From c1504f641fef0b7888c6c7d6afe63b7b4ab402c0 Mon Sep 17 00:00:00 2001
From: Jake Swann <jswann@axoft.us>
Date: Thu, 3 Oct 2024 13:39:10 -0400
Subject: [PATCH 01/42] Added vspacing_factor as a param for TracesWidget

---
 src/spikeinterface/widgets/traces.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/widgets/traces.py b/src/spikeinterface/widgets/traces.py
index 86f2350a85..f5dadc780f 100644
--- a/src/spikeinterface/widgets/traces.py
+++ b/src/spikeinterface/widgets/traces.py
@@ -52,6 +52,8 @@ class TracesWidget(BaseWidget):
         If dict, keys should be the same as recording keys
     scale : float, default: 1
         Scale factor for the traces
+    vspacing_factor : float, default: 1.5
+        Vertical spacing between channels as a multiple of maximum channel amplitude
     with_colorbar : bool, default: True
         When mode is "map", a colorbar is added
     tile_size : int, default: 1500
@@ -82,6 +84,7 @@ def __init__(
         tile_size=1500,
         seconds_per_row=0.2,
         scale=1,
+        vspacing_factor=1.5,
         with_colorbar=True,
         add_legend=True,
         backend=None,
@@ -168,7 +171,7 @@ def __init__(
         traces0 = list_traces[0]
         mean_channel_std = np.mean(np.std(traces0, axis=0))
         max_channel_amp = np.max(np.max(np.abs(traces0), axis=0))
-        vspacing = max_channel_amp * 1.5
+        vspacing = max_channel_amp * vspacing_factor
 
         if rec0.get_channel_groups() is None:
             color_groups = False

From e2fb8cc6985ab51c4d599122ab9643071bd950b9 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 15 Oct 2024 14:31:25 -0600
Subject: [PATCH 02/42] cap python

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a43ab63c8e..e535747428 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ authors = [
 ]
 description = "Python toolkit for analysis, visualization, and comparison of spike sorting output"
 readme = "README.md"
-requires-python = ">=3.9,<4.0"
+requires-python = ">=3.9,<3.14"  # Only numpy 2.0 supported on python 3.12 for windows. We need to wait for fix on neo
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: MIT License",

From 5347cba25a67566f0adc46b3dee8e24bfd1a545a Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 15 Oct 2024 14:55:52 -0600
Subject: [PATCH 03/42] Update pyproject.toml

Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e535747428..403988c980 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ authors = [
 ]
 description = "Python toolkit for analysis, visualization, and comparison of spike sorting output"
 readme = "README.md"
-requires-python = ">=3.9,<3.14"  # Only numpy 2.0 supported on python 3.12 for windows. We need to wait for fix on neo
+requires-python = ">=3.9,<3.13"  # Only numpy 2.0 supported on python 3.13 for windows. We need to wait for fix on neo
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: MIT License",

From 146d34a58f29165307bd5e00af7e6c4fbb8d2306 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Tue, 15 Oct 2024 17:16:02 -0400
Subject: [PATCH 04/42] remove writing text_file

---
 src/spikeinterface/sorters/basesorter.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/sorters/basesorter.py b/src/spikeinterface/sorters/basesorter.py
index 3502d27548..28948f81cc 100644
--- a/src/spikeinterface/sorters/basesorter.py
+++ b/src/spikeinterface/sorters/basesorter.py
@@ -145,9 +145,8 @@ def initialize_folder(cls, recording, output_folder, verbose, remove_existing_fo
         elif recording.check_serializability("pickle"):
             recording.dump(output_folder / "spikeinterface_recording.pickle", relative_to=output_folder)
         else:
-            # TODO: deprecate and finally remove this after 0.100
-            d = {"warning": "The recording is not serializable to json"}
-            rec_file.write_text(json.dumps(d, indent=4), encoding="utf8")
+            raise RuntimeError("This recording is not serializable and so can not be sorted. Consider `recording.save()` to save a "
+                               "compatible binary file.")
 
         return output_folder
 

From 5e832c9523a218a032c75d774c71c9188a8114ae Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 15 Oct 2024 21:19:30 +0000
Subject: [PATCH 05/42] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/spikeinterface/sorters/basesorter.py b/src/spikeinterface/sorters/basesorter.py
index 28948f81cc..c59fa29c05 100644
--- a/src/spikeinterface/sorters/basesorter.py
+++ b/src/spikeinterface/sorters/basesorter.py
@@ -145,8 +145,10 @@ def initialize_folder(cls, recording, output_folder, verbose, remove_existing_fo
         elif recording.check_serializability("pickle"):
             recording.dump(output_folder / "spikeinterface_recording.pickle", relative_to=output_folder)
         else:
-            raise RuntimeError("This recording is not serializable and so can not be sorted. Consider `recording.save()` to save a "
-                               "compatible binary file.")
+            raise RuntimeError(
+                "This recording is not serializable and so can not be sorted. Consider `recording.save()` to save a "
+                "compatible binary file."
+            )
 
         return output_folder
 

From b62e02ba244c40f9eb86e2206bc844e2be339a2d Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Mon, 21 Oct 2024 10:39:37 +0100
Subject: [PATCH 06/42] export_report without waveforms

---
 src/spikeinterface/widgets/unit_summary.py | 44 +++++++++++++---------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/src/spikeinterface/widgets/unit_summary.py b/src/spikeinterface/widgets/unit_summary.py
index 755e60ccbf..8aea6fd690 100644
--- a/src/spikeinterface/widgets/unit_summary.py
+++ b/src/spikeinterface/widgets/unit_summary.py
@@ -107,15 +107,18 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         # and use custum grid spec
         fig = self.figure
         nrows = 2
-        ncols = 3
+        ncols = 2
         if sorting_analyzer.has_extension("correlograms") or sorting_analyzer.has_extension("spike_amplitudes"):
             ncols += 1
+        if sorting_analyzer.has_extension("waveforms"):
+            ncols += 1
         if sorting_analyzer.has_extension("spike_amplitudes"):
             nrows += 1
         gs = fig.add_gridspec(nrows, ncols)
+        col_counter = 0
 
         if sorting_analyzer.has_extension("unit_locations"):
-            ax1 = fig.add_subplot(gs[:2, 0])
+            ax1 = fig.add_subplot(gs[:2, col_counter])
             # UnitLocationsPlotter().do_plot(dp.plot_data_unit_locations, ax=ax1)
             w = UnitLocationsWidget(
                 sorting_analyzer,
@@ -126,6 +129,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
                 ax=ax1,
                 **unitlocationswidget_kwargs,
             )
+            col_counter = col_counter + 1
 
             unit_locations = sorting_analyzer.get_extension("unit_locations").get_data(outputs="by_unit")
             unit_location = unit_locations[unit_id]
@@ -136,12 +140,13 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             ax1.set_xlabel(None)
             ax1.set_ylabel(None)
 
-        ax2 = fig.add_subplot(gs[:2, 1])
+        ax2 = fig.add_subplot(gs[:2, col_counter])
         w = UnitWaveformsWidget(
             sorting_analyzer,
             unit_ids=[unit_id],
             unit_colors=unit_colors,
             plot_templates=True,
+            plot_waveforms=sorting_analyzer.has_extension("waveforms"),
             same_axis=True,
             plot_legend=False,
             sparsity=sparsity,
@@ -149,24 +154,27 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             ax=ax2,
             **unitwaveformswidget_kwargs,
         )
+        col_counter = col_counter + 1
 
         ax2.set_title(None)
 
-        ax3 = fig.add_subplot(gs[:2, 2])
-        UnitWaveformDensityMapWidget(
-            sorting_analyzer,
-            unit_ids=[unit_id],
-            unit_colors=unit_colors,
-            use_max_channel=True,
-            same_axis=False,
-            backend="matplotlib",
-            ax=ax3,
-            **unitwaveformdensitymapwidget_kwargs,
-        )
-        ax3.set_ylabel(None)
+        if sorting_analyzer.has_extension("waveforms"):
+            ax3 = fig.add_subplot(gs[:2, col_counter])
+            UnitWaveformDensityMapWidget(
+                sorting_analyzer,
+                unit_ids=[unit_id],
+                unit_colors=unit_colors,
+                use_max_channel=True,
+                same_axis=False,
+                backend="matplotlib",
+                ax=ax3,
+                **unitwaveformdensitymapwidget_kwargs,
+            )
+            ax3.set_ylabel(None)
+            col_counter = col_counter + 1
 
         if sorting_analyzer.has_extension("correlograms"):
-            ax4 = fig.add_subplot(gs[:2, 3])
+            ax4 = fig.add_subplot(gs[:2, col_counter])
             AutoCorrelogramsWidget(
                 sorting_analyzer,
                 unit_ids=[unit_id],
@@ -180,8 +188,8 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             ax4.set_yticks([])
 
         if sorting_analyzer.has_extension("spike_amplitudes"):
-            ax5 = fig.add_subplot(gs[2, :3])
-            ax6 = fig.add_subplot(gs[2, 3])
+            ax5 = fig.add_subplot(gs[2, :col_counter])
+            ax6 = fig.add_subplot(gs[2, col_counter])
             axes = np.array([ax5, ax6])
             AmplitudesWidget(
                 sorting_analyzer,

From ebc6164064c72490cc1b9f539b1b2eb5f0eae9ea Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Mon, 21 Oct 2024 09:12:37 -0600
Subject: [PATCH 07/42] Update pyproject.toml

Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 403988c980..fc09ad9198 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ authors = [
 ]
 description = "Python toolkit for analysis, visualization, and comparison of spike sorting output"
 readme = "README.md"
-requires-python = ">=3.9,<3.13"  # Only numpy 2.0 supported on python 3.13 for windows. We need to wait for fix on neo
+requires-python = ">=3.9,<3.13"  # Only numpy 2.1 supported on python 3.13 for windows. We need to wait for fix on neo
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: MIT License",

From b5bd2fb1f4459689e05893a0524a8dab3543b5e8 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Wed, 23 Oct 2024 09:21:01 -0400
Subject: [PATCH 08/42] add error messaging around use of get data in templates

---
 .../core/analyzer_extension_core.py             | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/analyzer_extension_core.py b/src/spikeinterface/core/analyzer_extension_core.py
index bc5de63d07..e0b267ae72 100644
--- a/src/spikeinterface/core/analyzer_extension_core.py
+++ b/src/spikeinterface/core/analyzer_extension_core.py
@@ -380,7 +380,12 @@ def _set_params(self, ms_before: float = 1.0, ms_after: float = 2.0, operators=N
         assert isinstance(operators, list)
         for operator in operators:
             if isinstance(operator, str):
-                assert operator in ("average", "std", "median", "mad")
+                if operator not in ("average", "std", "median", "mad"):
+                    error_msg = (
+                        f"You have entered an operator {operator} in your `operators` argument which is "
+                        f"not supported. Please use any of ['average', 'std', 'median', 'mad'] instead."
+                    )
+                    raise ValueError(error_msg)
             else:
                 assert isinstance(operator, (list, tuple))
                 assert len(operator) == 2
@@ -549,9 +554,17 @@ def _get_data(self, operator="average", percentile=None, outputs="numpy"):
         if operator != "percentile":
             key = operator
         else:
-            assert percentile is not None, "You must provide percentile=..."
+            assert percentile is not None, "You must provide percentile=... if `operator=percentile`"
             key = f"percentile_{percentile}"
 
+        if key not in self.data.keys():
+            error_msg = (
+                f"You have entered `operator={key}`, but the only operators calculated are "
+                f"{list(self.data.keys())}. Please use one of these as your `operator` in the "
+                f"`get_data` function."
+            )
+            raise ValueError(error_msg)
+
         templates_array = self.data[key]
 
         if outputs == "numpy":

From 22d19d52217594a129fc474bde119a2370e8d0e4 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Wed, 23 Oct 2024 09:36:17 -0400
Subject: [PATCH 09/42] more docs stuff

---
 .../core/analyzer_extension_core.py           | 62 ++++++++++---------
 1 file changed, 34 insertions(+), 28 deletions(-)

diff --git a/src/spikeinterface/core/analyzer_extension_core.py b/src/spikeinterface/core/analyzer_extension_core.py
index e0b267ae72..7d644c9c00 100644
--- a/src/spikeinterface/core/analyzer_extension_core.py
+++ b/src/spikeinterface/core/analyzer_extension_core.py
@@ -22,21 +22,23 @@
 
 class ComputeRandomSpikes(AnalyzerExtension):
     """
-    AnalyzerExtension that select some random spikes.
+    AnalyzerExtension that select somes random spikes.
+    This is allows for a subsampling of spikes for further calculations and is important
+    for managing that amount of memory and speed of computation in the analyzer.
 
     This will be used by the `waveforms`/`templates` extensions.
 
-    This internally use `random_spikes_selection()` parameters are the same.
+    This internally use `random_spikes_selection()` parameters.
 
     Parameters
     ----------
-    method: "uniform" | "all", default: "uniform"
+    method : "uniform" | "all", default: "uniform"
         The method to select the spikes
-    max_spikes_per_unit: int, default: 500
+    max_spikes_per_unit : int, default: 500
         The maximum number of spikes per unit, ignored if method="all"
-    margin_size: int, default: None
+    margin_size : int, default: None
         A margin on each border of segments to avoid border spikes, ignored if method="all"
-    seed: int or None, default: None
+    seed : int or None, default: None
         A seed for the random generator, ignored if method="all"
 
     Returns
@@ -104,7 +106,7 @@ def get_random_spikes(self):
         return self._some_spikes
 
     def get_selected_indices_in_spike_train(self, unit_id, segment_index):
-        # usefull for Waveforms extractor backwars compatibility
+        # useful for Waveforms extractor backwars compatibility
         # In Waveforms extractor "selected_spikes" was a dict (key: unit_id) of list (segment_index) of indices of spikes in spiketrain
         sorting = self.sorting_analyzer.sorting
         random_spikes_indices = self.data["random_spikes_indices"]
@@ -133,16 +135,16 @@ class ComputeWaveforms(AnalyzerExtension):
 
     Parameters
     ----------
-    ms_before: float, default: 1.0
+    ms_before : float, default: 1.0
         The number of ms to extract before the spike events
-    ms_after: float, default: 2.0
+    ms_after : float, default: 2.0
         The number of ms to extract after the spike events
-    dtype: None | dtype, default: None
+    dtype : None | dtype, default: None
         The dtype of the waveforms. If None, the dtype of the recording is used.
 
     Returns
     -------
-    waveforms: np.ndarray
+    waveforms : np.ndarray
         Array with computed waveforms with shape (num_random_spikes, num_samples, num_channels)
     """
 
@@ -410,9 +412,13 @@ def _run(self, verbose=False, **job_kwargs):
             self._compute_and_append_from_waveforms(self.params["operators"])
 
         else:
-            for operator in self.params["operators"]:
-                if operator not in ("average", "std"):
-                    raise ValueError(f"Computing templates with operators {operator} needs the 'waveforms' extension")
+            bad_operator_list = [
+                operator for operator in self.params["operators"] if operator not in ("average", "std")
+            ]
+            if len(bad_operator_list) > 0:
+                raise ValueError(
+                    f"Computing templates with operators {bad_operator_list} requires the 'waveforms' extension"
+                )
 
             recording = self.sorting_analyzer.recording
             sorting = self.sorting_analyzer.sorting
@@ -446,7 +452,7 @@ def _run(self, verbose=False, **job_kwargs):
 
     def _compute_and_append_from_waveforms(self, operators):
         if not self.sorting_analyzer.has_extension("waveforms"):
-            raise ValueError(f"Computing templates with operators {operators} needs the 'waveforms' extension")
+            raise ValueError(f"Computing templates with operators {operators} requires the 'waveforms' extension")
 
         unit_ids = self.sorting_analyzer.unit_ids
         channel_ids = self.sorting_analyzer.channel_ids
@@ -471,7 +477,7 @@ def _compute_and_append_from_waveforms(self, operators):
 
         assert self.sorting_analyzer.has_extension(
             "random_spikes"
-        ), "compute templates requires the random_spikes extension. You can run sorting_analyzer.get_random_spikes()"
+        ), "compute 'templates' requires the random_spikes extension. You can run sorting_analyzer.compute('random_spikes')"
         some_spikes = self.sorting_analyzer.get_extension("random_spikes").get_random_spikes()
         for unit_index, unit_id in enumerate(unit_ids):
             spike_mask = some_spikes["unit_index"] == unit_index
@@ -579,7 +585,7 @@ def _get_data(self, operator="average", percentile=None, outputs="numpy"):
                 probe=self.sorting_analyzer.get_probe(),
             )
         else:
-            raise ValueError("outputs must be numpy or Templates")
+            raise ValueError("outputs must be `numpy` or `Templates`")
 
     def get_templates(self, unit_ids=None, operator="average", percentile=None, save=True, outputs="numpy"):
         """
@@ -589,26 +595,26 @@ def get_templates(self, unit_ids=None, operator="average", percentile=None, save
 
         Parameters
         ----------
-        unit_ids: list or None
+        unit_ids : list or None
             Unit ids to retrieve waveforms for
-        operator: "average" | "median" | "std" | "percentile", default: "average"
+        operator : "average" | "median" | "std" | "percentile", default: "average"
             The operator to compute the templates
-        percentile: float, default: None
+        percentile : float, default: None
             Percentile to use for operator="percentile"
-        save: bool, default True
+        save : bool, default: True
             In case, the operator is not computed yet it can be saved to folder or zarr
-        outputs: "numpy" | "Templates"
+        outputs : "numpy" | "Templates", default: "numpy"
             Whether to return a numpy array or a Templates object
 
         Returns
         -------
-        templates: np.array
+        templates : np.array | Templates
             The returned templates (num_units, num_samples, num_channels)
         """
         if operator != "percentile":
             key = operator
         else:
-            assert percentile is not None, "You must provide percentile=..."
+            assert percentile is not None, "You must provide percentile=... if `operator='percentile'`"
             key = f"pencentile_{percentile}"
 
         if key in self.data:
@@ -645,7 +651,7 @@ def get_templates(self, unit_ids=None, operator="average", percentile=None, save
                 is_scaled=self.sorting_analyzer.return_scaled,
             )
         else:
-            raise ValueError("outputs must be numpy or Templates")
+            raise ValueError("`outputs` must be 'numpy' or 'Templates'")
 
     def get_unit_template(self, unit_id, operator="average"):
         """
@@ -655,7 +661,7 @@ def get_unit_template(self, unit_id, operator="average"):
         ----------
         unit_id: str | int
             Unit id to retrieve waveforms for
-        operator: str
+        operator: str, default: "average"
              The operator to compute the templates
 
         Returns
@@ -713,13 +719,13 @@ def _set_params(self, num_chunks_per_segment=20, chunk_size=10000, seed=None):
         return params
 
     def _select_extension_data(self, unit_ids):
-        # this do not depend on units
+        # this does not depend on units
         return self.data
 
     def _merge_extension_data(
         self, merge_unit_groups, new_unit_ids, new_sorting_analyzer, keep_mask=None, verbose=False, **job_kwargs
     ):
-        # this do not depend on units
+        # this does not depend on units
         return self.data.copy()
 
     def _run(self, verbose=False):

From b1f11fbdcf3a9e94e77030f7da83368ed9ccea73 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Wed, 23 Oct 2024 09:38:03 -0400
Subject: [PATCH 10/42] fix typo

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

diff --git a/src/spikeinterface/core/analyzer_extension_core.py b/src/spikeinterface/core/analyzer_extension_core.py
index 7d644c9c00..2d9924554c 100644
--- a/src/spikeinterface/core/analyzer_extension_core.py
+++ b/src/spikeinterface/core/analyzer_extension_core.py
@@ -23,7 +23,7 @@
 class ComputeRandomSpikes(AnalyzerExtension):
     """
     AnalyzerExtension that select somes random spikes.
-    This is allows for a subsampling of spikes for further calculations and is important
+    This allows for a subsampling of spikes for further calculations and is important
     for managing that amount of memory and speed of computation in the analyzer.
 
     This will be used by the `waveforms`/`templates` extensions.

From f66ae7fc9c6cf66c5ca35d11dddedfbb2180080d Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Fri, 25 Oct 2024 08:28:41 +0100
Subject: [PATCH 11/42] Compute covariance matrix in float64.

---
 src/spikeinterface/preprocessing/whiten.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
index 195969ff79..91c74c423f 100644
--- a/src/spikeinterface/preprocessing/whiten.py
+++ b/src/spikeinterface/preprocessing/whiten.py
@@ -124,7 +124,7 @@ def __init__(self, parent_recording_segment, W, M, dtype, int_scale):
     def get_traces(self, start_frame, end_frame, channel_indices):
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, slice(None))
         traces_dtype = traces.dtype
-        # if uint --> force int
+        # if uint --> force float
         if traces_dtype.kind == "u":
             traces = traces.astype("float32")
 
@@ -185,6 +185,7 @@ def compute_whitening_matrix(
 
     """
     random_data = get_random_data_chunks(recording, concatenated=True, return_scaled=False, **random_chunk_kwargs)
+    random_data = random_data.astype(np.float64)
 
     regularize_kwargs = regularize_kwargs if regularize_kwargs is not None else {"method": "GraphicalLassoCV"}
 

From b5c260aed812d6fb6202ffdf13d35e28d79ff4e9 Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Fri, 25 Oct 2024 09:16:26 +0100
Subject: [PATCH 12/42] Update docstring.

---
 src/spikeinterface/preprocessing/whiten.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
index 91c74c423f..1c81f2ae42 100644
--- a/src/spikeinterface/preprocessing/whiten.py
+++ b/src/spikeinterface/preprocessing/whiten.py
@@ -19,6 +19,8 @@ class WhitenRecording(BasePreprocessor):
     recording : RecordingExtractor
         The recording extractor to be whitened.
     dtype : None or dtype, default: None
+        Datatype of the output recording (covariance matrix estimation
+        and whitening are performed in float64.
         If None the the parent dtype is kept.
         For integer dtype a int_scale must be also given.
     mode : "global" | "local", default: "global"
@@ -74,7 +76,8 @@ def __init__(
         dtype_ = fix_dtype(recording, dtype)
 
         if dtype_.kind == "i":
-            assert int_scale is not None, "For recording with dtype=int you must set dtype=float32 OR set a int_scale"
+            assert int_scale is not None, ("For recording with dtype=int you must set the output dtype to float "
+                                           " OR set a int_scale")
 
         if W is not None:
             W = np.asarray(W)

From 18cfb2b385d9cf5e18d622097a41631d94a0e9a8 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 25 Oct 2024 08:18:56 +0000
Subject: [PATCH 13/42] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/preprocessing/whiten.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
index 1c81f2ae42..4e3135c3e9 100644
--- a/src/spikeinterface/preprocessing/whiten.py
+++ b/src/spikeinterface/preprocessing/whiten.py
@@ -76,8 +76,9 @@ def __init__(
         dtype_ = fix_dtype(recording, dtype)
 
         if dtype_.kind == "i":
-            assert int_scale is not None, ("For recording with dtype=int you must set the output dtype to float "
-                                           " OR set a int_scale")
+            assert int_scale is not None, (
+                "For recording with dtype=int you must set the output dtype to float " " OR set a int_scale"
+            )
 
         if W is not None:
             W = np.asarray(W)

From 98e5db95aa36a415d520cfe758113fc7c5db9bac Mon Sep 17 00:00:00 2001
From: Samuel Garcia <sam.garcia.die@gmail.com>
Date: Fri, 25 Oct 2024 10:42:58 +0200
Subject: [PATCH 14/42] recording_slices in run_node_pipeline()

---
 src/spikeinterface/core/job_tools.py          | 22 +++++++++---------
 src/spikeinterface/core/node_pipeline.py      |  7 +++++-
 src/spikeinterface/core/recording_tools.py    |  2 +-
 .../core/tests/test_node_pipeline.py          | 23 +++++++++++++++----
 .../sortingcomponents/peak_detection.py       |  6 +++++
 5 files changed, 42 insertions(+), 18 deletions(-)

diff --git a/src/spikeinterface/core/job_tools.py b/src/spikeinterface/core/job_tools.py
index 27f05bb36b..7a6172369b 100644
--- a/src/spikeinterface/core/job_tools.py
+++ b/src/spikeinterface/core/job_tools.py
@@ -149,12 +149,12 @@ def divide_segment_into_chunks(num_frames, chunk_size):
 
 
 def divide_recording_into_chunks(recording, chunk_size):
-    all_chunks = []
+    recording_slices = []
     for segment_index in range(recording.get_num_segments()):
         num_frames = recording.get_num_samples(segment_index)
         chunks = divide_segment_into_chunks(num_frames, chunk_size)
-        all_chunks.extend([(segment_index, frame_start, frame_stop) for frame_start, frame_stop in chunks])
-    return all_chunks
+        recording_slices.extend([(segment_index, frame_start, frame_stop) for frame_start, frame_stop in chunks])
+    return recording_slices
 
 
 def ensure_n_jobs(recording, n_jobs=1):
@@ -387,13 +387,13 @@ def __init__(
                 f"chunk_duration={chunk_duration_str}",
             )
 
-    def run(self, all_chunks=None):
+    def run(self, recording_slices=None):
         """
         Runs the defined jobs.
         """
 
-        if all_chunks is None:
-            all_chunks = divide_recording_into_chunks(self.recording, self.chunk_size)
+        if recording_slices is None:
+            recording_slices = divide_recording_into_chunks(self.recording, self.chunk_size)
 
         if self.handle_returns:
             returns = []
@@ -402,17 +402,17 @@ def run(self, all_chunks=None):
 
         if self.n_jobs == 1:
             if self.progress_bar:
-                all_chunks = tqdm(all_chunks, ascii=True, desc=self.job_name)
+                recording_slices = tqdm(recording_slices, ascii=True, desc=self.job_name)
 
             worker_ctx = self.init_func(*self.init_args)
-            for segment_index, frame_start, frame_stop in all_chunks:
+            for segment_index, frame_start, frame_stop in recording_slices:
                 res = self.func(segment_index, frame_start, frame_stop, worker_ctx)
                 if self.handle_returns:
                     returns.append(res)
                 if self.gather_func is not None:
                     self.gather_func(res)
         else:
-            n_jobs = min(self.n_jobs, len(all_chunks))
+            n_jobs = min(self.n_jobs, len(recording_slices))
 
             # parallel
             with ProcessPoolExecutor(
@@ -421,10 +421,10 @@ def run(self, all_chunks=None):
                 mp_context=mp.get_context(self.mp_context),
                 initargs=(self.func, self.init_func, self.init_args, self.max_threads_per_process),
             ) as executor:
-                results = executor.map(function_wrapper, all_chunks)
+                results = executor.map(function_wrapper, recording_slices)
 
                 if self.progress_bar:
-                    results = tqdm(results, desc=self.job_name, total=len(all_chunks))
+                    results = tqdm(results, desc=self.job_name, total=len(recording_slices))
 
                 for res in results:
                     if self.handle_returns:
diff --git a/src/spikeinterface/core/node_pipeline.py b/src/spikeinterface/core/node_pipeline.py
index d90a20902d..8ca4ba7f3a 100644
--- a/src/spikeinterface/core/node_pipeline.py
+++ b/src/spikeinterface/core/node_pipeline.py
@@ -489,6 +489,7 @@ def run_node_pipeline(
     names=None,
     verbose=False,
     skip_after_n_peaks=None,
+    recording_slices=None,
 ):
     """
     Machinery to compute in parallel operations on peaks and traces.
@@ -540,6 +541,10 @@ def run_node_pipeline(
     skip_after_n_peaks : None | int
         Skip the computation after n_peaks.
         This is not an exact because internally this skip is done per worker in average.
+    recording_slices : None | list[tuple]
+        Optionaly give a list of slices to run the pipeline only on some chunks of the recording.
+        It must be a list of (segment_index, frame_start, frame_stop).
+        If None (default), the entire recording is computed.
 
     Returns
     -------
@@ -578,7 +583,7 @@ def run_node_pipeline(
         **job_kwargs,
     )
 
-    processor.run()
+    processor.run(recording_slices=recording_slices)
 
     outs = gather_func.finalize_buffers(squeeze_output=squeeze_output)
     return outs
diff --git a/src/spikeinterface/core/recording_tools.py b/src/spikeinterface/core/recording_tools.py
index 2ab74ce51e..4aabbfd587 100644
--- a/src/spikeinterface/core/recording_tools.py
+++ b/src/spikeinterface/core/recording_tools.py
@@ -806,7 +806,7 @@ def append_noise_chunk(res):
             gather_func=append_noise_chunk,
             **job_kwargs,
         )
-        executor.run(all_chunks=recording_slices)
+        executor.run(recording_slices=recording_slices)
         noise_levels_chunks = np.stack(noise_levels_chunks)
         noise_levels = np.mean(noise_levels_chunks, axis=0)
 
diff --git a/src/spikeinterface/core/tests/test_node_pipeline.py b/src/spikeinterface/core/tests/test_node_pipeline.py
index deef2291c6..400a71c424 100644
--- a/src/spikeinterface/core/tests/test_node_pipeline.py
+++ b/src/spikeinterface/core/tests/test_node_pipeline.py
@@ -4,7 +4,7 @@
 import shutil
 
 from spikeinterface import create_sorting_analyzer, get_template_extremum_channel, generate_ground_truth_recording
-
+from spikeinterface.core.job_tools import divide_recording_into_chunks
 
 # from spikeinterface.sortingcomponents.peak_detection import detect_peaks
 from spikeinterface.core.node_pipeline import (
@@ -191,8 +191,8 @@ def test_run_node_pipeline(cache_folder_creation):
             unpickled_node = pickle.loads(pickled_node)
 
 
-def test_skip_after_n_peaks():
-    recording, sorting = generate_ground_truth_recording(num_channels=10, num_units=10, durations=[10.0])
+def test_skip_after_n_peaks_and_recording_slices():
+    recording, sorting = generate_ground_truth_recording(num_channels=10, num_units=10, durations=[10.0], seed=2205)
 
     # job_kwargs = dict(chunk_duration="0.5s", n_jobs=2, progress_bar=False)
     job_kwargs = dict(chunk_duration="0.5s", n_jobs=1, progress_bar=False)
@@ -211,18 +211,31 @@ def test_skip_after_n_peaks():
     node1 = AmplitudeExtractionNode(recording, parents=[node0], param0=6.6, return_output=True)
     nodes = [node0, node1]
 
+    # skip
     skip_after_n_peaks = 30
     some_amplitudes = run_node_pipeline(
         recording, nodes, job_kwargs, gather_mode="memory", skip_after_n_peaks=skip_after_n_peaks
     )
-
     assert some_amplitudes.size >= skip_after_n_peaks
     assert some_amplitudes.size < spikes.size
 
+    # slices : 1 every 4
+    recording_slices = divide_recording_into_chunks(recording, 10_000)
+    recording_slices = recording_slices[::4]
+    some_amplitudes = run_node_pipeline(
+        recording, nodes, job_kwargs, gather_mode="memory", recording_slices=recording_slices
+    )
+    tolerance = 1.2
+    assert some_amplitudes.size < (spikes.size // 4) * tolerance
+
+
+    
+
+
 
 # the following is for testing locally with python or ipython. It is not used in ci or with pytest.
 if __name__ == "__main__":
     # folder = Path("./cache_folder/core")
     # test_run_node_pipeline(folder)
 
-    test_skip_after_n_peaks()
+    test_skip_after_n_peaks_and_recording_slices()
diff --git a/src/spikeinterface/sortingcomponents/peak_detection.py b/src/spikeinterface/sortingcomponents/peak_detection.py
index 5b1d33b334..233b16dcf7 100644
--- a/src/spikeinterface/sortingcomponents/peak_detection.py
+++ b/src/spikeinterface/sortingcomponents/peak_detection.py
@@ -57,6 +57,7 @@ def detect_peaks(
     folder=None,
     names=None,
     skip_after_n_peaks=None,
+    recording_slices=None,
     **kwargs,
 ):
     """Peak detection based on threshold crossing in term of k x MAD.
@@ -83,6 +84,10 @@ def detect_peaks(
     skip_after_n_peaks : None | int
         Skip the computation after n_peaks.
         This is not an exact because internally this skip is done per worker in average.
+    recording_slices : None | list[tuple]
+        Optionaly give a list of slices to run the pipeline only on some chunks of the recording.
+        It must be a list of (segment_index, frame_start, frame_stop).
+        If None (default), the entire recording is computed.
 
     {method_doc}
     {job_doc}
@@ -135,6 +140,7 @@ def detect_peaks(
         folder=folder,
         names=names,
         skip_after_n_peaks=skip_after_n_peaks,
+        recording_slices=recording_slices,
     )
     return outs
 

From aaa689fa9174e8576550528224431b9ea3e32759 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 25 Oct 2024 08:47:02 +0000
Subject: [PATCH 15/42] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/core/tests/test_node_pipeline.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/spikeinterface/core/tests/test_node_pipeline.py b/src/spikeinterface/core/tests/test_node_pipeline.py
index 400a71c424..028eaecf12 100644
--- a/src/spikeinterface/core/tests/test_node_pipeline.py
+++ b/src/spikeinterface/core/tests/test_node_pipeline.py
@@ -229,10 +229,6 @@ def test_skip_after_n_peaks_and_recording_slices():
     assert some_amplitudes.size < (spikes.size // 4) * tolerance
 
 
-    
-
-
-
 # the following is for testing locally with python or ipython. It is not used in ci or with pytest.
 if __name__ == "__main__":
     # folder = Path("./cache_folder/core")

From 3406f85ba35209dd557ca9c0b0c15c5c84219e7a Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Fri, 25 Oct 2024 06:39:35 -0400
Subject: [PATCH 16/42] Joe's comments

Co-authored-by: Joe Ziminski <55797454+JoeZiminski@users.noreply.github.com>
---
 src/spikeinterface/core/analyzer_extension_core.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/analyzer_extension_core.py b/src/spikeinterface/core/analyzer_extension_core.py
index 2d9924554c..55e0e34dcc 100644
--- a/src/spikeinterface/core/analyzer_extension_core.py
+++ b/src/spikeinterface/core/analyzer_extension_core.py
@@ -28,7 +28,7 @@ class ComputeRandomSpikes(AnalyzerExtension):
 
     This will be used by the `waveforms`/`templates` extensions.
 
-    This internally use `random_spikes_selection()` parameters.
+    This internally uses `random_spikes_selection()` parameters.
 
     Parameters
     ----------
@@ -106,7 +106,7 @@ def get_random_spikes(self):
         return self._some_spikes
 
     def get_selected_indices_in_spike_train(self, unit_id, segment_index):
-        # useful for Waveforms extractor backwars compatibility
+        # useful for WaveformExtractor backwards compatibility
         # In Waveforms extractor "selected_spikes" was a dict (key: unit_id) of list (segment_index) of indices of spikes in spiketrain
         sorting = self.sorting_analyzer.sorting
         random_spikes_indices = self.data["random_spikes_indices"]

From f55a9405040310064f716015f8d9b0c976b97923 Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Mon, 28 Oct 2024 14:28:05 +0000
Subject: [PATCH 17/42] Add 'shift start time' function.

---
 src/spikeinterface/core/baserecording.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 5e2e9e4014..b8a0420794 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -509,6 +509,26 @@ def reset_times(self):
             rs.t_start = None
             rs.sampling_frequency = self.sampling_frequency
 
+    def shift_start_time(self, shift, segment_index=None):
+        """
+        Shift the starting time of the times.
+
+        shift : int | float
+            The shift to apply to the first time point. If positive,
+            the current start time will be increased by `shift`. If
+            negative, the start time will be decreased.
+
+        segment_index : int | None
+            The segment on which to shift the times.
+        """
+        segment_index = self._check_segment_index(segment_index)
+        rs = self._recording_segments[segment_index]
+
+        if self.has_time_vector():
+            rs.time_vector += shift
+        else:
+            rs.t_start += shift
+
     def sample_index_to_time(self, sample_ind, segment_index=None):
         """
         Transform sample index into time in seconds

From d17181f3bd68f602780ad99e1b618aa3f793b8ad Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Tue, 29 Oct 2024 13:08:56 +0100
Subject: [PATCH 18/42] Update src/spikeinterface/preprocessing/whiten.py

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

diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
index 4e3135c3e9..505e8a330a 100644
--- a/src/spikeinterface/preprocessing/whiten.py
+++ b/src/spikeinterface/preprocessing/whiten.py
@@ -20,7 +20,7 @@ class WhitenRecording(BasePreprocessor):
         The recording extractor to be whitened.
     dtype : None or dtype, default: None
         Datatype of the output recording (covariance matrix estimation
-        and whitening are performed in float64.
+        and whitening are performed in float64).
         If None the the parent dtype is kept.
         For integer dtype a int_scale must be also given.
     mode : "global" | "local", default: "global"

From 7c953c2b1347dfbbb4058f5a9b7462f90d22c1dd Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Tue, 29 Oct 2024 12:19:26 +0000
Subject: [PATCH 19/42] Respond to Joe; add template_similarity check

---
 src/spikeinterface/exporters/report.py     |  8 +--
 src/spikeinterface/widgets/unit_summary.py | 82 +++++++++++-----------
 2 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/src/spikeinterface/exporters/report.py b/src/spikeinterface/exporters/report.py
index 3a4be9213a..484da83342 100644
--- a/src/spikeinterface/exporters/report.py
+++ b/src/spikeinterface/exporters/report.py
@@ -20,10 +20,10 @@ def export_report(
     **job_kwargs,
 ):
     """
-    Exports a SI spike sorting report. The report includes summary figures of the spike sorting output
-    (e.g. amplitude distributions, unit localization and depth VS amplitude) as well as unit-specific reports,
-    that include waveforms, templates, template maps, ISI distributions, and more.
-
+    Exports a SI spike sorting report. The report includes summary figures of the spike sorting output.
+    What is plotted depends on what has been calculated. Unit locations and unit waveforms are always included.
+    Unit waveform densities, correlograms and spike amplitudes are plotted if `waveforms`, `correlograms`
+    and 'template_similarity', and `spike_amplitudes` have been computed for the given `sorting_analyzer`.
 
     Parameters
     ----------
diff --git a/src/spikeinterface/widgets/unit_summary.py b/src/spikeinterface/widgets/unit_summary.py
index 8aea6fd690..d8cbeb7bb3 100644
--- a/src/spikeinterface/widgets/unit_summary.py
+++ b/src/spikeinterface/widgets/unit_summary.py
@@ -108,7 +108,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         fig = self.figure
         nrows = 2
         ncols = 2
-        if sorting_analyzer.has_extension("correlograms") or sorting_analyzer.has_extension("spike_amplitudes"):
+        if sorting_analyzer.has_extension("correlograms") and sorting_analyzer.has_extension("template_similarity"):
             ncols += 1
         if sorting_analyzer.has_extension("waveforms"):
             ncols += 1
@@ -117,31 +117,30 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         gs = fig.add_gridspec(nrows, ncols)
         col_counter = 0
 
-        if sorting_analyzer.has_extension("unit_locations"):
-            ax1 = fig.add_subplot(gs[:2, col_counter])
-            # UnitLocationsPlotter().do_plot(dp.plot_data_unit_locations, ax=ax1)
-            w = UnitLocationsWidget(
-                sorting_analyzer,
-                unit_ids=[unit_id],
-                unit_colors=unit_colors,
-                plot_legend=False,
-                backend="matplotlib",
-                ax=ax1,
-                **unitlocationswidget_kwargs,
-            )
-            col_counter = col_counter + 1
-
-            unit_locations = sorting_analyzer.get_extension("unit_locations").get_data(outputs="by_unit")
-            unit_location = unit_locations[unit_id]
-            x, y = unit_location[0], unit_location[1]
-            ax1.set_xlim(x - 80, x + 80)
-            ax1.set_ylim(y - 250, y + 250)
-            ax1.set_xticks([])
-            ax1.set_xlabel(None)
-            ax1.set_ylabel(None)
-
-        ax2 = fig.add_subplot(gs[:2, col_counter])
-        w = UnitWaveformsWidget(
+        # Unit locations and unit waveform plots are always generated
+        ax_unit_locations = fig.add_subplot(gs[:2, col_counter])
+        _ = UnitLocationsWidget(
+            sorting_analyzer,
+            unit_ids=[unit_id],
+            unit_colors=unit_colors,
+            plot_legend=False,
+            backend="matplotlib",
+            ax=ax_unit_locations,
+            **unitlocationswidget_kwargs,
+        )
+        col_counter += 1
+
+        unit_locations = sorting_analyzer.get_extension("unit_locations").get_data(outputs="by_unit")
+        unit_location = unit_locations[unit_id]
+        x, y = unit_location[0], unit_location[1]
+        ax_unit_locations.set_xlim(x - 80, x + 80)
+        ax_unit_locations.set_ylim(y - 250, y + 250)
+        ax_unit_locations.set_xticks([])
+        ax_unit_locations.set_xlabel(None)
+        ax_unit_locations.set_ylabel(None)
+
+        ax_unit_waveforms = fig.add_subplot(gs[:2, col_counter])
+        _ = UnitWaveformsWidget(
             sorting_analyzer,
             unit_ids=[unit_id],
             unit_colors=unit_colors,
@@ -151,15 +150,15 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             plot_legend=False,
             sparsity=sparsity,
             backend="matplotlib",
-            ax=ax2,
+            ax=ax_unit_waveforms,
             **unitwaveformswidget_kwargs,
         )
-        col_counter = col_counter + 1
+        col_counter += 1
 
-        ax2.set_title(None)
+        ax_unit_waveforms.set_title(None)
 
         if sorting_analyzer.has_extension("waveforms"):
-            ax3 = fig.add_subplot(gs[:2, col_counter])
+            ax_waveform_density = fig.add_subplot(gs[:2, col_counter])
             UnitWaveformDensityMapWidget(
                 sorting_analyzer,
                 unit_ids=[unit_id],
@@ -167,30 +166,31 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
                 use_max_channel=True,
                 same_axis=False,
                 backend="matplotlib",
-                ax=ax3,
+                ax=ax_waveform_density,
                 **unitwaveformdensitymapwidget_kwargs,
             )
-            ax3.set_ylabel(None)
-            col_counter = col_counter + 1
+            col_counter += 1
+            ax_waveform_density.set_ylabel(None)
 
-        if sorting_analyzer.has_extension("correlograms"):
-            ax4 = fig.add_subplot(gs[:2, col_counter])
+        if sorting_analyzer.has_extension("correlograms") and sorting_analyzer.has_extension("template_similarity"):
+            ax_correlograms = fig.add_subplot(gs[:2, col_counter])
             AutoCorrelogramsWidget(
                 sorting_analyzer,
                 unit_ids=[unit_id],
                 unit_colors=unit_colors,
                 backend="matplotlib",
-                ax=ax4,
+                ax=ax_correlograms,
                 **autocorrelogramswidget_kwargs,
             )
+            col_counter += 1
 
-            ax4.set_title(None)
-            ax4.set_yticks([])
+            ax_correlograms.set_title(None)
+            ax_correlograms.set_yticks([])
 
         if sorting_analyzer.has_extension("spike_amplitudes"):
-            ax5 = fig.add_subplot(gs[2, :col_counter])
-            ax6 = fig.add_subplot(gs[2, col_counter])
-            axes = np.array([ax5, ax6])
+            ax_spike_amps = fig.add_subplot(gs[2, : col_counter - 1])
+            ax_amps_distribution = fig.add_subplot(gs[2, col_counter - 1])
+            axes = np.array([ax_spike_amps, ax_amps_distribution])
             AmplitudesWidget(
                 sorting_analyzer,
                 unit_ids=[unit_id],

From 12538cc646f47b162b73190326d5b541121b2c1a Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Thu, 31 Oct 2024 17:49:29 +0000
Subject: [PATCH 20/42] Revert to float32.

---
 src/spikeinterface/preprocessing/whiten.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
index 505e8a330a..b9c106a5a2 100644
--- a/src/spikeinterface/preprocessing/whiten.py
+++ b/src/spikeinterface/preprocessing/whiten.py
@@ -20,7 +20,7 @@ class WhitenRecording(BasePreprocessor):
         The recording extractor to be whitened.
     dtype : None or dtype, default: None
         Datatype of the output recording (covariance matrix estimation
-        and whitening are performed in float64).
+        and whitening are performed in float32).
         If None the the parent dtype is kept.
         For integer dtype a int_scale must be also given.
     mode : "global" | "local", default: "global"
@@ -189,7 +189,7 @@ def compute_whitening_matrix(
 
     """
     random_data = get_random_data_chunks(recording, concatenated=True, return_scaled=False, **random_chunk_kwargs)
-    random_data = random_data.astype(np.float64)
+    random_data = random_data.astype(np.float32)
 
     regularize_kwargs = regularize_kwargs if regularize_kwargs is not None else {"method": "GraphicalLassoCV"}
 

From 035d61c38dbdb453a6461de424028d1466367bda Mon Sep 17 00:00:00 2001
From: Joe Ziminski <55797454+JoeZiminski@users.noreply.github.com>
Date: Thu, 31 Oct 2024 18:02:03 +0000
Subject: [PATCH 21/42] Fix string format error.

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

diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
index b9c106a5a2..fa33975a68 100644
--- a/src/spikeinterface/preprocessing/whiten.py
+++ b/src/spikeinterface/preprocessing/whiten.py
@@ -77,7 +77,7 @@ def __init__(
 
         if dtype_.kind == "i":
             assert int_scale is not None, (
-                "For recording with dtype=int you must set the output dtype to float " " OR set a int_scale"
+                "For recording with dtype=int you must set the output dtype to float OR set a int_scale"
             )
 
         if W is not None:

From 7b8d0a2c1c3e006d8a9a46257e0f06e034aa0a76 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 31 Oct 2024 18:02:31 +0000
Subject: [PATCH 22/42] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/preprocessing/whiten.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/preprocessing/whiten.py b/src/spikeinterface/preprocessing/whiten.py
index fa33975a68..57400c1199 100644
--- a/src/spikeinterface/preprocessing/whiten.py
+++ b/src/spikeinterface/preprocessing/whiten.py
@@ -76,9 +76,9 @@ def __init__(
         dtype_ = fix_dtype(recording, dtype)
 
         if dtype_.kind == "i":
-            assert int_scale is not None, (
-                "For recording with dtype=int you must set the output dtype to float OR set a int_scale"
-            )
+            assert (
+                int_scale is not None
+            ), "For recording with dtype=int you must set the output dtype to float OR set a int_scale"
 
         if W is not None:
             W = np.asarray(W)

From f34da1aff682828dfba78cd17034c0fc2cb40fda Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 1 Nov 2024 14:03:13 +0000
Subject: [PATCH 23/42] Make new index page with hover CSS.

---
 doc/_static/css/custom.css     |  20 +++
 doc/conf.py                    |   6 +-
 doc/index.rst                  |   1 +
 doc/tutorials_custom_index.rst | 254 +++++++++++++++++++++++++++++++++
 4 files changed, 279 insertions(+), 2 deletions(-)
 create mode 100644 doc/_static/css/custom.css
 create mode 100644 doc/tutorials_custom_index.rst

diff --git a/doc/_static/css/custom.css b/doc/_static/css/custom.css
new file mode 100644
index 0000000000..0c51da539e
--- /dev/null
+++ b/doc/_static/css/custom.css
@@ -0,0 +1,20 @@
+/* Center and make the title bold */
+.gallery-card .grid-item-card-title {
+    text-align: center;
+    font-weight: bold;
+}
+
+/* Default style for hover content (hidden) */
+.gallery-card .hover-content {
+    display: none;
+    text-align: center;
+}
+
+/* Show the hover content when hovering over the card */
+.gallery-card:hover .default-title {
+    display: none;
+}
+
+.gallery-card:hover .hover-content {
+    display: block;
+}
diff --git a/doc/conf.py b/doc/conf.py
index e3d58ca8f2..db16269991 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -109,8 +109,10 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
-
+html_static_path = ['_static']
+html_css_files = [
+    'css/custom.css',
+]
 html_favicon = "images/favicon-32x32.png"
 
 
diff --git a/doc/index.rst b/doc/index.rst
index ed443e4200..57a0c95443 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -51,6 +51,7 @@ SpikeInterface is made of several modules to deal with different aspects of the
 
     overview
     get_started/index
+    tutorials_custom_index
     tutorials/index
     how_to/index
     modules/index
diff --git a/doc/tutorials_custom_index.rst b/doc/tutorials_custom_index.rst
new file mode 100644
index 0000000000..46a7bea630
--- /dev/null
+++ b/doc/tutorials_custom_index.rst
@@ -0,0 +1,254 @@
+.. This page provides a custom index to the 'Tutorials' page, rather than the default sphinx-gallery
+.. generated page. The benefits of this are flexibility in design and inclusion of non-sphinx files in the index.
+..
+.. To update this index with a new documentation page
+.. 1) Copy the grid-item-card and associated ".. raw:: html" section.
+.. 2) change :link: to a link to your page. If this is an `.rst` file, point to the rst file directly.
+..    If it is a sphinx-gallery generated file, format the path as separated by underscore and prefix `sphx_glr`,
+..    pointing to the .py file. e.g. `tutorials/my/page.py` -> `sphx_glr_tutorials_my_page.py
+.. 3) Change :img-top: to point to the thumbnail image of your choosing. You can point to images generated
+..    in the sphinx gallery page if you wish.
+.. 4) In the `html` section, change the `default-title` to your pages title and `hover-content` to the subtitle.
+
+:orphan:
+
+TutorialsNew
+============
+
+Longer form tutorials about using SpikeInterface. Many of these are downloadable as notebooks or Python scripts so that you can "code along" with the tutorials.
+
+If you're new to SpikeInterface, we recommend trying out the :ref:`get_started/quickstart:Quickstart tutorial` first.
+
+Updating from legacy
+--------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorials/waveform_extractor_to_sorting_analyzer
+
+Core tutorials
+--------------
+
+These tutorials focus on the :py:mod:`spikeinterface.core` module.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_1_recording_extractor.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_1_recording_extractor_thumb.png
+      :img-alt: Recording objects
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Recording objects</div>
+         <div class="hover-content">Manage loaded recordings in SpikeInterface</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_2_sorting_extractor.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_2_sorting_extractor_thumb.png
+      :img-alt: Sorting objects
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Sorting objects</div>
+         <div class="hover-content">Explore sorting extractor features</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_3_handle_probe_info.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_3_handle_probe_info_thumb.png
+      :img-alt: Handling probe information
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Handling probe information</div>
+         <div class="hover-content">Handle and visualize probe information</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_4_sorting_analyzer.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_4_sorting_analyzer_thumb.png
+      :img-alt: SortingAnalyzer
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">SortingAnalyzer</div>
+         <div class="hover-content">Analyze sorting results with ease</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_5_append_concatenate_segments_thumb.png
+      :img-alt: Append/Concatenate segments
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Append and/or concatenate segments</div>
+         <div class="hover-content">Combine segments efficiently</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_core_plot_6_handle_times.py
+      :img-top: /tutorials/core/images/thumb/sphx_glr_plot_6_handle_times_thumb.png
+      :img-alt: Handle time information
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Handle time information</div>
+         <div class="hover-content">Manage and analyze time information</div>
+
+Extractors tutorials
+--------------------
+
+The :py:mod:`spikeinterface.extractors` module is designed to load and save recorded and sorted data, and to handle probe information.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_extractors_plot_1_read_various_formats.py
+      :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_1_read_various_formats_thumb.png
+      :img-alt: Read various formats
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Read various formats</div>
+         <div class="hover-content">Read different recording formats efficiently</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py
+      :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_2_working_with_unscaled_traces_thumb.png
+      :img-alt: Unscaled traces
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Working with unscaled traces</div>
+         <div class="hover-content">Learn about managing unscaled traces</div>
+
+Quality metrics tutorial
+------------------------
+
+The :code:`spikeinterface.qualitymetrics` module allows users to compute various quality metrics to assess the goodness of a spike sorting output.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py
+      :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_3_quality_mertics_thumb.png
+      :img-alt: Quality Metrics
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Quality Metrics</div>
+         <div class="hover-content">Evaluate sorting quality using metrics</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_qualitymetrics_plot_4_curation.py
+      :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_4_curation_thumb.png
+      :img-alt: Curation Tutorial
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Curation Tutorial</div>
+         <div class="hover-content">Learn how to curate spike sorting data</div>
+
+Comparison tutorial
+-------------------
+
+The :code:`spikeinterface.comparison` module allows you to compare sorter outputs or benchmark against ground truth.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py
+      :img-top: /tutorials/comparison/images/thumb/sphx_glr_plot_5_comparison_sorter_weaknesses_thumb.png
+      :img-alt: Sorter Comparison
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Sorter Comparison</div>
+         <div class="hover-content">Compare sorter outputs and assess weaknesses</div>
+
+Widgets tutorials
+-----------------
+
+The :code:`widgets` module contains several plotting routines (widgets) for visualizing recordings, sorting data, probe layout, and more.
+
+.. grid:: 1 2 2 3
+   :gutter: 2
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_1_rec_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_1_rec_gallery_thumb.png
+      :img-alt: Recording Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">RecordingExtractor Widgets</div>
+         <div class="hover-content">Visualize recordings with widgets</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_2_sort_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_2_sort_gallery_thumb.png
+      :img-alt: Sorting Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">SortingExtractor Widgets</div>
+         <div class="hover-content">Explore sorting data using widgets</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_3_waveforms_gallery_thumb.png
+      :img-alt: Waveforms Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Waveforms Widgets</div>
+         <div class="hover-content">Display waveforms using SpikeInterface</div>
+
+   .. grid-item-card::
+      :link-type: ref
+      :link: sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py
+      :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_4_peaks_gallery_thumb.png
+      :img-alt: Peaks Widgets
+      :class-card: gallery-card
+
+      .. raw:: html
+
+         <div class="grid-item-card-title default-title">Peaks Widgets</div>
+         <div class="hover-content">Visualize detected peaks</div>
+
+Download All Examples
+---------------------
+
+- :download:`Download all examples in Python source code </tutorials/tutorials_python.zip>`
+- :download:`Download all examples in Jupyter notebooks </tutorials/tutorials_jupyter.zip>`

From 7aa93490cca20916338629518800a1cbf976b8ff Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 1 Nov 2024 14:53:22 +0000
Subject: [PATCH 24/42] Remove CSS and update development docs.

---
 doc/_static/css/custom.css      |  20 -----
 doc/conf.py                     |   6 +-
 doc/development/development.rst |  19 +++++
 doc/index.rst                   |   1 -
 doc/tutorials_custom_index.rst  | 128 +++++++++-----------------------
 5 files changed, 56 insertions(+), 118 deletions(-)
 delete mode 100644 doc/_static/css/custom.css

diff --git a/doc/_static/css/custom.css b/doc/_static/css/custom.css
deleted file mode 100644
index 0c51da539e..0000000000
--- a/doc/_static/css/custom.css
+++ /dev/null
@@ -1,20 +0,0 @@
-/* Center and make the title bold */
-.gallery-card .grid-item-card-title {
-    text-align: center;
-    font-weight: bold;
-}
-
-/* Default style for hover content (hidden) */
-.gallery-card .hover-content {
-    display: none;
-    text-align: center;
-}
-
-/* Show the hover content when hovering over the card */
-.gallery-card:hover .default-title {
-    display: none;
-}
-
-.gallery-card:hover .hover-content {
-    display: block;
-}
diff --git a/doc/conf.py b/doc/conf.py
index db16269991..e3d58ca8f2 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -109,10 +109,8 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-html_css_files = [
-    'css/custom.css',
-]
+# html_static_path = ['_static']
+
 html_favicon = "images/favicon-32x32.png"
 
 
diff --git a/doc/development/development.rst b/doc/development/development.rst
index a91818a271..1638c41243 100644
--- a/doc/development/development.rst
+++ b/doc/development/development.rst
@@ -213,6 +213,25 @@ We use Sphinx to build the documentation. To build the documentation locally, yo
 
 This will build the documentation in the :code:`doc/_build/html` folder. You can open the :code:`index.html` file in your browser to see the documentation.
 
+Adding new documentation
+------------------------
+
+Documentation can be added as a
+`sphinx-gallery <https://sphinx-gallery.github.io/stable/index.html>`_
+python file ('tutorials')
+or a
+`sphinx rst <https://sphinx-tutorial.readthedocs.io/step-1/>`_
+file (all other sections).
+
+To add a new tutorial, add your ``.py`` file to ``spikeinterface/examples``.
+Then, update the ``spikeinterface/doc/tutorials_custom_index.rst`` file
+to make a new card linking to the page and an optional image. See
+``tutorials_custom_index.rst`` header for more information.
+
+For other sections, write your documentation in ``.rst`` format and add
+the page to the appropriate ``index.rst`` file found in the relevant
+folder (e.g. ``how_to/index.rst``).
+
 How to run code coverage locally
 --------------------------------
 To run code coverage locally, you can use the following command:
diff --git a/doc/index.rst b/doc/index.rst
index 57a0c95443..e6d8aa3fea 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -52,7 +52,6 @@ SpikeInterface is made of several modules to deal with different aspects of the
     overview
     get_started/index
     tutorials_custom_index
-    tutorials/index
     how_to/index
     modules/index
     api
diff --git a/doc/tutorials_custom_index.rst b/doc/tutorials_custom_index.rst
index 46a7bea630..4c7625d811 100644
--- a/doc/tutorials_custom_index.rst
+++ b/doc/tutorials_custom_index.rst
@@ -12,12 +12,14 @@
 
 :orphan:
 
-TutorialsNew
+Tutorials
 ============
 
-Longer form tutorials about using SpikeInterface. Many of these are downloadable as notebooks or Python scripts so that you can "code along" with the tutorials.
+Longer form tutorials about using SpikeInterface. Many of these are downloadable
+as notebooks or Python scripts so that you can "code along" with the tutorials.
 
-If you're new to SpikeInterface, we recommend trying out the :ref:`get_started/quickstart:Quickstart tutorial` first.
+If you're new to SpikeInterface, we recommend trying out the
+:ref:`get_started/quickstart:Quickstart tutorial` first.
 
 Updating from legacy
 --------------------
@@ -35,77 +37,53 @@ These tutorials focus on the :py:mod:`spikeinterface.core` module.
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Recording objects
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_1_recording_extractor.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_1_recording_extractor_thumb.png
       :img-alt: Recording objects
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Recording objects</div>
-         <div class="hover-content">Manage loaded recordings in SpikeInterface</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Sorting objects
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_2_sorting_extractor.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_2_sorting_extractor_thumb.png
       :img-alt: Sorting objects
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Sorting objects</div>
-         <div class="hover-content">Explore sorting extractor features</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Handling probe information
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_3_handle_probe_info.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_3_handle_probe_info_thumb.png
       :img-alt: Handling probe information
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Handling probe information</div>
-         <div class="hover-content">Handle and visualize probe information</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: SortingAnalyzer
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_4_sorting_analyzer.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_4_sorting_analyzer_thumb.png
       :img-alt: SortingAnalyzer
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">SortingAnalyzer</div>
-         <div class="hover-content">Analyze sorting results with ease</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Append and/or concatenate segments
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_5_append_concatenate_segments_thumb.png
       :img-alt: Append/Concatenate segments
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Append and/or concatenate segments</div>
-         <div class="hover-content">Combine segments efficiently</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Handle time information
       :link-type: ref
       :link: sphx_glr_tutorials_core_plot_6_handle_times.py
       :img-top: /tutorials/core/images/thumb/sphx_glr_plot_6_handle_times_thumb.png
       :img-alt: Handle time information
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Handle time information</div>
-         <div class="hover-content">Manage and analyze time information</div>
+      :text-align: center
 
 Extractors tutorials
 --------------------
@@ -115,29 +93,21 @@ The :py:mod:`spikeinterface.extractors` module is designed to load and save reco
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Read various formats
       :link-type: ref
       :link: sphx_glr_tutorials_extractors_plot_1_read_various_formats.py
       :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_1_read_various_formats_thumb.png
       :img-alt: Read various formats
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Read various formats</div>
-         <div class="hover-content">Read different recording formats efficiently</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Working with unscaled traces
       :link-type: ref
       :link: sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py
       :img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_2_working_with_unscaled_traces_thumb.png
       :img-alt: Unscaled traces
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Working with unscaled traces</div>
-         <div class="hover-content">Learn about managing unscaled traces</div>
+      :text-align: center
 
 Quality metrics tutorial
 ------------------------
@@ -147,29 +117,21 @@ The :code:`spikeinterface.qualitymetrics` module allows users to compute various
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Quality Metrics
       :link-type: ref
       :link: sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py
       :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_3_quality_mertics_thumb.png
       :img-alt: Quality Metrics
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Quality Metrics</div>
-         <div class="hover-content">Evaluate sorting quality using metrics</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Curation Tutorial
       :link-type: ref
       :link: sphx_glr_tutorials_qualitymetrics_plot_4_curation.py
       :img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_4_curation_thumb.png
       :img-alt: Curation Tutorial
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Curation Tutorial</div>
-         <div class="hover-content">Learn how to curate spike sorting data</div>
+      :text-align: center
 
 Comparison tutorial
 -------------------
@@ -179,17 +141,13 @@ The :code:`spikeinterface.comparison` module allows you to compare sorter output
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: Sorter Comparison
       :link-type: ref
       :link: sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py
       :img-top: /tutorials/comparison/images/thumb/sphx_glr_plot_5_comparison_sorter_weaknesses_thumb.png
       :img-alt: Sorter Comparison
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Sorter Comparison</div>
-         <div class="hover-content">Compare sorter outputs and assess weaknesses</div>
+      :text-align: center
 
 Widgets tutorials
 -----------------
@@ -199,53 +157,37 @@ The :code:`widgets` module contains several plotting routines (widgets) for visu
 .. grid:: 1 2 2 3
    :gutter: 2
 
-   .. grid-item-card::
+   .. grid-item-card:: RecordingExtractor Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_1_rec_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_1_rec_gallery_thumb.png
       :img-alt: Recording Widgets
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">RecordingExtractor Widgets</div>
-         <div class="hover-content">Visualize recordings with widgets</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: SortingExtractor Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_2_sort_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_2_sort_gallery_thumb.png
       :img-alt: Sorting Widgets
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">SortingExtractor Widgets</div>
-         <div class="hover-content">Explore sorting data using widgets</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Waveforms Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_3_waveforms_gallery_thumb.png
       :img-alt: Waveforms Widgets
       :class-card: gallery-card
+      :text-align: center
 
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Waveforms Widgets</div>
-         <div class="hover-content">Display waveforms using SpikeInterface</div>
-
-   .. grid-item-card::
+   .. grid-item-card:: Peaks Widgets
       :link-type: ref
       :link: sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py
       :img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_4_peaks_gallery_thumb.png
       :img-alt: Peaks Widgets
       :class-card: gallery-card
-
-      .. raw:: html
-
-         <div class="grid-item-card-title default-title">Peaks Widgets</div>
-         <div class="hover-content">Visualize detected peaks</div>
+      :text-align: center
 
 Download All Examples
 ---------------------

From 0e44185c2918a2d7b53cfe55879fde134c478b57 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Mon, 4 Nov 2024 11:05:26 +0100
Subject: [PATCH 25/42] Apply suggestions from code review

---
 src/spikeinterface/core/node_pipeline.py               | 2 +-
 src/spikeinterface/sortingcomponents/peak_detection.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/core/node_pipeline.py b/src/spikeinterface/core/node_pipeline.py
index 8ca4ba7f3a..53c2445c77 100644
--- a/src/spikeinterface/core/node_pipeline.py
+++ b/src/spikeinterface/core/node_pipeline.py
@@ -544,7 +544,7 @@ def run_node_pipeline(
     recording_slices : None | list[tuple]
         Optionaly give a list of slices to run the pipeline only on some chunks of the recording.
         It must be a list of (segment_index, frame_start, frame_stop).
-        If None (default), the entire recording is computed.
+        If None (default), the function iterates over the entire duration of the recording.
 
     Returns
     -------
diff --git a/src/spikeinterface/sortingcomponents/peak_detection.py b/src/spikeinterface/sortingcomponents/peak_detection.py
index 233b16dcf7..d03744f8f9 100644
--- a/src/spikeinterface/sortingcomponents/peak_detection.py
+++ b/src/spikeinterface/sortingcomponents/peak_detection.py
@@ -87,7 +87,7 @@ def detect_peaks(
     recording_slices : None | list[tuple]
         Optionaly give a list of slices to run the pipeline only on some chunks of the recording.
         It must be a list of (segment_index, frame_start, frame_stop).
-        If None (default), the entire recording is computed.
+        If None (default), the function iterates over the entire duration of the recording.
 
     {method_doc}
     {job_doc}

From 2faed131014fe46fd0fafddcb9b94872f889ca7c Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Mon, 4 Nov 2024 16:05:42 +0100
Subject: [PATCH 26/42] Remove the need of template_similarity extension for
 autocorrelogram plot

---
 src/spikeinterface/exporters/report.py          | 4 ++--
 src/spikeinterface/widgets/autocorrelograms.py  | 8 +++++++-
 src/spikeinterface/widgets/crosscorrelograms.py | 3 ++-
 src/spikeinterface/widgets/unit_summary.py      | 4 ++--
 4 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/exporters/report.py b/src/spikeinterface/exporters/report.py
index 484da83342..ab08401382 100644
--- a/src/spikeinterface/exporters/report.py
+++ b/src/spikeinterface/exporters/report.py
@@ -22,8 +22,8 @@ def export_report(
     """
     Exports a SI spike sorting report. The report includes summary figures of the spike sorting output.
     What is plotted depends on what has been calculated. Unit locations and unit waveforms are always included.
-    Unit waveform densities, correlograms and spike amplitudes are plotted if `waveforms`, `correlograms`
-    and 'template_similarity', and `spike_amplitudes` have been computed for the given `sorting_analyzer`.
+    Unit waveform densities, correlograms and spike amplitudes are plotted if `waveforms`, `correlograms`,
+    and `spike_amplitudes` have been computed for the given `sorting_analyzer`.
 
     Parameters
     ----------
diff --git a/src/spikeinterface/widgets/autocorrelograms.py b/src/spikeinterface/widgets/autocorrelograms.py
index c8acd93dc2..c211a277f8 100644
--- a/src/spikeinterface/widgets/autocorrelograms.py
+++ b/src/spikeinterface/widgets/autocorrelograms.py
@@ -9,7 +9,13 @@ class AutoCorrelogramsWidget(CrossCorrelogramsWidget):
     # the doc is copied form CrossCorrelogramsWidget
 
     def __init__(self, *args, **kargs):
-        CrossCorrelogramsWidget.__init__(self, *args, **kargs)
+        _ = kargs.pop("min_similarity_for_correlograms", 0.0)
+        CrossCorrelogramsWidget.__init__(
+            self,
+            *args,
+            **kargs,
+            min_similarity_for_correlograms=None,
+        )
 
     def plot_matplotlib(self, data_plot, **backend_kwargs):
         import matplotlib.pyplot as plt
diff --git a/src/spikeinterface/widgets/crosscorrelograms.py b/src/spikeinterface/widgets/crosscorrelograms.py
index cdb2041aa3..88dd803323 100644
--- a/src/spikeinterface/widgets/crosscorrelograms.py
+++ b/src/spikeinterface/widgets/crosscorrelograms.py
@@ -21,7 +21,8 @@ class CrossCorrelogramsWidget(BaseWidget):
         List of unit ids
     min_similarity_for_correlograms : float, default: 0.2
         For sortingview backend. Threshold for computing pair-wise cross-correlograms.
-        If template similarity between two units is below this threshold, the cross-correlogram is not displayed
+        If template similarity between two units is below this threshold, the cross-correlogram is not displayed.
+        For auto-correlograms plot, this is automatically set to None.
     window_ms : float, default: 100.0
         Window for CCGs in ms. If correlograms are already computed (e.g. with SortingAnalyzer),
         this argument is ignored
diff --git a/src/spikeinterface/widgets/unit_summary.py b/src/spikeinterface/widgets/unit_summary.py
index d8cbeb7bb3..9466110110 100644
--- a/src/spikeinterface/widgets/unit_summary.py
+++ b/src/spikeinterface/widgets/unit_summary.py
@@ -108,7 +108,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         fig = self.figure
         nrows = 2
         ncols = 2
-        if sorting_analyzer.has_extension("correlograms") and sorting_analyzer.has_extension("template_similarity"):
+        if sorting_analyzer.has_extension("correlograms"):
             ncols += 1
         if sorting_analyzer.has_extension("waveforms"):
             ncols += 1
@@ -172,7 +172,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             col_counter += 1
             ax_waveform_density.set_ylabel(None)
 
-        if sorting_analyzer.has_extension("correlograms") and sorting_analyzer.has_extension("template_similarity"):
+        if sorting_analyzer.has_extension("correlograms"):
             ax_correlograms = fig.add_subplot(gs[:2, col_counter])
             AutoCorrelogramsWidget(
                 sorting_analyzer,

From 2ba37a8b3990af3919a3c1b294700909d144a457 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Tue, 5 Nov 2024 15:58:45 +0100
Subject: [PATCH 27/42] Don't let decimate mess with times and skim tests

---
 src/spikeinterface/preprocessing/decimate.py  | 26 +++++++++----------
 .../preprocessing/tests/test_decimate.py      | 20 +++++++-------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/src/spikeinterface/preprocessing/decimate.py b/src/spikeinterface/preprocessing/decimate.py
index 334ebb02d2..c1b1cd9f80 100644
--- a/src/spikeinterface/preprocessing/decimate.py
+++ b/src/spikeinterface/preprocessing/decimate.py
@@ -63,18 +63,15 @@ def __init__(
                 f"Consider combining DecimateRecording with FrameSliceRecording for fine control on the recording start/end frames."
             )
         self._decimation_offset = decimation_offset
-        resample_rate = self._orig_samp_freq / self._decimation_factor
+        decimated_sampling_frequency = self._orig_samp_freq / self._decimation_factor
 
-        BasePreprocessor.__init__(self, recording, sampling_frequency=resample_rate)
+        BasePreprocessor.__init__(self, recording, sampling_frequency=decimated_sampling_frequency)
 
-        # in case there was a time_vector, it will be dropped for sanity.
-        # This is not necessary but consistent with ResampleRecording
         for parent_segment in recording._recording_segments:
-            parent_segment.time_vector = None
             self.add_recording_segment(
                 DecimateRecordingSegment(
                     parent_segment,
-                    resample_rate,
+                    decimated_sampling_frequency,
                     self._orig_samp_freq,
                     decimation_factor,
                     decimation_offset,
@@ -93,22 +90,25 @@ class DecimateRecordingSegment(BaseRecordingSegment):
     def __init__(
         self,
         parent_recording_segment,
-        resample_rate,
+        decimated_sampling_frequency,
         parent_rate,
         decimation_factor,
         decimation_offset,
         dtype,
     ):
-        if parent_recording_segment.t_start is None:
-            new_t_start = None
+        if parent_recording_segment.time_vector is not None:
+            time_vector = parent_recording_segment.time_vector[decimation_offset::decimation_factor]
+            decimated_sampling_frequency = None
         else:
-            new_t_start = parent_recording_segment.t_start + decimation_offset / parent_rate
+            time_vector = None
+            if parent_recording_segment.t_start is None:
+                t_start = None
+            else:
+                t_start = parent_recording_segment.t_start + decimation_offset / parent_rate
 
         # Do not use BasePreprocessorSegment bcause we have to reset the sampling rate!
         BaseRecordingSegment.__init__(
-            self,
-            sampling_frequency=resample_rate,
-            t_start=new_t_start,
+            self, sampling_frequency=decimated_sampling_frequency, t_start=t_start, time_vector=time_vector
         )
         self._parent_segment = parent_recording_segment
         self._decimation_factor = decimation_factor
diff --git a/src/spikeinterface/preprocessing/tests/test_decimate.py b/src/spikeinterface/preprocessing/tests/test_decimate.py
index 100972f762..adfcbd0d4a 100644
--- a/src/spikeinterface/preprocessing/tests/test_decimate.py
+++ b/src/spikeinterface/preprocessing/tests/test_decimate.py
@@ -8,19 +8,19 @@
 import numpy as np
 
 
-@pytest.mark.parametrize("N_segments", [1, 2])
-@pytest.mark.parametrize("decimation_offset", [0, 1, 9, 10, 11, 100, 101])
-@pytest.mark.parametrize("decimation_factor", [1, 9, 10, 11, 100, 101])
+@pytest.mark.parametrize("num_segments", [1, 2])
+@pytest.mark.parametrize("decimation_offset", [0, 5, 21, 101])
+@pytest.mark.parametrize("decimation_factor", [1, 7, 50])
 @pytest.mark.parametrize("start_frame", [0, 1, 5, None, 1000])
 @pytest.mark.parametrize("end_frame", [0, 1, 5, None, 1000])
-def test_decimate(N_segments, decimation_offset, decimation_factor, start_frame, end_frame):
+def test_decimate(num_segments, decimation_offset, decimation_factor, start_frame, end_frame):
     rec = generate_recording()
 
-    segment_num_samps = [101 + i for i in range(N_segments)]
+    segment_num_samps = [101 + i for i in range(num_segments)]
 
     rec = NumpyRecording([np.arange(2 * N).reshape(N, 2) for N in segment_num_samps], 1)
 
-    parent_traces = [rec.get_traces(i) for i in range(N_segments)]
+    parent_traces = [rec.get_traces(i) for i in range(num_segments)]
 
     if decimation_offset >= min(segment_num_samps) or decimation_offset >= decimation_factor:
         with pytest.raises(ValueError):
@@ -28,14 +28,14 @@ def test_decimate(N_segments, decimation_offset, decimation_factor, start_frame,
         return
 
     decimated_rec = DecimateRecording(rec, decimation_factor, decimation_offset=decimation_offset)
-    decimated_parent_traces = [parent_traces[i][decimation_offset::decimation_factor] for i in range(N_segments)]
+    decimated_parent_traces = [parent_traces[i][decimation_offset::decimation_factor] for i in range(num_segments)]
 
     if start_frame is None:
-        start_frame = max(decimated_rec.get_num_samples(i) for i in range(N_segments))
+        start_frame = max(decimated_rec.get_num_samples(i) for i in range(num_segments))
     if end_frame is None:
-        end_frame = max(decimated_rec.get_num_samples(i) for i in range(N_segments))
+        end_frame = max(decimated_rec.get_num_samples(i) for i in range(num_segments))
 
-    for i in range(N_segments):
+    for i in range(num_segments):
         assert decimated_rec.get_num_samples(i) == decimated_parent_traces[i].shape[0]
         assert np.all(
             decimated_rec.get_traces(i, start_frame, end_frame) == decimated_parent_traces[i][start_frame:end_frame]

From f90011803da2327d7ace74ff2a35b91b30c70d32 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Tue, 5 Nov 2024 16:35:27 +0100
Subject: [PATCH 28/42] More skimming and test decimate with times

---
 src/spikeinterface/preprocessing/decimate.py  |  1 +
 .../preprocessing/tests/test_decimate.py      | 57 +++++++++++++++----
 2 files changed, 47 insertions(+), 11 deletions(-)

diff --git a/src/spikeinterface/preprocessing/decimate.py b/src/spikeinterface/preprocessing/decimate.py
index c1b1cd9f80..2b47601fc2 100644
--- a/src/spikeinterface/preprocessing/decimate.py
+++ b/src/spikeinterface/preprocessing/decimate.py
@@ -99,6 +99,7 @@ def __init__(
         if parent_recording_segment.time_vector is not None:
             time_vector = parent_recording_segment.time_vector[decimation_offset::decimation_factor]
             decimated_sampling_frequency = None
+            t_start = None
         else:
             time_vector = None
             if parent_recording_segment.t_start is None:
diff --git a/src/spikeinterface/preprocessing/tests/test_decimate.py b/src/spikeinterface/preprocessing/tests/test_decimate.py
index adfcbd0d4a..dd521cbe9b 100644
--- a/src/spikeinterface/preprocessing/tests/test_decimate.py
+++ b/src/spikeinterface/preprocessing/tests/test_decimate.py
@@ -11,13 +11,8 @@
 @pytest.mark.parametrize("num_segments", [1, 2])
 @pytest.mark.parametrize("decimation_offset", [0, 5, 21, 101])
 @pytest.mark.parametrize("decimation_factor", [1, 7, 50])
-@pytest.mark.parametrize("start_frame", [0, 1, 5, None, 1000])
-@pytest.mark.parametrize("end_frame", [0, 1, 5, None, 1000])
-def test_decimate(num_segments, decimation_offset, decimation_factor, start_frame, end_frame):
-    rec = generate_recording()
-
-    segment_num_samps = [101 + i for i in range(num_segments)]
-
+def test_decimate(num_segments, decimation_offset, decimation_factor):
+    segment_num_samps = [20000, 40000]
     rec = NumpyRecording([np.arange(2 * N).reshape(N, 2) for N in segment_num_samps], 1)
 
     parent_traces = [rec.get_traces(i) for i in range(num_segments)]
@@ -30,10 +25,19 @@ def test_decimate(num_segments, decimation_offset, decimation_factor, start_fram
     decimated_rec = DecimateRecording(rec, decimation_factor, decimation_offset=decimation_offset)
     decimated_parent_traces = [parent_traces[i][decimation_offset::decimation_factor] for i in range(num_segments)]
 
-    if start_frame is None:
-        start_frame = max(decimated_rec.get_num_samples(i) for i in range(num_segments))
-    if end_frame is None:
-        end_frame = max(decimated_rec.get_num_samples(i) for i in range(num_segments))
+    for start_frame in [0, 1, 5, None, 1000]:
+        for end_frame in [0, 1, 5, None, 1000]:
+            if start_frame is None:
+                start_frame = max(decimated_rec.get_num_samples(i) for i in range(num_segments))
+            if end_frame is None:
+                end_frame = max(decimated_rec.get_num_samples(i) for i in range(num_segments))
+
+            for i in range(num_segments):
+                assert decimated_rec.get_num_samples(i) == decimated_parent_traces[i].shape[0]
+                assert np.all(
+                    decimated_rec.get_traces(i, start_frame, end_frame)
+                    == decimated_parent_traces[i][start_frame:end_frame]
+                )
 
     for i in range(num_segments):
         assert decimated_rec.get_num_samples(i) == decimated_parent_traces[i].shape[0]
@@ -42,5 +46,36 @@ def test_decimate(num_segments, decimation_offset, decimation_factor, start_fram
         )
 
 
+def test_decimate_with_times():
+    rec = generate_recording(durations=[5, 10])
+
+    # test with times
+    times = [rec.get_times(0) + 10, rec.get_times(1) + 20]
+    for i, t in enumerate(times):
+        rec.set_times(t, i)
+
+    decimation_factor = 2
+    decimation_offset = 1
+    decimated_rec = DecimateRecording(rec, decimation_factor, decimation_offset=decimation_offset)
+
+    for segment_index in range(rec.get_num_segments()):
+        assert np.allclose(
+            decimated_rec.get_times(segment_index),
+            rec.get_times(segment_index)[decimation_offset::decimation_factor],
+        )
+
+    # test with t_start
+    rec = generate_recording(durations=[5, 10])
+    t_starts = [10, 20]
+    for t_start, rec_segment in zip(t_starts, rec._recording_segments):
+        rec_segment.t_start = t_start
+    decimated_rec = DecimateRecording(rec, decimation_factor, decimation_offset=decimation_offset)
+    for segment_index in range(rec.get_num_segments()):
+        assert np.allclose(
+            decimated_rec.get_times(segment_index),
+            rec.get_times(segment_index)[decimation_offset::decimation_factor],
+        )
+
+
 if __name__ == "__main__":
     test_decimate()

From 2d843f8770a8587c32920d3af4dcc54bb8c05411 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Wed, 6 Nov 2024 10:09:56 +0100
Subject: [PATCH 29/42] Zach's comments

---
 src/spikeinterface/preprocessing/decimate.py            | 2 +-
 src/spikeinterface/preprocessing/tests/test_decimate.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/preprocessing/decimate.py b/src/spikeinterface/preprocessing/decimate.py
index 2b47601fc2..d5fc9d2025 100644
--- a/src/spikeinterface/preprocessing/decimate.py
+++ b/src/spikeinterface/preprocessing/decimate.py
@@ -105,7 +105,7 @@ def __init__(
             if parent_recording_segment.t_start is None:
                 t_start = None
             else:
-                t_start = parent_recording_segment.t_start + decimation_offset / parent_rate
+                t_start = parent_recording_segment.t_start + (decimation_offset / parent_rate)
 
         # Do not use BasePreprocessorSegment bcause we have to reset the sampling rate!
         BaseRecordingSegment.__init__(
diff --git a/src/spikeinterface/preprocessing/tests/test_decimate.py b/src/spikeinterface/preprocessing/tests/test_decimate.py
index dd521cbe9b..aab17560a6 100644
--- a/src/spikeinterface/preprocessing/tests/test_decimate.py
+++ b/src/spikeinterface/preprocessing/tests/test_decimate.py
@@ -9,7 +9,7 @@
 
 
 @pytest.mark.parametrize("num_segments", [1, 2])
-@pytest.mark.parametrize("decimation_offset", [0, 5, 21, 101])
+@pytest.mark.parametrize("decimation_offset", [0, 1, 5, 21, 101])
 @pytest.mark.parametrize("decimation_factor", [1, 7, 50])
 def test_decimate(num_segments, decimation_offset, decimation_factor):
     segment_num_samps = [20000, 40000]

From d6b4c1e7474c372c6d9f71787ddbe707854bd11f Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Thu, 7 Nov 2024 11:44:13 +0100
Subject: [PATCH 30/42] Fix cbin_file_path

---
 src/spikeinterface/extractors/cbin_ibl.py | 30 +++++++++++++++--------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index d7e5b58e11..88e1029ab0 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
+import warnings
 import numpy as np
 
 import probeinterface
@@ -30,8 +31,10 @@ class CompressedBinaryIblExtractor(BaseRecording):
     stream_name : {"ap", "lp"}, default: "ap".
         Whether to load AP or LFP band, one
         of "ap" or "lp".
-    cbin_file : str or None, default None
+    cbin_file_path : str or None, default None
         The cbin file of the recording. If None, searches in `folder_path` for file.
+    cbin_file : str or None, default None
+        (deprecated) The cbin file of the recording. If None, searches in `folder_path` for file.
 
     Returns
     -------
@@ -41,14 +44,21 @@ class CompressedBinaryIblExtractor(BaseRecording):
 
     installation_mesg = "To use the CompressedBinaryIblExtractor, install mtscomp: \n\n pip install mtscomp\n\n"
 
-    def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap", cbin_file=None):
+    def __init__(
+        self, folder_path=None, load_sync_channel=False, stream_name="ap", cbin_file_path=None, cbin_file=None
+    ):
         from neo.rawio.spikeglxrawio import read_meta_file
 
         try:
             import mtscomp
         except ImportError:
             raise ImportError(self.installation_mesg)
-        if cbin_file is None:
+        if cbin_file is not None:
+            warnings.warn(
+                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning
+            )
+            cbin_file_path = cbin_file
+        if cbin_file_path is None:
             folder_path = Path(folder_path)
             # check bands
             assert stream_name in ["ap", "lp"], "stream_name must be one of: 'ap', 'lp'"
@@ -60,17 +70,17 @@ def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap",
             assert (
                 len(curr_cbin_files) == 1
             ), f"There should only be one `*.cbin` file in the folder, but {print(curr_cbin_files)} have been found"
-            cbin_file = curr_cbin_files[0]
+            cbin_file_path = curr_cbin_files[0]
         else:
-            cbin_file = Path(cbin_file)
-            folder_path = cbin_file.parent
+            cbin_file_path = Path(cbin_file_path)
+            folder_path = cbin_file_path.parent
 
-        ch_file = cbin_file.with_suffix(".ch")
-        meta_file = cbin_file.with_suffix(".meta")
+        ch_file = cbin_file_path.with_suffix(".ch")
+        meta_file = cbin_file_path.with_suffix(".meta")
 
         # reader
         cbuffer = mtscomp.Reader()
-        cbuffer.open(cbin_file, ch_file)
+        cbuffer.open(cbin_file_path, ch_file)
 
         # meta data
         meta = read_meta_file(meta_file)
@@ -119,7 +129,7 @@ def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap",
         self._kwargs = {
             "folder_path": str(Path(folder_path).resolve()),
             "load_sync_channel": load_sync_channel,
-            "cbin_file": str(Path(cbin_file).resolve()),
+            "cbin_file_path": str(Path(cbin_file_path).resolve()),
         }
 
 

From e6f45056852e181fb8d6909c8a3365a08cb2c8f5 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Thu, 7 Nov 2024 15:56:48 +0100
Subject: [PATCH 31/42] Update src/spikeinterface/extractors/cbin_ibl.py

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

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index 88e1029ab0..357afde04e 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -55,7 +55,7 @@ def __init__(
             raise ImportError(self.installation_mesg)
         if cbin_file is not None:
             warnings.warn(
-                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning
+                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning, stacklevel=2
             )
             cbin_file_path = cbin_file
         if cbin_file_path is None:

From 471ce724faac7245766538880b7fcd196f49fa30 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 7 Nov 2024 14:57:14 +0000
Subject: [PATCH 32/42] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/spikeinterface/extractors/cbin_ibl.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index 357afde04e..8fe19f3d7e 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -55,7 +55,9 @@ def __init__(
             raise ImportError(self.installation_mesg)
         if cbin_file is not None:
             warnings.warn(
-                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead", DeprecationWarning, stacklevel=2
+                "The `cbin_file` argument is deprecated, please use `cbin_file_path` instead",
+                DeprecationWarning,
+                stacklevel=2,
             )
             cbin_file_path = cbin_file
         if cbin_file_path is None:

From f293303bef50073cb71add06e94410635615384b Mon Sep 17 00:00:00 2001
From: Pierre Yger <pierre.yger@gmail.com>
Date: Fri, 8 Nov 2024 16:06:30 +0100
Subject: [PATCH 33/42] Removing useless dependencies

---
 src/spikeinterface/postprocessing/template_metrics.py    | 2 +-
 src/spikeinterface/postprocessing/template_similarity.py | 2 +-
 src/spikeinterface/postprocessing/unit_locations.py      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/postprocessing/template_metrics.py b/src/spikeinterface/postprocessing/template_metrics.py
index 306e9594b8..6e7bcf21b8 100644
--- a/src/spikeinterface/postprocessing/template_metrics.py
+++ b/src/spikeinterface/postprocessing/template_metrics.py
@@ -97,7 +97,7 @@ class ComputeTemplateMetrics(AnalyzerExtension):
 
     extension_name = "template_metrics"
     depend_on = ["templates"]
-    need_recording = True
+    need_recording = False
     use_nodepipeline = False
     need_job_kwargs = False
 
diff --git a/src/spikeinterface/postprocessing/template_similarity.py b/src/spikeinterface/postprocessing/template_similarity.py
index cfa9d89fea..6c30e2730b 100644
--- a/src/spikeinterface/postprocessing/template_similarity.py
+++ b/src/spikeinterface/postprocessing/template_similarity.py
@@ -44,7 +44,7 @@ class ComputeTemplateSimilarity(AnalyzerExtension):
 
     extension_name = "template_similarity"
     depend_on = ["templates"]
-    need_recording = True
+    need_recording = False
     use_nodepipeline = False
     need_job_kwargs = False
     need_backward_compatibility_on_load = True
diff --git a/src/spikeinterface/postprocessing/unit_locations.py b/src/spikeinterface/postprocessing/unit_locations.py
index 4029fc88c7..3f6dd47eec 100644
--- a/src/spikeinterface/postprocessing/unit_locations.py
+++ b/src/spikeinterface/postprocessing/unit_locations.py
@@ -39,7 +39,7 @@ class ComputeUnitLocations(AnalyzerExtension):
 
     extension_name = "unit_locations"
     depend_on = ["templates"]
-    need_recording = True
+    need_recording = False
     use_nodepipeline = False
     need_job_kwargs = False
     need_backward_compatibility_on_load = True

From 620f8013b8bf4f1332a7802dd3f6804ce068493c Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 13:37:50 +0000
Subject: [PATCH 34/42] Apply to all segments if 'segment_index' is 'None'.

---
 src/spikeinterface/core/baserecording.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index b8a0420794..7392caa69b 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -521,13 +521,20 @@ def shift_start_time(self, shift, segment_index=None):
         segment_index : int | None
             The segment on which to shift the times.
         """
-        segment_index = self._check_segment_index(segment_index)
-        rs = self._recording_segments[segment_index]
+        self._check_segment_index(segment_index)
 
-        if self.has_time_vector():
-            rs.time_vector += shift
+        if segment_index is None:
+            segments_to_shift = range(self.get_num_segments())
         else:
-            rs.t_start += shift
+            segments_to_shift = (segment_index,)
+
+        for idx in segments_to_shift:
+            rs = self._recording_segments[idx]
+
+            if self.has_time_vector():
+                rs.time_vector += shift
+            else:
+                rs.t_start += shift
 
     def sample_index_to_time(self, sample_ind, segment_index=None):
         """

From 22d5dfc2a552e00d7b55d7c28681e25a1f51a711 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 13:39:34 +0000
Subject: [PATCH 35/42] Add type hints.

---
 src/spikeinterface/core/baserecording.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 7392caa69b..0af9c4bb6a 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -509,7 +509,7 @@ def reset_times(self):
             rs.t_start = None
             rs.sampling_frequency = self.sampling_frequency
 
-    def shift_start_time(self, shift, segment_index=None):
+    def shift_start_time(self, shift: int | float, segment_index: int | None = None) -> None:
         """
         Shift the starting time of the times.
 
@@ -536,15 +536,14 @@ def shift_start_time(self, shift, segment_index=None):
             else:
                 rs.t_start += shift
 
-    def sample_index_to_time(self, sample_ind, segment_index=None):
-        """
-        Transform sample index into time in seconds
-        """
+    def sample_index_to_time(self, sample_ind: int, segment_index: int | None = None):
+        """ """
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.sample_index_to_time(sample_ind)
 
-    def time_to_sample_index(self, time_s, segment_index=None):
+    def time_to_sample_index(self, time_s: float, segment_index: int | None = None):
+        """ """
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.time_to_sample_index(time_s)

From 458a3dcc201380740583ef1f075951e83ee77ed8 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 13:43:45 +0000
Subject: [PATCH 36/42] Update name and docstring.

---
 src/spikeinterface/core/baserecording.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 0af9c4bb6a..91f99f17b0 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -509,19 +509,24 @@ def reset_times(self):
             rs.t_start = None
             rs.sampling_frequency = self.sampling_frequency
 
-    def shift_start_time(self, shift: int | float, segment_index: int | None = None) -> None:
+    def shift_times(self, shift: int | float, segment_index: int | None = None) -> None:
         """
-        Shift the starting time of the times.
+        Shift all times by a scalar value. The default behaviour is to
+        shift all segments uniformly.
 
+        Parameters
+        ----------
         shift : int | float
-            The shift to apply to the first time point. If positive,
-            the current start time will be increased by `shift`. If
-            negative, the start time will be decreased.
+            The shift to apply. If positive, times will be increased by `shift`.
+            e.g. shifting by 1 will be like the recording started 1 second later.
+            If negative, the start time will be decreased i.e. as if the recording
+            started earlier.
 
         segment_index : int | None
-            The segment on which to shift the times.
+            The segment on which to shift the times. if `None`, all
+            segments will be shifted.
         """
-        self._check_segment_index(segment_index)
+        self._check_segment_index(segment_index)  # Check the segment index is valid only
 
         if segment_index is None:
             segments_to_shift = range(self.get_num_segments())

From 8845d3d7eb6caad8c6a5f0c12842f480766d3a26 Mon Sep 17 00:00:00 2001
From: chrishalcrow <57948917+chrishalcrow@users.noreply.github.com>
Date: Wed, 13 Nov 2024 14:40:16 +0000
Subject: [PATCH 37/42] Add verbose kwarg to mda write_recording

---
 src/spikeinterface/extractors/mdaextractors.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/spikeinterface/extractors/mdaextractors.py b/src/spikeinterface/extractors/mdaextractors.py
index f055e1d7c9..d2886d9e79 100644
--- a/src/spikeinterface/extractors/mdaextractors.py
+++ b/src/spikeinterface/extractors/mdaextractors.py
@@ -72,6 +72,7 @@ def write_recording(
         params_fname="params.json",
         geom_fname="geom.csv",
         dtype=None,
+        verbose=False,
         **job_kwargs,
     ):
         """Write a recording to file in MDA format.
@@ -93,6 +94,8 @@ def write_recording(
             File name of geom file
         dtype : dtype or None, default: None
             Data type to be used. If None dtype is same as recording traces.
+        verbose : bool
+            If True, shows progress bar when saving recording.
         **job_kwargs:
             Use by job_tools modules to set:
 
@@ -130,6 +133,7 @@ def write_recording(
             dtype=dtype,
             byte_offset=header_size,
             add_file_extension=False,
+            verbose=verbose,
             **job_kwargs,
         )
 

From 3e98c670a27671590613b7c1c4118780a8c47ce8 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:32:48 +0000
Subject: [PATCH 38/42] Add tests.

---
 .../core/tests/test_time_handling.py          | 92 ++++++++++++++++++-
 1 file changed, 89 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/core/tests/test_time_handling.py b/src/spikeinterface/core/tests/test_time_handling.py
index a129316ee7..9b7ed11bbb 100644
--- a/src/spikeinterface/core/tests/test_time_handling.py
+++ b/src/spikeinterface/core/tests/test_time_handling.py
@@ -15,7 +15,10 @@ class TestTimeHandling:
     is generated on the fly. Both time representations are tested here.
     """
 
-    # Fixtures #####
+    # #########################################################################
+    # Fixtures
+    # #########################################################################
+
     @pytest.fixture(scope="session")
     def time_vector_recording(self):
         """
@@ -95,7 +98,10 @@ def _get_fixture_data(self, request, fixture_name):
         raw_recording, times_recording, all_times = time_recording_fixture
         return (raw_recording, times_recording, all_times)
 
-    # Tests #####
+    # #########################################################################
+    # Tests
+    # #########################################################################
+
     def test_has_time_vector(self, time_vector_recording):
         """
         Test the `has_time_vector` function returns `False` before
@@ -305,7 +311,87 @@ def test_sorting_analyzer_get_durations_no_recording(self, time_vector_recording
 
         assert np.array_equal(sorting_analyzer.get_total_duration(), raw_recording.get_total_duration())
 
-    # Helpers ####
+    @pytest.mark.parametrize("fixture_name", ["time_vector_recording", "t_start_recording"])
+    @pytest.mark.parametrize("shift", [-123.456, 123.456])
+    def test_shift_time_all_segments(self, request, fixture_name, shift):
+        """
+        Shift the times in every segment using the `None` default, then
+        check that every segment of the recording is shifted as expected.
+        """
+        _, times_recording, all_times = self._get_fixture_data(request, fixture_name)
+
+        num_segments, orig_seg_data = self._store_all_times(times_recording)
+
+        times_recording.shift_times(shift)  # use default `segment_index=None`
+
+        for idx in range(num_segments):
+            assert np.allclose(
+                orig_seg_data[idx], times_recording.get_times(segment_index=idx) - shift, rtol=0, atol=1e-8
+            )
+
+    @pytest.mark.parametrize("fixture_name", ["time_vector_recording", "t_start_recording"])
+    @pytest.mark.parametrize("shift", [-123.456, 123.456])
+    def test_shift_times_different_segments(self, request, fixture_name, shift):
+        """
+        Shift each segment separately, and check the shifted segment only
+        is shifted as expected.
+        """
+        _, times_recording, all_times = self._get_fixture_data(request, fixture_name)
+
+        num_segments, orig_seg_data = self._store_all_times(times_recording)
+
+        # For each segment, shift the segment only and check the
+        # times are updated as expected.
+        for idx in range(num_segments):
+
+            scaler = idx + 2
+            times_recording.shift_times(shift * scaler, segment_index=idx)
+
+            assert np.allclose(
+                orig_seg_data[idx], times_recording.get_times(segment_index=idx) - shift * scaler, rtol=0, atol=1e-8
+            )
+
+            # Just do a little check that we are not
+            # accidentally changing some other segments,
+            # which should remain unchanged at this point in the loop.
+            if idx != num_segments - 1:
+                assert np.array_equal(orig_seg_data[idx + 1], times_recording.get_times(segment_index=idx + 1))
+
+    @pytest.mark.parametrize("fixture_name", ["time_vector_recording", "t_start_recording"])
+    def test_save_and_load_time_shift(self, request, fixture_name, tmp_path):
+        """
+        Save the shifted data and check the shift is propagated correctly.
+        """
+        _, times_recording, all_times = self._get_fixture_data(request, fixture_name)
+
+        shift = 100
+        times_recording.shift_times(shift=shift)
+
+        times_recording.save(folder=tmp_path / "my_file")
+
+        loaded_recording = si.load_extractor(tmp_path / "my_file")
+
+        for idx in range(times_recording.get_num_segments()):
+            assert np.array_equal(
+                times_recording.get_times(segment_index=idx), loaded_recording.get_times(segment_index=idx)
+            )
+
+    def _store_all_times(self, recording):
+        """
+        Convenience function to store original times of all segments to a dict.
+        """
+        num_segments = recording.get_num_segments()
+        seg_data = {}
+
+        for idx in range(num_segments):
+            seg_data[idx] = copy.deepcopy(recording.get_times(segment_index=idx))
+
+        return num_segments, seg_data
+
+    # #########################################################################
+    # Helpers
+    # #########################################################################
+
     def _check_times_match(self, recording, all_times):
         """
         For every segment in a recording, check the `get_times()`

From 4d7246a529e3d17747cf5a496a0a04bd97f4eb09 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:33:17 +0000
Subject: [PATCH 39/42] Fixes on shift function.

---
 src/spikeinterface/core/baserecording.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 91f99f17b0..4b545dc7c7 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -526,8 +526,6 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
             The segment on which to shift the times. if `None`, all
             segments will be shifted.
         """
-        self._check_segment_index(segment_index)  # Check the segment index is valid only
-
         if segment_index is None:
             segments_to_shift = range(self.get_num_segments())
         else:
@@ -536,7 +534,7 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
         for idx in segments_to_shift:
             rs = self._recording_segments[idx]
 
-            if self.has_time_vector():
+            if self.has_time_vector(segment_index=idx):
                 rs.time_vector += shift
             else:
                 rs.t_start += shift

From a1cf3367d18a549281208b25c622f2a1ee773226 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:35:32 +0000
Subject: [PATCH 40/42] Undo out of scope changes.

---
 src/spikeinterface/core/baserecording.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 4b545dc7c7..886f7db79f 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -539,14 +539,15 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
             else:
                 rs.t_start += shift
 
-    def sample_index_to_time(self, sample_ind: int, segment_index: int | None = None):
-        """ """
+    def sample_index_to_time(self, sample_ind, segment_index=None):
+        """
+        Transform sample index into time in seconds
+        """
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.sample_index_to_time(sample_ind)
 
-    def time_to_sample_index(self, time_s: float, segment_index: int | None = None):
-        """ """
+    def time_to_sample_index(self, time_s, segment_index=None):
         segment_index = self._check_segment_index(segment_index)
         rs = self._recording_segments[segment_index]
         return rs.time_to_sample_index(time_s)

From 469b3b0e36fdbc0571d37e100d99d6c741af1377 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Wed, 13 Nov 2024 18:37:20 +0000
Subject: [PATCH 41/42] Fix docstring.

---
 src/spikeinterface/core/baserecording.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/spikeinterface/core/baserecording.py b/src/spikeinterface/core/baserecording.py
index 886f7db79f..6d9d2a827f 100644
--- a/src/spikeinterface/core/baserecording.py
+++ b/src/spikeinterface/core/baserecording.py
@@ -511,8 +511,7 @@ def reset_times(self):
 
     def shift_times(self, shift: int | float, segment_index: int | None = None) -> None:
         """
-        Shift all times by a scalar value. The default behaviour is to
-        shift all segments uniformly.
+        Shift all times by a scalar value.
 
         Parameters
         ----------
@@ -523,8 +522,8 @@ def shift_times(self, shift: int | float, segment_index: int | None = None) -> N
             started earlier.
 
         segment_index : int | None
-            The segment on which to shift the times. if `None`, all
-            segments will be shifted.
+            The segment on which to shift the times.
+            If `None`, all segments will be shifted.
         """
         if segment_index is None:
             segments_to_shift = range(self.get_num_segments())

From 1e53a5e06b2a90956d72150826a8f590d673b5ce Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Tue, 19 Nov 2024 17:45:40 +0100
Subject: [PATCH 42/42] Update src/spikeinterface/extractors/cbin_ibl.py

Co-authored-by: Heberto Mayorquin <h.mayorquin@gmail.com>
---
 src/spikeinterface/extractors/cbin_ibl.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/extractors/cbin_ibl.py b/src/spikeinterface/extractors/cbin_ibl.py
index 8fe19f3d7e..728d352973 100644
--- a/src/spikeinterface/extractors/cbin_ibl.py
+++ b/src/spikeinterface/extractors/cbin_ibl.py
@@ -31,7 +31,7 @@ class CompressedBinaryIblExtractor(BaseRecording):
     stream_name : {"ap", "lp"}, default: "ap".
         Whether to load AP or LFP band, one
         of "ap" or "lp".
-    cbin_file_path : str or None, default None
+    cbin_file_path : str, Path or None, default None
         The cbin file of the recording. If None, searches in `folder_path` for file.
     cbin_file : str or None, default None
         (deprecated) The cbin file of the recording. If None, searches in `folder_path` for file.