/src/spikeinterface/core/tests/test_waveform_extractor.py
@@ -556,4 +556,5 @@ def test_non_json_object():
     # test_portability()
     # test_recordingless()
     # test_compute_sparsity()
-    test_non_json_object()
+    # test_non_json_object()
+    test_empty_sorting()

From 50f6fcf5322bf10f1b8310ac228921a975b17557 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Thu, 5 Oct 2023 12:16:50 +0200
Subject: [PATCH 09/27] small fix unrelated

---
 src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py b/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
index 364fc298c6..c921f42c6d 100644
--- a/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
+++ b/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
@@ -179,6 +179,8 @@ def plot(self):
 
     def _do_plot(self):
         import sklearn
+        import matplotlib.pyplot as plt
+        import matplotlib
 
         # compute similarity
         # take index of template (respect unit_ids order)

From 0798169827321ca8a823780baa377ed8d5820469 Mon Sep 17 00:00:00 2001
From: Garcia Samuel <sam.garcia.die@gmail.com>
Date: Thu, 5 Oct 2023 13:12:27 +0200
Subject: [PATCH 10/27] Update src/spikeinterface/core/waveform_extractor.py

---
 src/spikeinterface/core/waveform_extractor.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/core/waveform_extractor.py b/src/spikeinterface/core/waveform_extractor.py
index eb027faf81..0fc5694207 100644
--- a/src/spikeinterface/core/waveform_extractor.py
+++ b/src/spikeinterface/core/waveform_extractor.py
@@ -1507,7 +1507,7 @@ def extract_waveforms(
         If True and recording has gain_to_uV/offset_to_uV properties, waveforms are converted to uV.
     dtype: dtype or None
         Dtype of the output waveforms. If None, the recording dtype is maintained.
-    sparse: bool (default True)
+    sparse: bool, default: True
         If True, before extracting all waveforms the `precompute_sparsity()` function is run using
         a few spikes to get an estimate of dense templates to create a ChannelSparsity object.
         Then, the waveforms will be sparse at extraction time, which saves a lot of memory.

From 4293b2244be7b71aa0ce68f4dabad24d23318637 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 5 Oct 2023 11:17:03 +0000
Subject: [PATCH 11/27] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py b/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
index c921f42c6d..468b96ff3b 100644
--- a/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
+++ b/src/spikeinterface/widgets/_legacy_mpl_widgets/collisioncomp.py
@@ -44,7 +44,7 @@ def plot(self):
 
     def _do_plot(self):
         from matplotlib import pyplot as plt
-        
+
         fig = self.figure
 
         for ax in fig.axes:

From 3371915310a4bda8cbd9ecd8a5e2d2f3e0ee55b1 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Thu, 5 Oct 2023 15:36:46 +0200
Subject: [PATCH 12/27] Keep sparse=False in postprocessing tests

---
 .../postprocessing/tests/common_extension_tests.py             | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/spikeinterface/postprocessing/tests/common_extension_tests.py b/src/spikeinterface/postprocessing/tests/common_extension_tests.py
index 8f864e9b84..50e2ecdb57 100644
--- a/src/spikeinterface/postprocessing/tests/common_extension_tests.py
+++ b/src/spikeinterface/postprocessing/tests/common_extension_tests.py
@@ -57,6 +57,7 @@ def setUp(self):
             ms_before=3.0,
             ms_after=4.0,
             max_spikes_per_unit=500,
+            sparse=False,
             n_jobs=1,
             chunk_size=30000,
             overwrite=True,
@@ -92,6 +93,7 @@ def setUp(self):
             ms_before=3.0,
             ms_after=4.0,
             max_spikes_per_unit=500,
+            sparse=False,
             n_jobs=1,
             chunk_size=30000,
             overwrite=True,
@@ -112,6 +114,7 @@ def setUp(self):
             recording,
             sorting,
             mode="memory",
+            sparse=False,
             ms_before=3.0,
             ms_after=4.0,
             max_spikes_per_unit=500,

From f2fe6bbcedc5a1cca38918444afe52e3ae1bec19 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 5 Oct 2023 11:42:38 -0400
Subject: [PATCH 13/27] assert typo fixes round 1

---
 src/spikeinterface/core/base.py               |  6 +--
 src/spikeinterface/core/baserecording.py      |  6 +--
 src/spikeinterface/core/basesorting.py        |  2 +-
 .../core/binaryrecordingextractor.py          |  2 +-
 .../core/channelsaggregationrecording.py      |  4 +-
 src/spikeinterface/core/channelslice.py       |  4 +-
 .../core/frameslicerecording.py               |  2 +-
 src/spikeinterface/core/frameslicesorting.py  |  8 ++--
 src/spikeinterface/core/generate.py           |  4 +-
 src/spikeinterface/core/template_tools.py     | 41 ++++++++++---------
 .../core/unitsaggregationsorting.py           |  2 +-
 11 files changed, 41 insertions(+), 40 deletions(-)

diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
index 8b4f094c20..ba18cf09b6 100644
--- a/src/spikeinterface/core/base.py
+++ b/src/spikeinterface/core/base.py
@@ -45,7 +45,7 @@ def __init__(self, main_ids: Sequence) -> None:
         self._kwargs = {}
 
         # 'main_ids' will either be channel_ids or units_ids
-        # They is used for properties
+        # They are used for properties
         self._main_ids = np.array(main_ids)
 
         # dict at object level
@@ -984,7 +984,7 @@ def _load_extractor_from_dict(dic) -> BaseExtractor:
     class_name = None
 
     if "kwargs" not in dic:
-        raise Exception(f"This dict cannot be load into extractor {dic}")
+        raise Exception(f"This dict cannot be loaded into extractor {dic}")
 
     # Create new kwargs to avoid modifying the original dict["kwargs"]
     new_kwargs = dict()
@@ -1005,7 +1005,7 @@ def _load_extractor_from_dict(dic) -> BaseExtractor:
     assert extractor_class is not None and class_name is not None, "Could not load spikeinterface class"
     if not _check_same_version(class_name, dic["version"]):
         warnings.warn(
-            f"Versions are not the same. This might lead compatibility errors. "
+            f"Versions are not the same. This might lead to compatibility errors. "
             f"Using {class_name.split('.')[0]}=={dic['version']} is recommended"
         )
 
diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 08f187895b..d3572ef66b 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -305,7 +305,7 @@ def get_traces(
 
             if not self.has_scaled():
                 raise ValueError(
-                    "This recording do not support return_scaled=True (need gain_to_uV and offset_" "to_uV properties)"
+                    "This recording does not support return_scaled=True (need gain_to_uV and offset_" "to_uV properties)"
                 )
             else:
                 gains = self.get_property("gain_to_uV")
@@ -416,8 +416,8 @@ def set_times(self, times, segment_index=None, with_warning=True):
         if with_warning:
             warn(
                 "Setting times with Recording.set_times() is not recommended because "
-                "times are not always propagated to across preprocessing"
-                "Use use this carefully!"
+                "times are not always propagated across preprocessing"
+                "Use this carefully!"
             )
 
     def sample_index_to_time(self, sample_ind, segment_index=None):
diff --git a/src/spikeinterface/core/basesorting.py b/src/spikeinterface/core/basesorting.py
index e6d08d38f7..2a06a699cb 100644
--- a/src/spikeinterface/core/basesorting.py
+++ b/src/spikeinterface/core/basesorting.py
@@ -170,7 +170,7 @@ def register_recording(self, recording, check_spike_frames=True):
         if check_spike_frames:
             if has_exceeding_spikes(recording, self):
                 warnings.warn(
-                    "Some spikes are exceeding the recording's duration! "
+                    "Some spikes exceed the recording's duration! "
                     "Removing these excess spikes with `spikeinterface.curation.remove_excess_spikes()` "
                     "Might be necessary for further postprocessing."
                 )
diff --git a/src/spikeinterface/core/binaryrecordingextractor.py b/src/spikeinterface/core/binaryrecordingextractor.py
index 72a95637f6..b45290caa5 100644
--- a/src/spikeinterface/core/binaryrecordingextractor.py
+++ b/src/spikeinterface/core/binaryrecordingextractor.py
@@ -91,7 +91,7 @@ def __init__(
             file_path_list = [Path(file_paths)]
 
         if t_starts is not None:
-            assert len(t_starts) == len(file_path_list), "t_starts must be a list of same size than file_paths"
+            assert len(t_starts) == len(file_path_list), "t_starts must be a list of the same size as file_paths"
             t_starts = [float(t_start) for t_start in t_starts]
 
         dtype = np.dtype(dtype)
diff --git a/src/spikeinterface/core/channelsaggregationrecording.py b/src/spikeinterface/core/channelsaggregationrecording.py
index d36e168f8d..8714580821 100644
--- a/src/spikeinterface/core/channelsaggregationrecording.py
+++ b/src/spikeinterface/core/channelsaggregationrecording.py
@@ -104,11 +104,11 @@ def __init__(self, channel_map, parent_segments):
         times_kargs0 = parent_segment0.get_times_kwargs()
         if times_kargs0["time_vector"] is None:
             for ps in parent_segments:
-                assert ps.get_times_kwargs()["time_vector"] is None, "All segment should not have times set"
+                assert ps.get_times_kwargs()["time_vector"] is None, "All segments should not have times set"
         else:
             for ps in parent_segments:
                 assert ps.get_times_kwargs()["t_start"] == times_kargs0["t_start"], (
-                    "All segment should have the same " "t_start"
+                    "All segments should have the same " "t_start"
                 )
 
         BaseRecordingSegment.__init__(self, **times_kargs0)
diff --git a/src/spikeinterface/core/channelslice.py b/src/spikeinterface/core/channelslice.py
index ebd1b7db03..3a21e356a6 100644
--- a/src/spikeinterface/core/channelslice.py
+++ b/src/spikeinterface/core/channelslice.py
@@ -35,7 +35,7 @@ def __init__(self, parent_recording, channel_ids=None, renamed_channel_ids=None)
         ), "ChannelSliceRecording: renamed channel_ids must be the same size"
         assert (
             self._channel_ids.size == np.unique(self._channel_ids).size
-        ), "ChannelSliceRecording : channel_ids not unique"
+        ), "ChannelSliceRecording : channel_ids are not unique"
 
         sampling_frequency = parent_recording.get_sampling_frequency()
 
@@ -123,7 +123,7 @@ def __init__(self, parent_snippets, channel_ids=None, renamed_channel_ids=None):
         ), "ChannelSliceSnippets: renamed channel_ids must be the same size"
         assert (
             self._channel_ids.size == np.unique(self._channel_ids).size
-        ), "ChannelSliceSnippets : channel_ids not unique"
+        ), "ChannelSliceSnippets : channel_ids are not unique"
 
         sampling_frequency = parent_snippets.get_sampling_frequency()
 
diff --git a/src/spikeinterface/core/frameslicerecording.py b/src/spikeinterface/core/frameslicerecording.py
index 968f27c6ad..b8574c506f 100644
--- a/src/spikeinterface/core/frameslicerecording.py
+++ b/src/spikeinterface/core/frameslicerecording.py
@@ -27,7 +27,7 @@ class FrameSliceRecording(BaseRecording):
     def __init__(self, parent_recording, start_frame=None, end_frame=None):
         channel_ids = parent_recording.get_channel_ids()
 
-        assert parent_recording.get_num_segments() == 1, "FrameSliceRecording work only with one segment"
+        assert parent_recording.get_num_segments() == 1, "FrameSliceRecording only works with one segment"
 
         parent_size = parent_recording.get_num_samples(0)
         if start_frame is None:
diff --git a/src/spikeinterface/core/frameslicesorting.py b/src/spikeinterface/core/frameslicesorting.py
index 5da5350f06..ed1391b0e2 100644
--- a/src/spikeinterface/core/frameslicesorting.py
+++ b/src/spikeinterface/core/frameslicesorting.py
@@ -36,7 +36,7 @@ class FrameSliceSorting(BaseSorting):
     def __init__(self, parent_sorting, start_frame=None, end_frame=None, check_spike_frames=True):
         unit_ids = parent_sorting.get_unit_ids()
 
-        assert parent_sorting.get_num_segments() == 1, "FrameSliceSorting work only with one segment"
+        assert parent_sorting.get_num_segments() == 1, "FrameSliceSorting only works with one segment"
 
         if start_frame is None:
             start_frame = 0
@@ -49,10 +49,10 @@ def __init__(self, parent_sorting, start_frame=None, end_frame=None, check_spike
                 end_frame = parent_n_samples
             assert (
                 end_frame <= parent_n_samples
-            ), "`end_frame` should be smaller than the sortings total number of samples."
+            ), "`end_frame` should be smaller than the sortings' total number of samples."
             assert (
                 start_frame <= parent_n_samples
-            ), "`start_frame` should be smaller than the sortings total number of samples."
+            ), "`start_frame` should be smaller than the sortings' total number of samples."
             if check_spike_frames and has_exceeding_spikes(parent_sorting._recording, parent_sorting):
                 raise ValueError(
                     "The sorting object has spikes exceeding the recording duration. You have to remove those spikes "
@@ -67,7 +67,7 @@ def __init__(self, parent_sorting, start_frame=None, end_frame=None, check_spike
                 end_frame = max_spike_time + 1
 
         assert start_frame < end_frame, (
-            "`start_frame` should be greater than `end_frame`. "
+            "`start_frame` should be less than `end_frame`. "
             "This may be due to start_frame >= max_spike_time, if the end frame "
             "was not specified explicitly."
         )
diff --git a/src/spikeinterface/core/generate.py b/src/spikeinterface/core/generate.py
index 06a5ec96ec..0c67404069 100644
--- a/src/spikeinterface/core/generate.py
+++ b/src/spikeinterface/core/generate.py
@@ -1101,11 +1101,11 @@ def __init__(
             # handle also upsampling and jitter
             upsample_factor = templates.shape[3]
         elif templates.ndim == 5:
-            # handle also dirft
+            # handle also drift
             raise NotImplementedError("Drift will be implented soon...")
             # upsample_factor = templates.shape[3]
         else:
-            raise ValueError("templates have wring dim should 3 or 4")
+            raise ValueError("templates have wrong dim should 3 or 4")
 
         if upsample_factor is not None:
             assert upsample_vector is not None
diff --git a/src/spikeinterface/core/template_tools.py b/src/spikeinterface/core/template_tools.py
index 95278b76da..552642751c 100644
--- a/src/spikeinterface/core/template_tools.py
+++ b/src/spikeinterface/core/template_tools.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 import numpy as np
 import warnings
 
@@ -5,7 +6,7 @@
 from .recording_tools import get_channel_distances, get_noise_levels
 
 
-def get_template_amplitudes(waveform_extractor, peak_sign: str = "neg", mode: str = "extremum"):
+def get_template_amplitudes(waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "extremum"):
     """
     Get amplitude per channel for each unit.
 
@@ -13,9 +14,9 @@ def get_template_amplitudes(waveform_extractor, peak_sign: str = "neg", mode: st
     ----------
     waveform_extractor: WaveformExtractor
         The waveform extractor
-    peak_sign: str
-        Sign of the template to compute best channels ('neg', 'pos', 'both')
-    mode: str
+    peak_sign: "neg" | "pos" | "both", default: "neg"
+        Sign of the template to compute best channels
+    mode: "extremum" | "at_index", default: "extremum"
         'extremum':  max or min
         'at_index': take value at spike index
 
@@ -24,8 +25,8 @@ def get_template_amplitudes(waveform_extractor, peak_sign: str = "neg", mode: st
     peak_values: dict
         Dictionary with unit ids as keys and template amplitudes as values
     """
-    assert peak_sign in ("both", "neg", "pos")
-    assert mode in ("extremum", "at_index")
+    assert peak_sign in ("both", "neg", "pos"), "'peak_sign' must be 'both', 'neg', or 'pos'"
+    assert mode in ("extremum", "at_index"), "'mode' must be 'extremum' or 'at_index'"
     unit_ids = waveform_extractor.sorting.unit_ids
 
     before = waveform_extractor.nbefore
@@ -57,7 +58,7 @@ def get_template_amplitudes(waveform_extractor, peak_sign: str = "neg", mode: st
 
 
 def get_template_extremum_channel(
-    waveform_extractor, peak_sign: str = "neg", mode: str = "extremum", outputs: str = "id"
+    waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "extremum", outputs: "id" | "index" = "id"
 ):
     """
     Compute the channel with the extremum peak for each unit.
@@ -66,12 +67,12 @@ def get_template_extremum_channel(
     ----------
     waveform_extractor: WaveformExtractor
         The waveform extractor
-    peak_sign: str
-        Sign of the template to compute best channels ('neg', 'pos', 'both')
-    mode: str
+    peak_sign: "neg" | "pos" | "both", default: "neg"
+        Sign of the template to compute best channels
+    mode: "extremum" | "at_index", default: "extremum"
         'extremum':  max or min
         'at_index': take value at spike index
-    outputs: str
+    outputs: "id" | "index", default: "id"
         * 'id': channel id
         * 'index': channel index
 
@@ -159,7 +160,7 @@ def get_template_channel_sparsity(
 get_template_channel_sparsity.__doc__ = get_template_channel_sparsity.__doc__.format(_sparsity_doc)
 
 
-def get_template_extremum_channel_peak_shift(waveform_extractor, peak_sign: str = "neg"):
+def get_template_extremum_channel_peak_shift(waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg"):
     """
     In some situations spike sorters could return a spike index with a small shift related to the waveform peak.
     This function estimates and return these alignment shifts for the mean template.
@@ -169,8 +170,8 @@ def get_template_extremum_channel_peak_shift(waveform_extractor, peak_sign: str
     ----------
     waveform_extractor: WaveformExtractor
         The waveform extractor
-    peak_sign: str
-        Sign of the template to compute best channels ('neg', 'pos', 'both')
+    peak_sign: "neg" | "pos" | "both", default: "neg"
+        Sign of the template to compute best channels
 
     Returns
     -------
@@ -203,7 +204,7 @@ def get_template_extremum_channel_peak_shift(waveform_extractor, peak_sign: str
     return shifts
 
 
-def get_template_extremum_amplitude(waveform_extractor, peak_sign: str = "neg", mode: str = "at_index"):
+def get_template_extremum_amplitude(waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "at_index"):
     """
     Computes amplitudes on the best channel.
 
@@ -211,9 +212,9 @@ def get_template_extremum_amplitude(waveform_extractor, peak_sign: str = "neg",
     ----------
     waveform_extractor: WaveformExtractor
         The waveform extractor
-    peak_sign: str
-        Sign of the template to compute best channels ('neg', 'pos', 'both')
-    mode: str
+    peak_sign:  "neg" | "pos" | "both"
+        Sign of the template to compute best channels
+    mode: "extremum" | "at_index", default: "at_index"
         Where the amplitude is computed
         'extremum':  max or min
         'at_index': take value at spike index
@@ -223,8 +224,8 @@ def get_template_extremum_amplitude(waveform_extractor, peak_sign: str = "neg",
     amplitudes: dict
         Dictionary with unit ids as keys and amplitudes as values
     """
-    assert peak_sign in ("both", "neg", "pos")
-    assert mode in ("extremum", "at_index")
+    assert peak_sign in ("both", "neg", "pos"), "'peak_sign' must be  'neg' or 'pos' or 'both'"
+    assert mode in ("extremum", "at_index"), "'mode' must be 'extremum' or 'at_index'"
     unit_ids = waveform_extractor.sorting.unit_ids
 
     before = waveform_extractor.nbefore
diff --git a/src/spikeinterface/core/unitsaggregationsorting.py b/src/spikeinterface/core/unitsaggregationsorting.py
index 32158f00df..4e98864ba9 100644
--- a/src/spikeinterface/core/unitsaggregationsorting.py
+++ b/src/spikeinterface/core/unitsaggregationsorting.py
@@ -95,7 +95,7 @@ def __init__(self, sorting_list, renamed_unit_ids=None):
                 try:
                     property_dict[prop_name] = np.concatenate((property_dict[prop_name], values))
                 except Exception as e:
-                    print(f"Skipping property '{prop_name}' for shape inconsistency")
+                    print(f"Skipping property '{prop_name}' due to shape inconsistency")
                     del property_dict[prop_name]
                     break
         for prop_name, prop_values in property_dict.items():

From 2417b9af67a652f38e32cf24f749f9c7706554e9 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 5 Oct 2023 12:11:01 -0400
Subject: [PATCH 14/27] add asserts msgs and fix typos

---
 src/spikeinterface/preprocessing/clip.py             |  2 +-
 src/spikeinterface/preprocessing/common_reference.py |  2 +-
 .../preprocessing/detect_bad_channels.py             |  4 ++--
 src/spikeinterface/preprocessing/filter.py           |  6 +++---
 src/spikeinterface/preprocessing/filter_opencl.py    | 12 ++++++------
 .../preprocessing/highpass_spatial_filter.py         |  2 +-
 src/spikeinterface/preprocessing/normalize_scale.py  |  4 ++--
 src/spikeinterface/preprocessing/phase_shift.py      |  2 +-
 8 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/src/spikeinterface/preprocessing/clip.py b/src/spikeinterface/preprocessing/clip.py
index a2349c1ee9..cc18d51d2e 100644
--- a/src/spikeinterface/preprocessing/clip.py
+++ b/src/spikeinterface/preprocessing/clip.py
@@ -97,7 +97,7 @@ def __init__(
         chunk_size=500,
         seed=0,
     ):
-        assert direction in ("upper", "lower", "both")
+        assert direction in ("upper", "lower", "both"), "'direction' must be 'upper', 'lower', or 'both'"
 
         if fill_value is None or quantile_threshold is not None:
             random_data = get_random_data_chunks(
diff --git a/src/spikeinterface/preprocessing/common_reference.py b/src/spikeinterface/preprocessing/common_reference.py
index d2ac227217..6d6ce256de 100644
--- a/src/spikeinterface/preprocessing/common_reference.py
+++ b/src/spikeinterface/preprocessing/common_reference.py
@@ -83,7 +83,7 @@ def __init__(
                 ref_channel_ids = np.asarray(ref_channel_ids)
                 assert np.all(
                     [ch in recording.get_channel_ids() for ch in ref_channel_ids]
-                ), "Some wrong 'ref_channel_ids'!"
+                ), "Some 'ref_channel_ids' are wrong!"
         elif reference == "local":
             assert groups is None, "With 'local' CAR, the group option should not be used."
             closest_inds, dist = get_closest_channels(recording)
diff --git a/src/spikeinterface/preprocessing/detect_bad_channels.py b/src/spikeinterface/preprocessing/detect_bad_channels.py
index cc4e8601e2..e6e2836a35 100644
--- a/src/spikeinterface/preprocessing/detect_bad_channels.py
+++ b/src/spikeinterface/preprocessing/detect_bad_channels.py
@@ -211,9 +211,9 @@ def detect_bad_channels(
 
         if bad_channel_ids.size > recording.get_num_channels() / 3:
             warnings.warn(
-                "Over 1/3 of channels are detected as bad. In the precense of a high"
+                "Over 1/3 of channels are detected as bad. In the presence of a high"
                 "number of dead / noisy channels, bad channel detection may fail "
-                "(erroneously label good channels as dead)."
+                "(good channels may be erroneously labeled as dead)."
             )
 
     elif method == "neighborhood_r2":
diff --git a/src/spikeinterface/preprocessing/filter.py b/src/spikeinterface/preprocessing/filter.py
index 51c1fb4ad6..b31088edf7 100644
--- a/src/spikeinterface/preprocessing/filter.py
+++ b/src/spikeinterface/preprocessing/filter.py
@@ -71,10 +71,10 @@ def __init__(
     ):
         import scipy.signal
 
-        assert filter_mode in ("sos", "ba")
+        assert filter_mode in ("sos", "ba"), "'filter' mode must be 'sos' or 'ba'"
         fs = recording.get_sampling_frequency()
         if coeff is None:
-            assert btype in ("bandpass", "highpass")
+            assert btype in ("bandpass", "highpass"), "'bytpe' must be 'bandpass' or 'highpass'"
             # coefficient
             # self.coeff is 'sos' or 'ab' style
             filter_coeff = scipy.signal.iirfilter(
@@ -258,7 +258,7 @@ def __init__(self, recording, freq=3000, q=30, margin_ms=5.0, dtype=None):
         if dtype.kind == "u":
             raise TypeError(
                 "The notch filter only supports signed types. Use the 'dtype' argument"
-                "to specify a signed type (e.g. 'int16', 'float32'"
+                "to specify a signed type (e.g. 'int16', 'float32')"
             )
 
         BasePreprocessor.__init__(self, recording, dtype=dtype)
diff --git a/src/spikeinterface/preprocessing/filter_opencl.py b/src/spikeinterface/preprocessing/filter_opencl.py
index 790279d647..d3a08297c6 100644
--- a/src/spikeinterface/preprocessing/filter_opencl.py
+++ b/src/spikeinterface/preprocessing/filter_opencl.py
@@ -50,9 +50,9 @@ def __init__(
         margin_ms=5.0,
     ):
         assert HAVE_PYOPENCL, "You need to install pyopencl (and GPU driver!!)"
-
-        assert btype in ("bandpass", "lowpass", "highpass", "bandstop")
-        assert filter_mode in ("sos",)
+        btype_modes = ("bandpass", "lowpass", "highpass", "bandstop")
+        assert btype in btype_modes, f"'btype' must be in {btype_modes}"
+        assert filter_mode in ("sos",), "'filter_mode' must be 'sos'"
 
         # coefficient
         sf = recording.get_sampling_frequency()
@@ -96,8 +96,8 @@ def __init__(self, parent_recording_segment, executor, margin):
         self.margin = margin
 
     def get_traces(self, start_frame, end_frame, channel_indices):
-        assert start_frame is not None, "FilterOpenCLRecording work with fixed chunk_size"
-        assert end_frame is not None, "FilterOpenCLRecording work with fixed chunk_size"
+        assert start_frame is not None, "FilterOpenCLRecording only works with fixed chunk_size"
+        assert end_frame is not None, "FilterOpenCLRecording only works with fixed chunk_size"
 
         chunk_size = end_frame - start_frame
         if chunk_size != self.executor.chunk_size:
@@ -157,7 +157,7 @@ def process(self, traces):
 
         if traces.shape[0] != self.full_size:
             if self.full_size is not None:
-                print(f"Warning : chunk_size have change {self.chunk_size} {traces.shape[0]}, need recompile CL!!!")
+                print(f"Warning : chunk_size has changed {self.chunk_size} {traces.shape[0]}, need to recompile CL!!!")
             self.create_buffers_and_compile()
 
         event = pyopencl.enqueue_copy(self.queue, self.input_cl, traces)
diff --git a/src/spikeinterface/preprocessing/highpass_spatial_filter.py b/src/spikeinterface/preprocessing/highpass_spatial_filter.py
index aa98410568..4df4a409bc 100644
--- a/src/spikeinterface/preprocessing/highpass_spatial_filter.py
+++ b/src/spikeinterface/preprocessing/highpass_spatial_filter.py
@@ -212,7 +212,7 @@ def get_traces(self, start_frame, end_frame, channel_indices):
             traces = traces * self.taper[np.newaxis, :]
 
         # apply actual HP filter
-        import scipy
+        import scipy.signal
 
         traces = scipy.signal.sosfiltfilt(self.sos_filter, traces, axis=1)
 
diff --git a/src/spikeinterface/preprocessing/normalize_scale.py b/src/spikeinterface/preprocessing/normalize_scale.py
index 7d43982853..bd53866b6a 100644
--- a/src/spikeinterface/preprocessing/normalize_scale.py
+++ b/src/spikeinterface/preprocessing/normalize_scale.py
@@ -68,7 +68,7 @@ def __init__(
         dtype="float32",
         **random_chunk_kwargs,
     ):
-        assert mode in ("pool_channel", "by_channel")
+        assert mode in ("pool_channel", "by_channel"), "'mode' must be 'pool_channel' or 'by_channel'"
 
         random_data = get_random_data_chunks(recording, **random_chunk_kwargs)
 
@@ -260,7 +260,7 @@ def __init__(
         dtype="float32",
         **random_chunk_kwargs,
     ):
-        assert mode in ("median+mad", "mean+std")
+        assert mode in ("median+mad", "mean+std"), "'mode' must be 'median+mad' or 'mean+std'"
 
         # fix dtype
         dtype_ = fix_dtype(recording, dtype)
diff --git a/src/spikeinterface/preprocessing/phase_shift.py b/src/spikeinterface/preprocessing/phase_shift.py
index 9c8b2589a0..237f32eca4 100644
--- a/src/spikeinterface/preprocessing/phase_shift.py
+++ b/src/spikeinterface/preprocessing/phase_shift.py
@@ -42,7 +42,7 @@ def __init__(self, recording, margin_ms=40.0, inter_sample_shift=None, dtype=Non
             assert "inter_sample_shift" in recording.get_property_keys(), "'inter_sample_shift' is not a property!"
             sample_shifts = recording.get_property("inter_sample_shift")
         else:
-            assert len(inter_sample_shift) == recording.get_num_channels(), "sample "
+            assert len(inter_sample_shift) == recording.get_num_channels(), "the 'inter_sample_shift' must be same size at the num_channels "
             sample_shifts = np.asarray(inter_sample_shift)
 
         margin = int(margin_ms * recording.get_sampling_frequency() / 1000.0)

From 9db087de50bd4b132b5e42c743dcf17fa8a9106b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 5 Oct 2023 16:27:04 +0000
Subject: [PATCH 15/27] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/core/baserecording.py        |  3 ++-
 src/spikeinterface/core/template_tools.py       | 13 ++++++++++---
 src/spikeinterface/preprocessing/phase_shift.py |  4 +++-
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index d3572ef66b..2977211c25 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -305,7 +305,8 @@ def get_traces(
 
             if not self.has_scaled():
                 raise ValueError(
-                    "This recording does not support return_scaled=True (need gain_to_uV and offset_" "to_uV properties)"
+                    "This recording does not support return_scaled=True (need gain_to_uV and offset_"
+                    "to_uV properties)"
                 )
             else:
                 gains = self.get_property("gain_to_uV")
diff --git a/src/spikeinterface/core/template_tools.py b/src/spikeinterface/core/template_tools.py
index 552642751c..b6022e27c0 100644
--- a/src/spikeinterface/core/template_tools.py
+++ b/src/spikeinterface/core/template_tools.py
@@ -6,7 +6,9 @@
 from .recording_tools import get_channel_distances, get_noise_levels
 
 
-def get_template_amplitudes(waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "extremum"):
+def get_template_amplitudes(
+    waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "extremum"
+):
     """
     Get amplitude per channel for each unit.
 
@@ -58,7 +60,10 @@ def get_template_amplitudes(waveform_extractor, peak_sign: "neg" | "pos" | "both
 
 
 def get_template_extremum_channel(
-    waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "extremum", outputs: "id" | "index" = "id"
+    waveform_extractor,
+    peak_sign: "neg" | "pos" | "both" = "neg",
+    mode: "extremum" | "at_index" = "extremum",
+    outputs: "id" | "index" = "id",
 ):
     """
     Compute the channel with the extremum peak for each unit.
@@ -204,7 +209,9 @@ def get_template_extremum_channel_peak_shift(waveform_extractor, peak_sign: "neg
     return shifts
 
 
-def get_template_extremum_amplitude(waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "at_index"):
+def get_template_extremum_amplitude(
+    waveform_extractor, peak_sign: "neg" | "pos" | "both" = "neg", mode: "extremum" | "at_index" = "at_index"
+):
     """
     Computes amplitudes on the best channel.
 
diff --git a/src/spikeinterface/preprocessing/phase_shift.py b/src/spikeinterface/preprocessing/phase_shift.py
index 237f32eca4..bdba55038d 100644
--- a/src/spikeinterface/preprocessing/phase_shift.py
+++ b/src/spikeinterface/preprocessing/phase_shift.py
@@ -42,7 +42,9 @@ def __init__(self, recording, margin_ms=40.0, inter_sample_shift=None, dtype=Non
             assert "inter_sample_shift" in recording.get_property_keys(), "'inter_sample_shift' is not a property!"
             sample_shifts = recording.get_property("inter_sample_shift")
         else:
-            assert len(inter_sample_shift) == recording.get_num_channels(), "the 'inter_sample_shift' must be same size at the num_channels "
+            assert (
+                len(inter_sample_shift) == recording.get_num_channels()
+            ), "the 'inter_sample_shift' must be same size at the num_channels "
             sample_shifts = np.asarray(inter_sample_shift)
 
         margin = int(margin_ms * recording.get_sampling_frequency() / 1000.0)

From 57078791382deed5fe73c4799bd352e6c3e0ee80 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Thu, 5 Oct 2023 18:39:27 +0200
Subject: [PATCH 16/27] Fix ipywidgets with explicit dense/sparse waveforms

---
 .../widgets/tests/test_widgets.py             | 102 +++++++++---------
 1 file changed, 51 insertions(+), 51 deletions(-)

diff --git a/src/spikeinterface/widgets/tests/test_widgets.py b/src/spikeinterface/widgets/tests/test_widgets.py
index f44878927d..da16136fa9 100644
--- a/src/spikeinterface/widgets/tests/test_widgets.py
+++ b/src/spikeinterface/widgets/tests/test_widgets.py
@@ -49,28 +49,28 @@ def setUpClass(cls):
 
         cls.num_units = len(cls.sorting.get_unit_ids())
         if (cache_folder / "mearec_test").is_dir():
-            cls.we = load_waveforms(cache_folder / "mearec_test")
+            cls.we_dense = load_waveforms(cache_folder / "mearec_test")
         else:
-            cls.we = extract_waveforms(cls.recording, cls.sorting, cache_folder / "mearec_test")
+            cls.we_dense = extract_waveforms(cls.recording, cls.sorting, cache_folder / "mearec_test", sparse=False)
 
         sw.set_default_plotter_backend("matplotlib")
 
         metric_names = ["snr", "isi_violation", "num_spikes"]
-        _ = compute_spike_amplitudes(cls.we)
-        _ = compute_unit_locations(cls.we)
-        _ = compute_spike_locations(cls.we)
-        _ = compute_quality_metrics(cls.we, metric_names=metric_names)
-        _ = compute_template_metrics(cls.we)
-        _ = compute_correlograms(cls.we)
-        _ = compute_template_similarity(cls.we)
+        _ = compute_spike_amplitudes(cls.we_dense)
+        _ = compute_unit_locations(cls.we_dense)
+        _ = compute_spike_locations(cls.we_dense)
+        _ = compute_quality_metrics(cls.we_dense, metric_names=metric_names)
+        _ = compute_template_metrics(cls.we_dense)
+        _ = compute_correlograms(cls.we_dense)
+        _ = compute_template_similarity(cls.we_dense)
 
         # make sparse waveforms
-        cls.sparsity_radius = compute_sparsity(cls.we, method="radius", radius_um=50)
-        cls.sparsity_best = compute_sparsity(cls.we, method="best_channels", num_channels=5)
+        cls.sparsity_radius = compute_sparsity(cls.we_dense, method="radius", radius_um=50)
+        cls.sparsity_best = compute_sparsity(cls.we_dense, method="best_channels", num_channels=5)
         if (cache_folder / "mearec_test_sparse").is_dir():
             cls.we_sparse = load_waveforms(cache_folder / "mearec_test_sparse")
         else:
-            cls.we_sparse = cls.we.save(folder=cache_folder / "mearec_test_sparse", sparsity=cls.sparsity_radius)
+            cls.we_sparse = cls.we_dense.save(folder=cache_folder / "mearec_test_sparse", sparsity=cls.sparsity_radius)
 
         cls.skip_backends = ["ipywidgets", "ephyviewer"]
 
@@ -124,17 +124,17 @@ def test_plot_unit_waveforms(self):
         possible_backends = list(sw.UnitWaveformsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_unit_waveforms(self.we, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_unit_waveforms(self.we_dense, backend=backend, **self.backend_kwargs[backend])
                 unit_ids = self.sorting.unit_ids[:6]
                 sw.plot_unit_waveforms(
-                    self.we,
+                    self.we_dense,
                     sparsity=self.sparsity_radius,
                     unit_ids=unit_ids,
                     backend=backend,
                     **self.backend_kwargs[backend],
                 )
                 sw.plot_unit_waveforms(
-                    self.we,
+                    self.we_dense,
                     sparsity=self.sparsity_best,
                     unit_ids=unit_ids,
                     backend=backend,
@@ -148,10 +148,10 @@ def test_plot_unit_templates(self):
         possible_backends = list(sw.UnitWaveformsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_unit_templates(self.we, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_unit_templates(self.we_dense, backend=backend, **self.backend_kwargs[backend])
                 unit_ids = self.sorting.unit_ids[:6]
                 sw.plot_unit_templates(
-                    self.we,
+                    self.we_dense,
                     sparsity=self.sparsity_radius,
                     unit_ids=unit_ids,
                     backend=backend,
@@ -171,7 +171,7 @@ def test_plot_unit_waveforms_density_map(self):
             if backend not in self.skip_backends:
                 unit_ids = self.sorting.unit_ids[:2]
                 sw.plot_unit_waveforms_density_map(
-                    self.we, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend]
+                    self.we_dense, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend]
                 )
 
     def test_plot_unit_waveforms_density_map_sparsity_radius(self):
@@ -180,7 +180,7 @@ def test_plot_unit_waveforms_density_map_sparsity_radius(self):
             if backend not in self.skip_backends:
                 unit_ids = self.sorting.unit_ids[:2]
                 sw.plot_unit_waveforms_density_map(
-                    self.we,
+                    self.we_dense,
                     sparsity=self.sparsity_radius,
                     same_axis=False,
                     unit_ids=unit_ids,
@@ -234,11 +234,11 @@ def test_amplitudes(self):
         possible_backends = list(sw.AmplitudesWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_amplitudes(self.we, backend=backend, **self.backend_kwargs[backend])
-                unit_ids = self.we.unit_ids[:4]
-                sw.plot_amplitudes(self.we, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_amplitudes(self.we_dense, backend=backend, **self.backend_kwargs[backend])
+                unit_ids = self.we_dense.unit_ids[:4]
+                sw.plot_amplitudes(self.we_dense, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_amplitudes(
-                    self.we, unit_ids=unit_ids, plot_histograms=True, backend=backend, **self.backend_kwargs[backend]
+                    self.we_dense, unit_ids=unit_ids, plot_histograms=True, backend=backend, **self.backend_kwargs[backend]
                 )
                 sw.plot_amplitudes(
                     self.we_sparse,
@@ -252,9 +252,9 @@ def test_plot_all_amplitudes_distributions(self):
         possible_backends = list(sw.AllAmplitudesDistributionsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                unit_ids = self.we.unit_ids[:4]
+                unit_ids = self.we_dense.unit_ids[:4]
                 sw.plot_all_amplitudes_distributions(
-                    self.we, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend]
+                    self.we_dense, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend]
                 )
                 sw.plot_all_amplitudes_distributions(
                     self.we_sparse, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend]
@@ -264,7 +264,7 @@ def test_unit_locations(self):
         possible_backends = list(sw.UnitLocationsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_unit_locations(self.we, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_unit_locations(self.we_dense, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_unit_locations(
                     self.we_sparse, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend]
                 )
@@ -273,7 +273,7 @@ def test_spike_locations(self):
         possible_backends = list(sw.SpikeLocationsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_spike_locations(self.we, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_spike_locations(self.we_dense, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_spike_locations(
                     self.we_sparse, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend]
                 )
@@ -282,28 +282,28 @@ def test_similarity(self):
         possible_backends = list(sw.TemplateSimilarityWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_template_similarity(self.we, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_template_similarity(self.we_dense, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_template_similarity(self.we_sparse, backend=backend, **self.backend_kwargs[backend])
 
     def test_quality_metrics(self):
         possible_backends = list(sw.QualityMetricsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_quality_metrics(self.we, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_quality_metrics(self.we_dense, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_quality_metrics(self.we_sparse, backend=backend, **self.backend_kwargs[backend])
 
     def test_template_metrics(self):
         possible_backends = list(sw.TemplateMetricsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_template_metrics(self.we, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_template_metrics(self.we_dense, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_template_metrics(self.we_sparse, backend=backend, **self.backend_kwargs[backend])
 
     def test_plot_unit_depths(self):
         possible_backends = list(sw.UnitDepthsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_unit_depths(self.we, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_unit_depths(self.we_dense, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_unit_depths(self.we_sparse, backend=backend, **self.backend_kwargs[backend])
 
     def test_plot_unit_summary(self):
@@ -311,17 +311,17 @@ def test_plot_unit_summary(self):
         for backend in possible_backends:
             if backend not in self.skip_backends:
                 sw.plot_unit_summary(
-                    self.we, self.we.sorting.unit_ids[0], backend=backend, **self.backend_kwargs[backend]
+                    self.we_dense, self.we_dense.sorting.unit_ids[0], backend=backend, **self.backend_kwargs[backend]
                 )
                 sw.plot_unit_summary(
-                    self.we_sparse, self.we.sorting.unit_ids[0], backend=backend, **self.backend_kwargs[backend]
+                    self.we_sparse, self.we_sparse.sorting.unit_ids[0], backend=backend, **self.backend_kwargs[backend]
                 )
 
     def test_sorting_summary(self):
         possible_backends = list(sw.SortingSummaryWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_sorting_summary(self.we, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_sorting_summary(self.we_dense, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_sorting_summary(self.we_sparse, backend=backend, **self.backend_kwargs[backend])
 
     def test_plot_agreement_matrix(self):
@@ -355,23 +355,23 @@ def test_plot_rasters(self):
     mytest = TestWidgets()
     mytest.setUpClass()
 
-    # mytest.test_plot_unit_waveforms_density_map()
-    # mytest.test_plot_unit_summary()
-    # mytest.test_plot_all_amplitudes_distributions()
-    # mytest.test_plot_traces()
-    # mytest.test_plot_unit_waveforms()
-    # mytest.test_plot_unit_templates()
-    # mytest.test_plot_unit_templates()
-    # mytest.test_plot_unit_depths()
-    # mytest.test_plot_unit_templates()
-    # mytest.test_plot_unit_summary()
-    # mytest.test_unit_locations()
-    # mytest.test_quality_metrics()
-    # mytest.test_template_metrics()
-    # mytest.test_amplitudes()
-    # mytest.test_plot_agreement_matrix()
-    # mytest.test_plot_confusion_matrix()
-    # mytest.test_plot_probe_map()
+    mytest.test_plot_unit_waveforms_density_map()
+    mytest.test_plot_unit_summary()
+    mytest.test_plot_all_amplitudes_distributions()
+    mytest.test_plot_traces()
+    mytest.test_plot_unit_waveforms()
+    mytest.test_plot_unit_templates()
+    mytest.test_plot_unit_templates()
+    mytest.test_plot_unit_depths()
+    mytest.test_plot_unit_templates()
+    mytest.test_plot_unit_summary()
+    mytest.test_unit_locations()
+    mytest.test_quality_metrics()
+    mytest.test_template_metrics()
+    mytest.test_amplitudes()
+    mytest.test_plot_agreement_matrix()
+    mytest.test_plot_confusion_matrix()
+    mytest.test_plot_probe_map()
     mytest.test_plot_rasters()
 
     # plt.ion()

From 3ac58086dd8d46e02d433ee840378617d5d42e9d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 6 Oct 2023 06:31:41 +0000
Subject: [PATCH 17/27] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/widgets/tests/test_widgets.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/widgets/tests/test_widgets.py b/src/spikeinterface/widgets/tests/test_widgets.py
index da16136fa9..ca53d85648 100644
--- a/src/spikeinterface/widgets/tests/test_widgets.py
+++ b/src/spikeinterface/widgets/tests/test_widgets.py
@@ -238,7 +238,11 @@ def test_amplitudes(self):
                 unit_ids = self.we_dense.unit_ids[:4]
                 sw.plot_amplitudes(self.we_dense, unit_ids=unit_ids, backend=backend, **self.backend_kwargs[backend])
                 sw.plot_amplitudes(
-                    self.we_dense, unit_ids=unit_ids, plot_histograms=True, backend=backend, **self.backend_kwargs[backend]
+                    self.we_dense,
+                    unit_ids=unit_ids,
+                    plot_histograms=True,
+                    backend=backend,
+                    **self.backend_kwargs[backend],
                 )
                 sw.plot_amplitudes(
                     self.we_sparse,
@@ -264,7 +268,9 @@ def test_unit_locations(self):
         possible_backends = list(sw.UnitLocationsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_unit_locations(self.we_dense, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_unit_locations(
+                    self.we_dense, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend]
+                )
                 sw.plot_unit_locations(
                     self.we_sparse, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend]
                 )
@@ -273,7 +279,9 @@ def test_spike_locations(self):
         possible_backends = list(sw.SpikeLocationsWidget.get_possible_backends())
         for backend in possible_backends:
             if backend not in self.skip_backends:
-                sw.plot_spike_locations(self.we_dense, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend])
+                sw.plot_spike_locations(
+                    self.we_dense, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend]
+                )
                 sw.plot_spike_locations(
                     self.we_sparse, with_channel_ids=True, backend=backend, **self.backend_kwargs[backend]
                 )

From 3448e1ec4b19d5f5091ba6a2792362cf35a9f941 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 6 Oct 2023 08:57:56 +0200
Subject: [PATCH 18/27] Fix plot_traces with ipywidgets when channel_ids is not
 None

---
 src/spikeinterface/widgets/traces.py           | 10 ++++++----
 src/spikeinterface/widgets/utils_ipywidgets.py | 16 ++++++++++++++--
 2 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/widgets/traces.py b/src/spikeinterface/widgets/traces.py
index 9b6716e8f3..2783b6a369 100644
--- a/src/spikeinterface/widgets/traces.py
+++ b/src/spikeinterface/widgets/traces.py
@@ -138,9 +138,10 @@ def __init__(
 
         # colors is a nested dict by layer and channels
         # lets first create black for all channels and layer
+        # all color are generated for ipywidgets
         colors = {}
         for k in layer_keys:
-            colors[k] = {chan_id: "k" for chan_id in channel_ids}
+            colors[k] = {chan_id: "k" for chan_id in rec0.channel_ids}
 
         if color_groups:
             channel_groups = rec0.get_channel_groups(channel_ids=channel_ids)
@@ -149,7 +150,7 @@ def __init__(
             group_colors = get_some_colors(groups, color_engine="auto")
 
             channel_colors = {}
-            for i, chan_id in enumerate(channel_ids):
+            for i, chan_id in enumerate(rec0.channel_ids):
                 group = channel_groups[i]
                 channel_colors[chan_id] = group_colors[group]
 
@@ -159,12 +160,12 @@ def __init__(
         elif color is not None:
             # old behavior one color for all channel
             # if multi layer then black for all
-            colors[layer_keys[0]] = {chan_id: color for chan_id in channel_ids}
+            colors[layer_keys[0]] = {chan_id: color for chan_id in rec0.channel_ids}
         elif color is None and len(recordings) > 1:
             # several layer
             layer_colors = get_some_colors(layer_keys)
             for k in layer_keys:
-                colors[k] = {chan_id: layer_colors[k] for chan_id in channel_ids}
+                colors[k] = {chan_id: layer_colors[k] for chan_id in rec0.channel_ids}
         else:
             # color is None unique layer : all channels black
             pass
@@ -336,6 +337,7 @@ def plot_ipywidgets(self, data_plot, **backend_kwargs):
         )
         self.scaler = ScaleWidget()
         self.channel_selector = ChannelSelector(self.rec0.channel_ids)
+        self.channel_selector.value = data_plot["channel_ids"]
 
         left_sidebar = W.VBox(
             children=[
diff --git a/src/spikeinterface/widgets/utils_ipywidgets.py b/src/spikeinterface/widgets/utils_ipywidgets.py
index 6e872eca55..5bbe31302c 100644
--- a/src/spikeinterface/widgets/utils_ipywidgets.py
+++ b/src/spikeinterface/widgets/utils_ipywidgets.py
@@ -235,8 +235,7 @@ def __init__(self, channel_ids, **kwargs):
         self.slider.observe(self.on_slider_changed, names=["value"], type="change")
         self.selector.observe(self.on_selector_changed, names=["value"], type="change")
 
-        # TODO external value change
-        # self.observe(self.value_changed, names=['value'], type="change")
+        self.observe(self.value_changed, names=['value'], type="change")
 
     def on_slider_changed(self, change=None):
         i0, i1 = self.slider.value
@@ -259,6 +258,19 @@ def on_selector_changed(self, change=None):
             self.slider.observe(self.on_slider_changed, names=["value"], type="change")
 
         self.value = channel_ids
+    
+    def value_changed(self, change=None):
+        self.selector.unobserve(self.on_selector_changed, names=["value"], type="change")
+        self.selector.value = change["new"]
+        self.selector.observe(self.on_selector_changed, names=["value"], type="change")
+
+        channel_ids = self.selector.value
+        self.slider.unobserve(self.on_slider_changed, names=["value"], type="change")
+        i0 = self.channel_ids.index(channel_ids[0])
+        i1 = self.channel_ids.index(channel_ids[-1]) + 1
+        self.slider.value = (i0, i1)
+        self.slider.observe(self.on_slider_changed, names=["value"], type="change")
+
 
 
 class ScaleWidget(W.VBox):

From e51bb75f226c7c2be97c4a6ceeae460a7c610efe Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 6 Oct 2023 09:25:35 +0200
Subject: [PATCH 19/27] Fix order_channel_by_depth in ipywidgets Fix
 order_channel_by_depth when channel_ids is given.

---
 src/spikeinterface/widgets/traces.py | 58 +++++++++++++++-------------
 1 file changed, 32 insertions(+), 26 deletions(-)

diff --git a/src/spikeinterface/widgets/traces.py b/src/spikeinterface/widgets/traces.py
index 2783b6a369..802f90c62a 100644
--- a/src/spikeinterface/widgets/traces.py
+++ b/src/spikeinterface/widgets/traces.py
@@ -88,6 +88,26 @@ def __init__(
         else:
             raise ValueError("plot_traces recording must be recording or dict or list")
 
+        if "location" in rec0.get_property_keys():
+            channel_locations = rec0.get_channel_locations()
+        else:
+            channel_locations = None
+
+        if order_channel_by_depth and channel_locations is not None:
+            from ..preprocessing import depth_order
+            rec0 = depth_order(rec0)
+            recordings = {k: depth_order(rec) for k, rec in recordings.items()}
+
+            if channel_ids is not None:
+                # ensure that channel_ids are in the good order
+                channel_ids_ = list(rec0.channel_ids)
+                order = np.argsort([channel_ids_.index(c) for c in channel_ids])
+                channel_ids = list(np.array(channel_ids)[order])
+
+        if channel_ids is None:
+            channel_ids = rec0.channel_ids
+
+
         layer_keys = list(recordings.keys())
 
         if segment_index is None:
@@ -95,19 +115,6 @@ def __init__(
                 raise ValueError("You must provide segment_index=...")
             segment_index = 0
 
-        if channel_ids is None:
-            channel_ids = rec0.channel_ids
-
-        if "location" in rec0.get_property_keys():
-            channel_locations = rec0.get_channel_locations()
-        else:
-            channel_locations = None
-
-        if order_channel_by_depth:
-            if channel_locations is not None:
-                order, _ = order_channels_by_depth(rec0, channel_ids)
-        else:
-            order = None
 
         fs = rec0.get_sampling_frequency()
         if time_range is None:
@@ -124,7 +131,7 @@ def __init__(
         cmap = cmap
 
         times, list_traces, frame_range, channel_ids = _get_trace_list(
-            recordings, channel_ids, time_range, segment_index, order, return_scaled
+            recordings, channel_ids, time_range, segment_index, return_scaled=return_scaled
         )
 
         # stat for auto scaling done on the first layer
@@ -202,7 +209,6 @@ def __init__(
             show_channel_ids=show_channel_ids,
             add_legend=add_legend,
             order_channel_by_depth=order_channel_by_depth,
-            order=order,
             tile_size=tile_size,
             num_timepoints_per_row=int(seconds_per_row * fs),
             return_scaled=return_scaled,
@@ -337,7 +343,7 @@ def plot_ipywidgets(self, data_plot, **backend_kwargs):
         )
         self.scaler = ScaleWidget()
         self.channel_selector = ChannelSelector(self.rec0.channel_ids)
-        self.channel_selector.value = data_plot["channel_ids"]
+        self.channel_selector.value = list(data_plot["channel_ids"])
 
         left_sidebar = W.VBox(
             children=[
@@ -400,17 +406,17 @@ def _mode_changed(self, change=None):
     def _retrieve_traces(self, change=None):
         channel_ids = np.array(self.channel_selector.value)
 
-        if self.data_plot["order_channel_by_depth"]:
-            order, _ = order_channels_by_depth(self.rec0, channel_ids)
-        else:
-            order = None
+        # if self.data_plot["order_channel_by_depth"]:
+        #     order, _ = order_channels_by_depth(self.rec0, channel_ids)
+        # else:
+        #     order = None
 
         start_frame, end_frame, segment_index = self.time_slider.value
         time_range = np.array([start_frame, end_frame]) / self.rec0.sampling_frequency
 
         self._selected_recordings = {k: self.recordings[k] for k in self._get_layers()}
         times, list_traces, frame_range, channel_ids = _get_trace_list(
-            self._selected_recordings, channel_ids, time_range, segment_index, order, self.return_scaled
+            self._selected_recordings, channel_ids, time_range, segment_index, return_scaled=self.return_scaled
         )
 
         self._channel_ids = channel_ids
@@ -525,7 +531,7 @@ def plot_ephyviewer(self, data_plot, **backend_kwargs):
         app.exec()
 
 
-def _get_trace_list(recordings, channel_ids, time_range, segment_index, order=None, return_scaled=False):
+def _get_trace_list(recordings, channel_ids, time_range, segment_index, return_scaled=False):
     # function also used in ipywidgets plotter
     k0 = list(recordings.keys())[0]
     rec0 = recordings[k0]
@@ -552,11 +558,11 @@ def _get_trace_list(recordings, channel_ids, time_range, segment_index, order=No
             return_scaled=return_scaled,
         )
 
-        if order is not None:
-            traces = traces[:, order]
+        # if order is not None:
+        #     traces = traces[:, order]
         list_traces.append(traces)
 
-    if order is not None:
-        channel_ids = np.array(channel_ids)[order]
+    # if order is not None:
+    #     channel_ids = np.array(channel_ids)[order]
 
     return times, list_traces, frame_range, channel_ids

From bc3234cc4ce7d35cd62e0c29e33e38002f43ecd0 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 6 Oct 2023 09:52:20 +0200
Subject: [PATCH 20/27] More fix in widgets due to sparse=True by default

---
 .../tests/test_widgets_legacy.py              |  6 +-
 .../widgets/tests/test_widgets.py             | 57 +++++++++----------
 2 files changed, 31 insertions(+), 32 deletions(-)

diff --git a/src/spikeinterface/widgets/_legacy_mpl_widgets/tests/test_widgets_legacy.py b/src/spikeinterface/widgets/_legacy_mpl_widgets/tests/test_widgets_legacy.py
index 39eb80e2e5..8814e0131a 100644
--- a/src/spikeinterface/widgets/_legacy_mpl_widgets/tests/test_widgets_legacy.py
+++ b/src/spikeinterface/widgets/_legacy_mpl_widgets/tests/test_widgets_legacy.py
@@ -32,10 +32,10 @@ def setUp(self):
 
         self.num_units = len(self._sorting.get_unit_ids())
         #  self._we = extract_waveforms(self._rec, self._sorting, './toy_example', load_if_exists=True)
-        if (cache_folder / "mearec_test").is_dir():
-            self._we = load_waveforms(cache_folder / "mearec_test")
+        if (cache_folder / "mearec_test_old_api").is_dir():
+            self._we = load_waveforms(cache_folder / "mearec_test_old_api")
         else:
-            self._we = extract_waveforms(self._rec, self._sorting, cache_folder / "mearec_test")
+            self._we = extract_waveforms(self._rec, self._sorting, cache_folder / "mearec_test_old_api", sparse=False)
 
         self._amplitudes = compute_spike_amplitudes(self._we, peak_sign="neg", outputs="by_unit")
         self._gt_comp = sc.compare_sorter_to_ground_truth(self._sorting, self._sorting)
diff --git a/src/spikeinterface/widgets/tests/test_widgets.py b/src/spikeinterface/widgets/tests/test_widgets.py
index ca53d85648..5f1a936a6e 100644
--- a/src/spikeinterface/widgets/tests/test_widgets.py
+++ b/src/spikeinterface/widgets/tests/test_widgets.py
@@ -48,22 +48,21 @@ def setUpClass(cls):
         cls.sorting = se.MEArecSortingExtractor(local_path)
 
         cls.num_units = len(cls.sorting.get_unit_ids())
-        if (cache_folder / "mearec_test").is_dir():
-            cls.we_dense = load_waveforms(cache_folder / "mearec_test")
+        if (cache_folder / "mearec_test_dense").is_dir():
+            cls.we_dense = load_waveforms(cache_folder / "mearec_test_dense")
         else:
-            cls.we_dense = extract_waveforms(cls.recording, cls.sorting, cache_folder / "mearec_test", sparse=False)
+            cls.we_dense = extract_waveforms(cls.recording, cls.sorting, cache_folder / "mearec_test_dense", sparse=False)
+            metric_names = ["snr", "isi_violation", "num_spikes"]
+            _ = compute_spike_amplitudes(cls.we_dense)
+            _ = compute_unit_locations(cls.we_dense)
+            _ = compute_spike_locations(cls.we_dense)
+            _ = compute_quality_metrics(cls.we_dense, metric_names=metric_names)
+            _ = compute_template_metrics(cls.we_dense)
+            _ = compute_correlograms(cls.we_dense)
+            _ = compute_template_similarity(cls.we_dense)
 
         sw.set_default_plotter_backend("matplotlib")
 
-        metric_names = ["snr", "isi_violation", "num_spikes"]
-        _ = compute_spike_amplitudes(cls.we_dense)
-        _ = compute_unit_locations(cls.we_dense)
-        _ = compute_spike_locations(cls.we_dense)
-        _ = compute_quality_metrics(cls.we_dense, metric_names=metric_names)
-        _ = compute_template_metrics(cls.we_dense)
-        _ = compute_correlograms(cls.we_dense)
-        _ = compute_template_similarity(cls.we_dense)
-
         # make sparse waveforms
         cls.sparsity_radius = compute_sparsity(cls.we_dense, method="radius", radius_um=50)
         cls.sparsity_best = compute_sparsity(cls.we_dense, method="best_channels", num_channels=5)
@@ -363,24 +362,24 @@ def test_plot_rasters(self):
     mytest = TestWidgets()
     mytest.setUpClass()
 
-    mytest.test_plot_unit_waveforms_density_map()
-    mytest.test_plot_unit_summary()
-    mytest.test_plot_all_amplitudes_distributions()
-    mytest.test_plot_traces()
-    mytest.test_plot_unit_waveforms()
-    mytest.test_plot_unit_templates()
-    mytest.test_plot_unit_templates()
-    mytest.test_plot_unit_depths()
-    mytest.test_plot_unit_templates()
-    mytest.test_plot_unit_summary()
-    mytest.test_unit_locations()
-    mytest.test_quality_metrics()
-    mytest.test_template_metrics()
-    mytest.test_amplitudes()
+    # mytest.test_plot_unit_waveforms_density_map()
+    # mytest.test_plot_unit_summary()
+    # mytest.test_plot_all_amplitudes_distributions()
+    # mytest.test_plot_traces()
+    # mytest.test_plot_unit_waveforms()
+    # mytest.test_plot_unit_templates()
+    # mytest.test_plot_unit_templates()
+    # mytest.test_plot_unit_depths()
+    # mytest.test_plot_unit_templates()
+    # mytest.test_plot_unit_summary()
+    # mytest.test_unit_locations()
+    # mytest.test_quality_metrics()
+    # mytest.test_template_metrics()
+    # mytest.test_amplitudes()
     mytest.test_plot_agreement_matrix()
-    mytest.test_plot_confusion_matrix()
-    mytest.test_plot_probe_map()
-    mytest.test_plot_rasters()
+    # mytest.test_plot_confusion_matrix()
+    # mytest.test_plot_probe_map()
+    # mytest.test_plot_rasters()
 
     # plt.ion()
     plt.show()

From 7cd60ac434288e7eb9d43684e0b575396f70daaa Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 6 Oct 2023 07:52:41 +0000
Subject: [PATCH 21/27] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/widgets/tests/test_widgets.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/widgets/tests/test_widgets.py b/src/spikeinterface/widgets/tests/test_widgets.py
index 5f1a936a6e..1a2fdf38d9 100644
--- a/src/spikeinterface/widgets/tests/test_widgets.py
+++ b/src/spikeinterface/widgets/tests/test_widgets.py
@@ -51,7 +51,9 @@ def setUpClass(cls):
         if (cache_folder / "mearec_test_dense").is_dir():
             cls.we_dense = load_waveforms(cache_folder / "mearec_test_dense")
         else:
-            cls.we_dense = extract_waveforms(cls.recording, cls.sorting, cache_folder / "mearec_test_dense", sparse=False)
+            cls.we_dense = extract_waveforms(
+                cls.recording, cls.sorting, cache_folder / "mearec_test_dense", sparse=False
+            )
             metric_names = ["snr", "isi_violation", "num_spikes"]
             _ = compute_spike_amplitudes(cls.we_dense)
             _ = compute_unit_locations(cls.we_dense)
@@ -366,7 +368,7 @@ def test_plot_rasters(self):
     # mytest.test_plot_unit_summary()
     # mytest.test_plot_all_amplitudes_distributions()
     # mytest.test_plot_traces()
-    # mytest.test_plot_unit_waveforms()
+    # mytest.test_plot_unit_waveforms()
     # mytest.test_plot_unit_templates()
     # mytest.test_plot_unit_templates()
     # mytest.test_plot_unit_depths()

From 5c5f32fb0df19cb5faf7e24c11758639c1740f18 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 6 Oct 2023 09:53:33 +0200
Subject: [PATCH 22/27] yep

---
 src/spikeinterface/widgets/traces.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/widgets/traces.py b/src/spikeinterface/widgets/traces.py
index 802f90c62a..d010c96a27 100644
--- a/src/spikeinterface/widgets/traces.py
+++ b/src/spikeinterface/widgets/traces.py
@@ -88,7 +88,7 @@ def __init__(
         else:
             raise ValueError("plot_traces recording must be recording or dict or list")
 
-        if "location" in rec0.get_property_keys():
+        if rec0.has_channel_locations():
             channel_locations = rec0.get_channel_locations()
         else:
             channel_locations = None

From 986d6d9f26417740dd7162e671db3082363930f6 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 6 Oct 2023 10:20:20 +0200
Subject: [PATCH 23/27] Fix fix with sparse waveform extractor

---
 src/spikeinterface/exporters/tests/test_export_to_phy.py | 6 +++---
 src/spikeinterface/exporters/to_phy.py                   | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/exporters/tests/test_export_to_phy.py b/src/spikeinterface/exporters/tests/test_export_to_phy.py
index 7528f0ebf9..39bb875ea8 100644
--- a/src/spikeinterface/exporters/tests/test_export_to_phy.py
+++ b/src/spikeinterface/exporters/tests/test_export_to_phy.py
@@ -78,7 +78,7 @@ def test_export_to_phy_by_property():
     recording = recording.save(folder=rec_folder)
     sorting = sorting.save(folder=sort_folder)
 
-    waveform_extractor = extract_waveforms(recording, sorting, waveform_folder)
+    waveform_extractor = extract_waveforms(recording, sorting, waveform_folder, sparse=False)
     sparsity_group = compute_sparsity(waveform_extractor, method="by_property", by_property="group")
     export_to_phy(
         waveform_extractor,
@@ -96,7 +96,7 @@ def test_export_to_phy_by_property():
 
     # Remove one channel
     recording_rm = recording.channel_slice([0, 2, 3, 4, 5, 6, 7])
-    waveform_extractor_rm = extract_waveforms(recording_rm, sorting, waveform_folder_rm)
+    waveform_extractor_rm = extract_waveforms(recording_rm, sorting, waveform_folder_rm, sparse=False)
     sparsity_group = compute_sparsity(waveform_extractor_rm, method="by_property", by_property="group")
 
     export_to_phy(
@@ -130,7 +130,7 @@ def test_export_to_phy_by_sparsity():
         if f.is_dir():
             shutil.rmtree(f)
 
-    waveform_extractor = extract_waveforms(recording, sorting, waveform_folder)
+    waveform_extractor = extract_waveforms(recording, sorting, waveform_folder, sparse=False)
     sparsity_radius = compute_sparsity(waveform_extractor, method="radius", radius_um=50.0)
     export_to_phy(
         waveform_extractor,
diff --git a/src/spikeinterface/exporters/to_phy.py b/src/spikeinterface/exporters/to_phy.py
index ebc810b953..31a452f389 100644
--- a/src/spikeinterface/exporters/to_phy.py
+++ b/src/spikeinterface/exporters/to_phy.py
@@ -94,6 +94,7 @@ def export_to_phy(
 
     if waveform_extractor.is_sparse():
         used_sparsity = waveform_extractor.sparsity
+        assert sparsity is None
     elif sparsity is not None:
         used_sparsity = sparsity
     else:

From 63494f2a44424085d7ad22935313f9cbd2c8b88c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 6 Oct 2023 09:11:43 +0000
Subject: [PATCH 24/27] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/widgets/traces.py           | 3 +--
 src/spikeinterface/widgets/utils_ipywidgets.py | 5 ++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/spikeinterface/widgets/traces.py b/src/spikeinterface/widgets/traces.py
index d010c96a27..7a4306b284 100644
--- a/src/spikeinterface/widgets/traces.py
+++ b/src/spikeinterface/widgets/traces.py
@@ -95,6 +95,7 @@ def __init__(
 
         if order_channel_by_depth and channel_locations is not None:
             from ..preprocessing import depth_order
+
             rec0 = depth_order(rec0)
             recordings = {k: depth_order(rec) for k, rec in recordings.items()}
 
@@ -107,7 +108,6 @@ def __init__(
         if channel_ids is None:
             channel_ids = rec0.channel_ids
 
-
         layer_keys = list(recordings.keys())
 
         if segment_index is None:
@@ -115,7 +115,6 @@ def __init__(
                 raise ValueError("You must provide segment_index=...")
             segment_index = 0
 
-
         fs = rec0.get_sampling_frequency()
         if time_range is None:
             time_range = (0, 1.0)
diff --git a/src/spikeinterface/widgets/utils_ipywidgets.py b/src/spikeinterface/widgets/utils_ipywidgets.py
index 5bbe31302c..58dd5c7f32 100644
--- a/src/spikeinterface/widgets/utils_ipywidgets.py
+++ b/src/spikeinterface/widgets/utils_ipywidgets.py
@@ -235,7 +235,7 @@ def __init__(self, channel_ids, **kwargs):
         self.slider.observe(self.on_slider_changed, names=["value"], type="change")
         self.selector.observe(self.on_selector_changed, names=["value"], type="change")
 
-        self.observe(self.value_changed, names=['value'], type="change")
+        self.observe(self.value_changed, names=["value"], type="change")
 
     def on_slider_changed(self, change=None):
         i0, i1 = self.slider.value
@@ -258,7 +258,7 @@ def on_selector_changed(self, change=None):
             self.slider.observe(self.on_slider_changed, names=["value"], type="change")
 
         self.value = channel_ids
-    
+
     def value_changed(self, change=None):
         self.selector.unobserve(self.on_selector_changed, names=["value"], type="change")
         self.selector.value = change["new"]
@@ -272,7 +272,6 @@ def value_changed(self, change=None):
         self.slider.observe(self.on_slider_changed, names=["value"], type="change")
 
 
-
 class ScaleWidget(W.VBox):
     value = traitlets.Float()
 

From 5660de282ac43d96324184d47aa2d951910d6fec Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Fri, 6 Oct 2023 11:16:24 +0200
Subject: [PATCH 25/27] Simplify parsing in cellexplorer

---
 src/spikeinterface/extractors/cellexplorersortingextractor.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/spikeinterface/extractors/cellexplorersortingextractor.py b/src/spikeinterface/extractors/cellexplorersortingextractor.py
index 0096a40a79..0980e89f1c 100644
--- a/src/spikeinterface/extractors/cellexplorersortingextractor.py
+++ b/src/spikeinterface/extractors/cellexplorersortingextractor.py
@@ -118,7 +118,6 @@ def __init__(
         spike_times = spikes_data["times"]
 
         # CellExplorer reports spike times in units seconds; SpikeExtractors uses time units of sampling frames
-        unit_ids = unit_ids[:].astype(int).tolist()
         unit_ids = [str(unit_id) for unit_id in unit_ids]
         spiketrains_dict = {unit_id: spike_times[index] for index, unit_id in enumerate(unit_ids)}
         for unit_id in unit_ids:

From c0d4c60095f9704f9b27adfb5fa0f4867adfaf10 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 6 Oct 2023 11:38:15 +0200
Subject: [PATCH 26/27] oups

---
 src/spikeinterface/widgets/traces.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/widgets/traces.py b/src/spikeinterface/widgets/traces.py
index d010c96a27..ce34af0bfa 100644
--- a/src/spikeinterface/widgets/traces.py
+++ b/src/spikeinterface/widgets/traces.py
@@ -88,7 +88,7 @@ def __init__(
         else:
             raise ValueError("plot_traces recording must be recording or dict or list")
 
-        if rec0.has_channel_locations():
+        if rec0.has_channel_location():
             channel_locations = rec0.get_channel_locations()
         else:
             channel_locations = None

From 2907934928719cf8d0403a2c55628645483187f7 Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 6 Oct 2023 11:48:37 +0200
Subject: [PATCH 27/27] clean

---
 src/spikeinterface/widgets/traces.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/spikeinterface/widgets/traces.py b/src/spikeinterface/widgets/traces.py
index 5a8212302c..fc8b30eb05 100644
--- a/src/spikeinterface/widgets/traces.py
+++ b/src/spikeinterface/widgets/traces.py
@@ -557,11 +557,6 @@ def _get_trace_list(recordings, channel_ids, time_range, segment_index, return_s
             return_scaled=return_scaled,
         )
 
-        # if order is not None:
-        #     traces = traces[:, order]
         list_traces.append(traces)
 
-    # if order is not None:
-    #     channel_ids = np.array(channel_ids)[order]
-
     return times, list_traces, frame_range, channel_ids