From 0bf2b08248b836c6323524c1f54cf3690cd6c5f8 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 11:14:08 -0600
Subject: [PATCH 01/12] use strings as ids in generators

---
 src/spikeinterface/core/generate.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/core/generate.py b/src/spikeinterface/core/generate.py
index 0316b3bab1..d03c08b480 100644
--- a/src/spikeinterface/core/generate.py
+++ b/src/spikeinterface/core/generate.py
@@ -134,7 +134,7 @@ def generate_sorting(
     seed = _ensure_seed(seed)
     rng = np.random.default_rng(seed)
     num_segments = len(durations)
-    unit_ids = np.arange(num_units)
+    unit_ids = [str(id) for id in np.arange(num_units)]
 
     spikes = []
     for segment_index in range(num_segments):
@@ -1111,7 +1111,7 @@ def __init__(
 
         """
 
-        unit_ids = np.arange(num_units)
+        unit_ids = [str(id) for id in np.arange(num_units)]
         super().__init__(sampling_frequency, unit_ids)
 
         self.num_units = num_units
@@ -1280,7 +1280,7 @@ def __init__(
         noise_block_size: int = 30000,
     ):
 
-        channel_ids = np.arange(num_channels)
+        channel_ids = [str(id) for id in np.arange(num_channels)]
         dtype = np.dtype(dtype).name  # Cast to string for serialization
         if dtype not in ("float32", "float64"):
             raise ValueError(f"'dtype' must be 'float32' or 'float64' but is {dtype}")

From 212a974ea7fa17eacb91f37495c764dc2eb8f828 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 12:16:16 -0600
Subject: [PATCH 02/12] change to strings

---
 src/spikeinterface/core/basesorting.py        |  2 +-
 src/spikeinterface/core/generate.py           |  7 ++++--
 .../core/tests/test_basesnippets.py           | 10 ++++-----
 .../test_channelsaggregationrecording.py      |  6 +++--
 .../core/tests/test_sortinganalyzer.py        | 14 ++++++------
 .../core/tests/test_unitsselectionsorting.py  | 22 +++++++++++--------
 6 files changed, 35 insertions(+), 26 deletions(-)

diff --git a/src/spikeinterface/core/basesorting.py b/src/spikeinterface/core/basesorting.py
index 2af48407a3..9a0e242d62 100644
--- a/src/spikeinterface/core/basesorting.py
+++ b/src/spikeinterface/core/basesorting.py
@@ -135,7 +135,7 @@ def get_total_duration(self) -> float:
 
     def get_unit_spike_train(
         self,
-        unit_id,
+        unit_id: str | int,
         segment_index: Union[int, None] = None,
         start_frame: Union[int, None] = None,
         end_frame: Union[int, None] = None,
diff --git a/src/spikeinterface/core/generate.py b/src/spikeinterface/core/generate.py
index d03c08b480..5824a75ab8 100644
--- a/src/spikeinterface/core/generate.py
+++ b/src/spikeinterface/core/generate.py
@@ -2,7 +2,7 @@
 import math
 import warnings
 import numpy as np
-from typing import Literal
+from typing import Literal, Optional
 from math import ceil
 
 from .basesorting import SpikeVectorSortingSegment
@@ -1138,6 +1138,7 @@ def __init__(
                 firing_rates=firing_rates,
                 refractory_period_seconds=self.refractory_period_seconds,
                 seed=segment_seed,
+                unit_ids=unit_ids,
                 t_start=None,
             )
             self.add_sorting_segment(segment)
@@ -1161,6 +1162,7 @@ def __init__(
         firing_rates: float | np.ndarray,
         refractory_period_seconds: float | np.ndarray,
         seed: int,
+        unit_ids: list[str],
         t_start: Optional[float] = None,
     ):
         self.num_units = num_units
@@ -1177,7 +1179,8 @@ def __init__(
             self.refractory_period_seconds = np.full(num_units, self.refractory_period_seconds, dtype="float64")
 
         self.segment_seed = seed
-        self.units_seed = {unit_id: self.segment_seed + hash(unit_id) for unit_id in range(num_units)}
+        self.units_seed = {unit_id: abs(self.segment_seed + hash(unit_id)) for unit_id in unit_ids}
+
         self.num_samples = math.ceil(sampling_frequency * duration)
         super().__init__(t_start)
 
diff --git a/src/spikeinterface/core/tests/test_basesnippets.py b/src/spikeinterface/core/tests/test_basesnippets.py
index 64f7f76819..f243dd9d9f 100644
--- a/src/spikeinterface/core/tests/test_basesnippets.py
+++ b/src/spikeinterface/core/tests/test_basesnippets.py
@@ -41,8 +41,8 @@ def test_BaseSnippets(create_cache_folder):
     assert snippets.get_num_segments() == len(duration)
     assert snippets.get_num_channels() == num_channels
 
-    assert np.all(snippets.ids_to_indices([0, 1, 2]) == [0, 1, 2])
-    assert np.all(snippets.ids_to_indices([0, 1, 2], prefer_slice=True) == slice(0, 3, None))
+    assert np.all(snippets.ids_to_indices(["0", "1", "2"]) == [0, 1, 2])
+    assert np.all(snippets.ids_to_indices(["0", "1", "2"], prefer_slice=True) == slice(0, 3, None))
 
     # annotations / properties
     snippets.annotate(gre="ta")
@@ -60,7 +60,7 @@ def test_BaseSnippets(create_cache_folder):
     )
 
     # missing property
-    snippets.set_property("string_property", ["ciao", "bello"], ids=[0, 1])
+    snippets.set_property("string_property", ["ciao", "bello"], ids=["0", "1"])
     values = snippets.get_property("string_property")
     assert values[2] == ""
 
@@ -70,14 +70,14 @@ def test_BaseSnippets(create_cache_folder):
         snippets.set_property,
         key="string_property_nan",
         values=["hola", "chabon"],
-        ids=[0, 1],
+        ids=["0", "1"],
         missing_value=np.nan,
     )
 
     # int properties without missing values raise an error
     assert_raises(Exception, snippets.set_property, key="int_property", values=[5, 6], ids=[1, 2])
 
-    snippets.set_property("int_property", [5, 6], ids=[1, 2], missing_value=200)
+    snippets.set_property("int_property", [5, 6], ids=["1", "2"], missing_value=200)
     values = snippets.get_property("int_property")
     assert values.dtype.kind == "i"
 
diff --git a/src/spikeinterface/core/tests/test_channelsaggregationrecording.py b/src/spikeinterface/core/tests/test_channelsaggregationrecording.py
index 118b6092a9..99d6890dfd 100644
--- a/src/spikeinterface/core/tests/test_channelsaggregationrecording.py
+++ b/src/spikeinterface/core/tests/test_channelsaggregationrecording.py
@@ -38,10 +38,12 @@ def test_channelsaggregationrecording():
 
         assert np.allclose(traces1_1, recording_agg.get_traces(channel_ids=[str(channel_ids[1])], segment_index=seg))
         assert np.allclose(
-            traces2_0, recording_agg.get_traces(channel_ids=[str(num_channels + channel_ids[0])], segment_index=seg)
+            traces2_0,
+            recording_agg.get_traces(channel_ids=[str(num_channels + int(channel_ids[0]))], segment_index=seg),
         )
         assert np.allclose(
-            traces3_2, recording_agg.get_traces(channel_ids=[str(2 * num_channels + channel_ids[2])], segment_index=seg)
+            traces3_2,
+            recording_agg.get_traces(channel_ids=[str(2 * num_channels + int(channel_ids[2]))], segment_index=seg),
         )
         # all traces
         traces1 = recording1.get_traces(segment_index=seg)
diff --git a/src/spikeinterface/core/tests/test_sortinganalyzer.py b/src/spikeinterface/core/tests/test_sortinganalyzer.py
index 35ab18b5f2..899993d840 100644
--- a/src/spikeinterface/core/tests/test_sortinganalyzer.py
+++ b/src/spikeinterface/core/tests/test_sortinganalyzer.py
@@ -76,8 +76,8 @@ def test_SortingAnalyzer_binary_folder(tmp_path, dataset):
 
     # test select_units see https://github.com/SpikeInterface/spikeinterface/issues/3041
     # this bug requires that we have an info.json file so we calculate templates above
-    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=[1])
-    assert len(select_units_sorting_analyer.unit_ids) == 1
+    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=["1"])
+    assert len(select_units_sorting_analyer.unit_ids) == "1"
 
     folder = tmp_path / "test_SortingAnalyzer_binary_folder"
     if folder.exists():
@@ -121,11 +121,11 @@ def test_SortingAnalyzer_zarr(tmp_path, dataset):
 
     # test select_units see https://github.com/SpikeInterface/spikeinterface/issues/3041
     # this bug requires that we have an info.json file so we calculate templates above
-    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=[1])
-    assert len(select_units_sorting_analyer.unit_ids) == 1
-    remove_units_sorting_analyer = sorting_analyzer.remove_units(remove_unit_ids=[1])
+    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=["1"])
+    assert len(select_units_sorting_analyer.unit_ids) == "1"
+    remove_units_sorting_analyer = sorting_analyzer.remove_units(remove_unit_ids=["1"])
     assert len(remove_units_sorting_analyer.unit_ids) == len(sorting_analyzer.unit_ids) - 1
-    assert 1 not in remove_units_sorting_analyer.unit_ids
+    assert "1" not in remove_units_sorting_analyer.unit_ids
 
     # test no compression
     sorting_analyzer_no_compression = create_sorting_analyzer(
@@ -358,7 +358,7 @@ def _check_sorting_analyzers(sorting_analyzer, original_sorting, cache_folder):
                 shutil.rmtree(folder)
         else:
             folder = None
-        sorting_analyzer4 = sorting_analyzer.merge_units(merge_unit_groups=[[0, 1]], format=format, folder=folder)
+        sorting_analyzer4 = sorting_analyzer.merge_units(merge_unit_groups=[["0", "1"]], format=format, folder=folder)
 
         if format != "memory":
             if format == "zarr":
diff --git a/src/spikeinterface/core/tests/test_unitsselectionsorting.py b/src/spikeinterface/core/tests/test_unitsselectionsorting.py
index 1e72b0ab28..3ecb702aa2 100644
--- a/src/spikeinterface/core/tests/test_unitsselectionsorting.py
+++ b/src/spikeinterface/core/tests/test_unitsselectionsorting.py
@@ -10,25 +10,29 @@
 def test_basic_functions():
     sorting = generate_sorting(num_units=3, durations=[0.100, 0.100], sampling_frequency=30000.0)
 
-    sorting2 = UnitsSelectionSorting(sorting, unit_ids=[0, 2])
-    assert np.array_equal(sorting2.unit_ids, [0, 2])
+    sorting2 = UnitsSelectionSorting(sorting, unit_ids=["0", "2"])
+    assert np.array_equal(sorting2.unit_ids, ["0", "2"])
     assert sorting2.get_parent() == sorting
 
-    sorting3 = UnitsSelectionSorting(sorting, unit_ids=[0, 2], renamed_unit_ids=["a", "b"])
+    sorting3 = UnitsSelectionSorting(sorting, unit_ids=["0", "2"], renamed_unit_ids=["a", "b"])
     assert np.array_equal(sorting3.unit_ids, ["a", "b"])
 
     assert np.array_equal(
-        sorting.get_unit_spike_train(0, segment_index=0), sorting2.get_unit_spike_train(0, segment_index=0)
+        sorting.get_unit_spike_train(unit_id="0", segment_index=0),
+        sorting2.get_unit_spike_train(unit_id="0", segment_index=0),
     )
     assert np.array_equal(
-        sorting.get_unit_spike_train(0, segment_index=0), sorting3.get_unit_spike_train("a", segment_index=0)
+        sorting.get_unit_spike_train(unit_id="0", segment_index=0),
+        sorting3.get_unit_spike_train(unit_id="a", segment_index=0),
     )
 
     assert np.array_equal(
-        sorting.get_unit_spike_train(2, segment_index=0), sorting2.get_unit_spike_train(2, segment_index=0)
+        sorting.get_unit_spike_train(unit_id="2", segment_index=0),
+        sorting2.get_unit_spike_train(unit_id="2", segment_index=0),
     )
     assert np.array_equal(
-        sorting.get_unit_spike_train(2, segment_index=0), sorting3.get_unit_spike_train("b", segment_index=0)
+        sorting.get_unit_spike_train(unit_id="2", segment_index=0),
+        sorting3.get_unit_spike_train(unit_id="b", segment_index=0),
     )
 
 
@@ -36,13 +40,13 @@ def test_failure_with_non_unique_unit_ids():
     seed = 10
     sorting = generate_sorting(num_units=3, durations=[0.100], sampling_frequency=30000.0, seed=seed)
     with pytest.raises(AssertionError):
-        sorting2 = UnitsSelectionSorting(sorting, unit_ids=[0, 2], renamed_unit_ids=["a", "a"])
+        sorting2 = UnitsSelectionSorting(sorting, unit_ids=["0", "2"], renamed_unit_ids=["a", "a"])
 
 
 def test_custom_cache_spike_vector():
     sorting = generate_sorting(num_units=3, durations=[0.100, 0.100], sampling_frequency=30000.0)
 
-    sub_sorting = UnitsSelectionSorting(sorting, unit_ids=[2, 0], renamed_unit_ids=["b", "a"])
+    sub_sorting = UnitsSelectionSorting(sorting, unit_ids=["2", "0"], renamed_unit_ids=["b", "a"])
     cached_spike_vector = sub_sorting.to_spike_vector(use_cache=True)
     computed_spike_vector = sub_sorting.to_spike_vector(use_cache=False)
     assert np.all(cached_spike_vector == computed_spike_vector)

From c36e49e6c5057496cd59ab74f23c805732bf708c Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 12:24:41 -0600
Subject: [PATCH 03/12] keep sorting analyzer tests as they were

---
 src/spikeinterface/core/tests/test_sortinganalyzer.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/spikeinterface/core/tests/test_sortinganalyzer.py b/src/spikeinterface/core/tests/test_sortinganalyzer.py
index 899993d840..8d8beaa491 100644
--- a/src/spikeinterface/core/tests/test_sortinganalyzer.py
+++ b/src/spikeinterface/core/tests/test_sortinganalyzer.py
@@ -31,6 +31,14 @@ def get_dataset():
         noise_kwargs=dict(noise_levels=5.0, strategy="tile_pregenerated"),
         seed=2205,
     )
+
+    # TODO: the tests or the sorting analyzer make assumptions about the ids being integers
+    # So keeping this the way it was
+    integer_channel_ids = [int(id) for id in recording.get_channel_ids()]
+    integer_unit_ids = [int(id) for id in sorting.get_unit_ids()]
+
+    recording = recording.rename_channels(new_channel_ids=integer_channel_ids)
+    sorting = sorting.rename_units(new_unit_ids=integer_unit_ids)
     return recording, sorting
 
 
@@ -358,7 +366,7 @@ def _check_sorting_analyzers(sorting_analyzer, original_sorting, cache_folder):
                 shutil.rmtree(folder)
         else:
             folder = None
-        sorting_analyzer4 = sorting_analyzer.merge_units(merge_unit_groups=[["0", "1"]], format=format, folder=folder)
+        sorting_analyzer4 = sorting_analyzer.merge_units(merge_unit_groups=[[0, 1]], format=format, folder=folder)
 
         if format != "memory":
             if format == "zarr":

From 3dd6b359daa86252878e480dddbe9dc719e98c2b Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 12:27:04 -0600
Subject: [PATCH 04/12] fully restore sorting anlayzer

---
 .../core/tests/test_sortinganalyzer.py               | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/spikeinterface/core/tests/test_sortinganalyzer.py b/src/spikeinterface/core/tests/test_sortinganalyzer.py
index 8d8beaa491..15f089f784 100644
--- a/src/spikeinterface/core/tests/test_sortinganalyzer.py
+++ b/src/spikeinterface/core/tests/test_sortinganalyzer.py
@@ -84,8 +84,8 @@ def test_SortingAnalyzer_binary_folder(tmp_path, dataset):
 
     # test select_units see https://github.com/SpikeInterface/spikeinterface/issues/3041
     # this bug requires that we have an info.json file so we calculate templates above
-    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=["1"])
-    assert len(select_units_sorting_analyer.unit_ids) == "1"
+    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=[1])
+    assert len(select_units_sorting_analyer.unit_ids) == 1
 
     folder = tmp_path / "test_SortingAnalyzer_binary_folder"
     if folder.exists():
@@ -129,11 +129,11 @@ def test_SortingAnalyzer_zarr(tmp_path, dataset):
 
     # test select_units see https://github.com/SpikeInterface/spikeinterface/issues/3041
     # this bug requires that we have an info.json file so we calculate templates above
-    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=["1"])
-    assert len(select_units_sorting_analyer.unit_ids) == "1"
-    remove_units_sorting_analyer = sorting_analyzer.remove_units(remove_unit_ids=["1"])
+    select_units_sorting_analyer = sorting_analyzer.select_units(unit_ids=[1])
+    assert len(select_units_sorting_analyer.unit_ids) == 1
+    remove_units_sorting_analyer = sorting_analyzer.remove_units(remove_unit_ids=[1])
     assert len(remove_units_sorting_analyer.unit_ids) == len(sorting_analyzer.unit_ids) - 1
-    assert "1" not in remove_units_sorting_analyer.unit_ids
+    assert 1 not in remove_units_sorting_analyer.unit_ids
 
     # test no compression
     sorting_analyzer_no_compression = create_sorting_analyzer(

From 61f40187cb372f64a2752136c6df461bbad89705 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 12:41:22 -0600
Subject: [PATCH 05/12] fix mda extractor

---
 src/spikeinterface/extractors/tests/test_mdaextractors.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/spikeinterface/extractors/tests/test_mdaextractors.py b/src/spikeinterface/extractors/tests/test_mdaextractors.py
index 0ef6697c6c..78e6afb65e 100644
--- a/src/spikeinterface/extractors/tests/test_mdaextractors.py
+++ b/src/spikeinterface/extractors/tests/test_mdaextractors.py
@@ -9,6 +9,12 @@ def test_mda_extractors(create_cache_folder):
     cache_folder = create_cache_folder
     rec, sort = generate_ground_truth_recording(durations=[10.0], num_units=10)
 
+    ids_as_integers = [id for id in range(rec.get_num_channels())]
+    rec = rec.rename_channels(new_channel_ids=ids_as_integers)
+
+    ids_as_integers = [id for id in range(sort.get_num_units())]
+    sort = sort.rename_units(new_unit_ids=ids_as_integers)
+
     MdaRecordingExtractor.write_recording(rec, cache_folder / "mdatest")
     rec_mda = MdaRecordingExtractor(cache_folder / "mdatest")
     probe = rec_mda.get_probe()

From 0429152bfa7141b4c1428fc960833d9141da2168 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 13:11:51 -0600
Subject: [PATCH 06/12] fix preprocessing

---
 src/spikeinterface/preprocessing/tests/test_clip.py       | 8 ++++----
 .../preprocessing/tests/test_interpolate_bad_channels.py  | 4 +++-
 .../preprocessing/tests/test_normalize_scale.py           | 2 +-
 src/spikeinterface/preprocessing/tests/test_rectify.py    | 2 +-
 4 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/spikeinterface/preprocessing/tests/test_clip.py b/src/spikeinterface/preprocessing/tests/test_clip.py
index 724ba2c963..c18c7d37af 100644
--- a/src/spikeinterface/preprocessing/tests/test_clip.py
+++ b/src/spikeinterface/preprocessing/tests/test_clip.py
@@ -14,12 +14,12 @@ def test_clip():
     rec1 = clip(rec, a_min=-1.5)
     rec1.save(verbose=False)
 
-    traces0 = rec0.get_traces(segment_index=0, channel_ids=[1])
+    traces0 = rec0.get_traces(segment_index=0, channel_ids=["1"])
     assert traces0.shape[1] == 1
 
     assert np.all(-2 <= traces0[0] <= 3)
 
-    traces1 = rec1.get_traces(segment_index=0, channel_ids=[0, 1])
+    traces1 = rec1.get_traces(segment_index=0, channel_ids=["0", "1"])
     assert traces1.shape[1] == 2
 
     assert np.all(-1.5 <= traces1[1])
@@ -34,11 +34,11 @@ def test_blank_staturation():
     rec1 = blank_staturation(rec, quantile_threshold=0.01, direction="both", chunk_size=10000)
     rec1.save(verbose=False)
 
-    traces0 = rec0.get_traces(segment_index=0, channel_ids=[1])
+    traces0 = rec0.get_traces(segment_index=0, channel_ids=["1"])
     assert traces0.shape[1] == 1
     assert np.all(traces0 < 3.0)
 
-    traces1 = rec1.get_traces(segment_index=0, channel_ids=[0])
+    traces1 = rec1.get_traces(segment_index=0, channel_ids=["0"])
     assert traces1.shape[1] == 1
     # use a smaller value to be sure
     a_min = rec1._recording_segments[0].a_min
diff --git a/src/spikeinterface/preprocessing/tests/test_interpolate_bad_channels.py b/src/spikeinterface/preprocessing/tests/test_interpolate_bad_channels.py
index 1189f04f7d..06bde4e3d1 100644
--- a/src/spikeinterface/preprocessing/tests/test_interpolate_bad_channels.py
+++ b/src/spikeinterface/preprocessing/tests/test_interpolate_bad_channels.py
@@ -163,7 +163,9 @@ def test_output_values():
     expected_weights = np.r_[np.tile(np.exp(-2), 3), np.exp(-4)]
     expected_weights /= np.sum(expected_weights)
 
-    si_interpolated_recording = spre.interpolate_bad_channels(recording, bad_channel_indexes, sigma_um=1, p=1)
+    si_interpolated_recording = spre.interpolate_bad_channels(
+        recording, bad_channel_ids=bad_channel_ids, sigma_um=1, p=1
+    )
     si_interpolated = si_interpolated_recording.get_traces()
 
     expected_ts = si_interpolated[:, 1:] @ expected_weights
diff --git a/src/spikeinterface/preprocessing/tests/test_normalize_scale.py b/src/spikeinterface/preprocessing/tests/test_normalize_scale.py
index 576b570832..151752e0e6 100644
--- a/src/spikeinterface/preprocessing/tests/test_normalize_scale.py
+++ b/src/spikeinterface/preprocessing/tests/test_normalize_scale.py
@@ -15,7 +15,7 @@ def test_normalize_by_quantile():
     rec2 = normalize_by_quantile(rec, mode="by_channel")
     rec2.save(verbose=False)
 
-    traces = rec2.get_traces(segment_index=0, channel_ids=[1])
+    traces = rec2.get_traces(segment_index=0, channel_ids=["1"])
     assert traces.shape[1] == 1
 
     rec2 = normalize_by_quantile(rec, mode="pool_channel")
diff --git a/src/spikeinterface/preprocessing/tests/test_rectify.py b/src/spikeinterface/preprocessing/tests/test_rectify.py
index b8bb31015e..a2a06e7a1f 100644
--- a/src/spikeinterface/preprocessing/tests/test_rectify.py
+++ b/src/spikeinterface/preprocessing/tests/test_rectify.py
@@ -15,7 +15,7 @@ def test_rectify():
     rec2 = rectify(rec)
     rec2.save(verbose=False)
 
-    traces = rec2.get_traces(segment_index=0, channel_ids=[1])
+    traces = rec2.get_traces(segment_index=0, channel_ids=["1"])
     assert traces.shape[1] == 1
 
     # import matplotlib.pyplot as plt

From 6d70a154426a2391e6712fb38b27dcf0fbd95a05 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 13:18:20 -0600
Subject: [PATCH 07/12] fix quality metrics

---
 src/spikeinterface/qualitymetrics/tests/conftest.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/spikeinterface/qualitymetrics/tests/conftest.py b/src/spikeinterface/qualitymetrics/tests/conftest.py
index 01fa16c8d7..ac1789a375 100644
--- a/src/spikeinterface/qualitymetrics/tests/conftest.py
+++ b/src/spikeinterface/qualitymetrics/tests/conftest.py
@@ -16,6 +16,11 @@ def small_sorting_analyzer():
         seed=1205,
     )
 
+    channel_ids_as_integers = [id for id in range(recording.get_num_channels())]
+    unit_ids_as_integers = [id for id in range(sorting.get_num_units())]
+    recording = recording.rename_channels(new_channel_ids=channel_ids_as_integers)
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_integers)
+
     sorting = sorting.select_units([2, 7, 0], ["#3", "#9", "#4"])
 
     sorting_analyzer = create_sorting_analyzer(recording=recording, sorting=sorting, format="memory")
@@ -60,6 +65,11 @@ def sorting_analyzer_simple():
         seed=1205,
     )
 
+    channel_ids_as_integers = [id for id in range(recording.get_num_channels())]
+    unit_ids_as_integers = [id for id in range(sorting.get_num_units())]
+    recording = recording.rename_channels(new_channel_ids=channel_ids_as_integers)
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_integers)
+
     sorting_analyzer = create_sorting_analyzer(sorting, recording, format="memory", sparse=True)
 
     sorting_analyzer.compute("random_spikes", max_spikes_per_unit=300, seed=1205)

From d94ccf1e56bf1c8cd0d89b71bbba42817c59106f Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 13:45:55 -0600
Subject: [PATCH 08/12] fix post processing

---
 .../postprocessing/tests/test_multi_extensions.py            | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/spikeinterface/postprocessing/tests/test_multi_extensions.py b/src/spikeinterface/postprocessing/tests/test_multi_extensions.py
index bf0000135c..be0070d94a 100644
--- a/src/spikeinterface/postprocessing/tests/test_multi_extensions.py
+++ b/src/spikeinterface/postprocessing/tests/test_multi_extensions.py
@@ -23,6 +23,11 @@ def get_dataset():
         seed=2205,
     )
 
+    channel_ids_as_integers = [id for id in range(recording.get_num_channels())]
+    unit_ids_as_integers = [id for id in range(sorting.get_num_units())]
+    recording = recording.rename_channels(new_channel_ids=channel_ids_as_integers)
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_integers)
+
     # since templates are going to be averaged and this might be a problem for amplitude scaling
     # we select the 3 units with the largest templates to split
     analyzer_raw = create_sorting_analyzer(sorting, recording, format="memory", sparse=False)

From 7f461db713a377725ea51888859930401d224a98 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 13:48:07 -0600
Subject: [PATCH 09/12] fix motion

---
 src/spikeinterface/sortingcomponents/tests/common.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/spikeinterface/sortingcomponents/tests/common.py b/src/spikeinterface/sortingcomponents/tests/common.py
index 01e4445a13..d5e5b6be1b 100644
--- a/src/spikeinterface/sortingcomponents/tests/common.py
+++ b/src/spikeinterface/sortingcomponents/tests/common.py
@@ -21,4 +21,10 @@ def make_dataset():
         noise_kwargs=dict(noise_levels=5.0, strategy="on_the_fly"),
         seed=2205,
     )
+
+    channel_ids_as_integers = [id for id in range(recording.get_num_channels())]
+    unit_ids_as_integers = [id for id in range(sorting.get_num_units())]
+    recording = recording.rename_channels(new_channel_ids=channel_ids_as_integers)
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_integers)
+
     return recording, sorting

From 33359cc1f1646545d7beb2a16bad8528e019d428 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Tue, 17 Dec 2024 14:21:07 -0600
Subject: [PATCH 10/12] fix curation

---
 src/spikeinterface/curation/tests/common.py              | 5 +++++
 .../curation/tests/test_sortingview_curation.py          | 9 +++++++++
 2 files changed, 14 insertions(+)

diff --git a/src/spikeinterface/curation/tests/common.py b/src/spikeinterface/curation/tests/common.py
index 9cd20f4bfc..e9c4c4a463 100644
--- a/src/spikeinterface/curation/tests/common.py
+++ b/src/spikeinterface/curation/tests/common.py
@@ -19,6 +19,11 @@ def make_sorting_analyzer(sparse=True):
         seed=2205,
     )
 
+    channel_ids_as_integers = [id for id in range(recording.get_num_channels())]
+    unit_ids_as_integers = [id for id in range(sorting.get_num_units())]
+    recording = recording.rename_channels(new_channel_ids=channel_ids_as_integers)
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_integers)
+
     sorting_analyzer = create_sorting_analyzer(sorting=sorting, recording=recording, format="memory", sparse=sparse)
     sorting_analyzer.compute("random_spikes")
     sorting_analyzer.compute("waveforms", **job_kwargs)
diff --git a/src/spikeinterface/curation/tests/test_sortingview_curation.py b/src/spikeinterface/curation/tests/test_sortingview_curation.py
index 945aca7937..ff80be365d 100644
--- a/src/spikeinterface/curation/tests/test_sortingview_curation.py
+++ b/src/spikeinterface/curation/tests/test_sortingview_curation.py
@@ -49,6 +49,9 @@ def test_gh_curation():
     Test curation using GitHub URI.
     """
     sorting = generate_sorting(num_units=10)
+    unit_ids_as_int = [id for id in range(sorting.get_num_units())]
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_int)
+
     # curated link:
     # https://figurl.org/f?v=npm://@fi-sci/figurl-sortingview@12/dist&d=sha1://058ab901610aa9d29df565595a3cc2a81a1b08e5
     gh_uri = "gh://SpikeInterface/spikeinterface/main/src/spikeinterface/curation/tests/sv-sorting-curation.json"
@@ -76,6 +79,8 @@ def test_sha1_curation():
     Test curation using SHA1 URI.
     """
     sorting = generate_sorting(num_units=10)
+    unit_ids_as_int = [id for id in range(sorting.get_num_units())]
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_int)
 
     # from SHA1
     # curated link:
@@ -105,6 +110,8 @@ def test_json_curation():
     Test curation using a JSON file.
     """
     sorting = generate_sorting(num_units=10)
+    unit_ids_as_int = [id for id in range(sorting.get_num_units())]
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_int)
 
     # from curation.json
     json_file = parent_folder / "sv-sorting-curation.json"
@@ -248,6 +255,8 @@ def test_json_no_merge_curation():
     Test curation with no merges using a JSON file.
     """
     sorting = generate_sorting(num_units=10)
+    unit_ids_as_int = [id for id in range(sorting.get_num_units())]
+    sorting = sorting.rename_units(new_unit_ids=unit_ids_as_int)
 
     json_file = parent_folder / "sv-sorting-curation-no-merge.json"
     sorting_curated = apply_sortingview_curation(sorting, uri_or_json=json_file)

From bb48b63a05e6e933bce31e380f97f83cfb3cddb9 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Thu, 19 Dec 2024 11:03:57 -0600
Subject: [PATCH 11/12] Update src/spikeinterface/core/generate.py

Co-authored-by: Alessio Buccino <alejoe9187@gmail.com>
---
 src/spikeinterface/core/generate.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/core/generate.py b/src/spikeinterface/core/generate.py
index 5824a75ab8..118ce384f3 100644
--- a/src/spikeinterface/core/generate.py
+++ b/src/spikeinterface/core/generate.py
@@ -1111,7 +1111,7 @@ def __init__(
 
         """
 
-        unit_ids = [str(id) for id in np.arange(num_units)]
+        unit_ids = [str(idx) for idx in np.arange(num_units)]
         super().__init__(sampling_frequency, unit_ids)
 
         self.num_units = num_units

From 2f26983798026145f9455cacb5e312f11efc4bf3 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Thu, 19 Dec 2024 11:04:03 -0600
Subject: [PATCH 12/12] Update src/spikeinterface/core/generate.py

Co-authored-by: Alessio Buccino <alejoe9187@gmail.com>
---
 src/spikeinterface/core/generate.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/core/generate.py b/src/spikeinterface/core/generate.py
index 118ce384f3..fb10f26a2e 100644
--- a/src/spikeinterface/core/generate.py
+++ b/src/spikeinterface/core/generate.py
@@ -134,7 +134,7 @@ def generate_sorting(
     seed = _ensure_seed(seed)
     rng = np.random.default_rng(seed)
     num_segments = len(durations)
-    unit_ids = [str(id) for id in np.arange(num_units)]
+    unit_ids = [str(idx) for idx in np.arange(num_units)]
 
     spikes = []
     for segment_index in range(num_segments):