more warnings

docs/conversion_examples_gallery/sorting/blackrock.rst

@@ -19,7 +19,7 @@ Convert Blackrock sorting data to NWB using
     >>>
     >>> file_path = f"{ECEPHY_DATA_PATH}/blackrock/FileSpec2.3001.nev"
     >>> # Change the file_path to the location of the file in your system
-    >>> interface = BlackrockSortingInterface(file_path=file_path, verbose=False)
+    >>> interface = BlackrockSortingInterface(file_path=file_path, sampling_frequency=30000.0, verbose=False)
     >>>
     >>> # Extract what metadata we can from the source files
     >>> metadata = interface.get_metadata()

docs/conversion_examples_gallery/sorting/neuralynx.rst

@@ -20,7 +20,8 @@ Convert Neuralynx data to NWB using
     >>>
     >>> folder_path = f"{ECEPHY_DATA_PATH}/neuralynx/Cheetah_v5.5.1/original_data"
     >>> # Change the folder_path to the location of the data in your system
-    >>> interface = NeuralynxSortingInterface(folder_path=folder_path, verbose=False)
+    >>> # The stream is optional but is used to specify the sampling frequency of the data
+    >>> interface = NeuralynxSortingInterface(folder_path=folder_path, verbose=False, stream_id="0")
     >>>
     >>> metadata = interface.get_metadata()
     >>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=ZoneInfo("US/Pacific")).isoformat()

src/neuroconv/tools/testing/data_interface_mixins.py

@@ -639,7 +639,7 @@ def check_read_nwb(self, nwbfile_path: str):
                 else:
                     renamed_unit_ids = np.arange(len(sorting.unit_ids))
 
-                sorting_renamed = sorting.rename_units(new_unit_ids=sorting.unit_ids)
+                sorting_renamed = sorting.rename_units(new_unit_ids=renamed_unit_ids)
             check_sortings_equal(SX1=sorting_renamed, SX2=nwb_sorting)
 
     def check_interface_set_aligned_segment_timestamps(self):

tests/test_minimal/test_tools/test_backend_and_dataset_configuration/test_helpers/test_get_default_dataset_io_configurations_appended_files.py

@@ -31,7 +31,7 @@ def generate_nwbfile_with_existing_time_series() -> NWBFile:
 
 @pytest.fixture(scope="session")
 def hdf5_nwbfile_path(tmpdir_factory):
-    nwbfile_path = tmpdir_factory.mktemp("data").join("test_default_dataset_configurations_hdf5_nwbfile_.nwb.h5")
+    nwbfile_path = tmpdir_factory.mktemp("data").join("test_default_dataset_configurations_hdf5_nwbfile_.nwb")
     if not Path(nwbfile_path).exists():
         nwbfile = generate_nwbfile_with_existing_time_series()
         with NWBHDF5IO(path=str(nwbfile_path), mode="w") as io:

tests/test_on_data/ecephys/test_raw_recordings.py

@@ -97,9 +97,7 @@ class TestConverter(NWBConverter):
                 renamed_channel_ids = recording.get_property("channel_name")
             else:
                 renamed_channel_ids = recording.get_channel_ids().astype("str")
-            recording = recording.channel_slice(
-                channel_ids=recording.get_channel_ids(), renamed_channel_ids=renamed_channel_ids
-            )
+            recording = recording.rename_channels(new_channel_ids=renamed_channel_ids)
 
             # Edge case that only occurs in testing, but should eventually be fixed nonetheless
             # The NwbRecordingExtractor on spikeinterface experiences an issue when duplicated channel_ids

tests/test_on_data/ecephys/test_spikeglx_converter.py

@@ -212,15 +212,15 @@ def test_electrode_table_writing(tmp_path):
     # Test round trip with spikeinterface
     recording_extractor_ap = NwbRecordingExtractor(
         file_path=nwbfile_path,
-        electrical_series_name="ElectricalSeriesAP",
+        electrical_series_path="acquisition/ElectricalSeriesAP",
     )
 
     channel_ids = recording_extractor_ap.get_channel_ids()
     np.testing.assert_array_equal(channel_ids, expected_channel_names_ap)
 
     recording_extractor_lf = NwbRecordingExtractor(
         file_path=nwbfile_path,
-        electrical_series_name="ElectricalSeriesLF",
+        electrical_series_path="acquisition/ElectricalSeriesLF",
     )
 
     channel_ids = recording_extractor_lf.get_channel_ids()

tests/test_on_data/ecephys/test_spikeglx_metadata.py

@@ -1,7 +1,6 @@
 import datetime
 
 import probeinterface as pi
-import pytest
 from numpy.testing import assert_array_equal
 from spikeinterface.extractors import SpikeGLXRecordingExtractor
 
@@ -38,7 +37,8 @@ def test_spikelgx_recording_property_addition():
     expected_contact_ids = probe.contact_ids
 
     # Initialize the interface and get the added properties
-    interface = SpikeGLXRecordingInterface(file_path=ap_file_path)
+    folder_path = ap_file_path.parent
+    interface = SpikeGLXRecordingInterface(folder_path=folder_path, stream_id="imec0.ap")
     group_name = interface.recording_extractor.get_property("group_name")
     contact_shapes = interface.recording_extractor.get_property("contact_shapes")
     shank_ids = interface.recording_extractor.get_property("shank_ids")
@@ -48,21 +48,3 @@ def test_spikelgx_recording_property_addition():
     assert_array_equal(contact_shapes, expected_contact_shapes)
     assert_array_equal(shank_ids, expected_shank_ids)
     assert_array_equal(contact_ids, expected_contact_ids)
-
-
-@pytest.mark.skip(reason="Legacy spikeextractors cannot read new GIN file.")
-def test_matching_recording_property_addition_between_backends():
-    """Test that the extracted properties match with both backends"""
-    folder_path = SPIKEGLX_PATH / "Noise4Sam_g0" / "Noise4Sam_g0_imec0"
-    ap_file_path = folder_path / "Noise4Sam_g0_t0.imec0.ap.bin"
-
-    interface_new = SpikeGLXRecordingInterface(file_path=ap_file_path)
-    shank_electrode_number_new = interface_new.recording_extractor.get_property("shank_electrode_number")
-    group_name_new = interface_new.recording_extractor.get_property("group_name")
-
-    interface_old = SpikeGLXRecordingInterface(file_path=ap_file_path, spikeextractors_backend=True)
-    shank_electrode_number_old = interface_old.recording_extractor.get_property("shank_electrode_number")
-    group_name_old = interface_old.recording_extractor.get_property("group_name")
-
-    assert_array_equal(shank_electrode_number_new, shank_electrode_number_old)
-    assert_array_equal(group_name_new, group_name_old)