Merge branch 'main' into main

Author: jakeswann1

.github/scripts/determine_testing_environment.py

@@ -48,7 +48,7 @@
     elif changed_file.name == "nwbextractors.py":
         extractors_changed = True  # There are NWB tests that are not streaming
         stream_extractors_changed = True
-    elif changed_file.name == "iblextractors.py":
+    elif changed_file.name == "iblextractors.py" or changed_file.name == "test_iblextractors.py":
         stream_extractors_changed = True
     elif "core" in changed_file.parts:
         core_changed = True

doc/api.rst

@@ -143,7 +143,9 @@ Non-NEO-based
     .. autofunction:: read_mcsh5
     .. autofunction:: read_mda_recording
     .. autofunction:: read_mda_sorting
-    .. autofunction:: read_nwb
+    .. autofunction:: read_nwb_sorting
+    .. autofunction:: read_nwb_recording
+    .. autofunction:: read_nwb_timeseries
     .. autofunction:: read_phy
     .. autofunction:: read_shybrid_recording
     .. autofunction:: read_shybrid_sorting

pyproject.toml

@@ -67,15 +67,13 @@ extractors = [
     "sonpy;python_version<'3.10'",
     "lxml", # lxml for neuroscope
     "scipy",
-    "ONE-api>=2.7.0,<3.0.0", # alf sorter and streaming IBL
-    "ibllib>=2.36.0,<3.0.0", # streaming IBL
+    "ibllib", # streaming IBL
     "pymatreader>=0.0.32", # For cell explorer matlab files
     "zugbruecke>=0.2; sys_platform!='win32'", # For plexon2
 ]
 
 streaming_extractors = [
-    "ONE-api>=2.7.0,<3.0.0", # alf sorter and streaming IBL
-    "ibllib>=2.36.0,<3.0.0", # streaming IBL
+    "ibllib", # streaming IBL
     # Following dependencies are for streaming with nwb files
     "pynwb>=2.6.0",
     "fsspec",
@@ -140,7 +138,7 @@ test_extractors = [
 ]
 
 test_preprocessing = [
-    # "ibllib>=2.36.0", # for IBL
+    "ibllib", # for IBL
     "torch",
 ]
 
@@ -154,7 +152,7 @@ test = [
     "huggingface_hub",
 
     # preprocessing
-    "ibllib>=2.36.0", # for IBL
+    "ibllib", # for IBL
 
     # streaming templates
     "s3fs",

src/spikeinterface/core/base.py

@@ -47,6 +47,9 @@ class BaseExtractor:
     # these properties are skipped by default in copy_metadata
     _skip_properties = []
 
+    # kwargs which can be precomputed before being used by the extractor
+    _precomputable_kwarg_names = []
+
     installation_mesg = ""
     installed = True
 

src/spikeinterface/core/numpyextractors.py

@@ -367,12 +367,20 @@ def from_times_and_labels(times_list, labels_list, sampling_frequency, unit_ids=
 
     @staticmethod
     def from_times_labels(times_list, labels_list, sampling_frequency, unit_ids=None) -> "NumpySorting":
+        warning_msg = (
+            "`from_times_labels` is deprecated and will be removed in 0.104.0. Note this function requires"
+            "samples rather than times so should not be used for clarity purposes. For those working in samples please"
+            "use `from_samples_and_labels` instead. For those working in time units (seconds) please use "
+            "`from_times_and_labels` instead."
+        )
+
         warnings.warn(
-            "from_times_labels is deprecated and will be removed in 0.104.0, use from_sample_and_labels instead",
+            warning_msg,
             DeprecationWarning,
             stacklevel=2,
         )
-        return NumpySorting.from_times_and_labels(times_list, labels_list, sampling_frequency, unit_ids)
+        # despite the naming of the original function this required samples
+        return NumpySorting.from_samples_and_labels(times_list, labels_list, sampling_frequency, unit_ids)
 
     @staticmethod
     def from_unit_dict(units_dict_list, sampling_frequency) -> "NumpySorting":

src/spikeinterface/extractors/tests/test_iblextractors.py

@@ -1,3 +1,4 @@
+import sys
 from re import escape
 from unittest import TestCase
 
@@ -10,9 +11,11 @@
 EID = "e2b845a1-e313-4a08-bc61-a5f662ed295e"
 PID = "80f6ffdd-f692-450f-ab19-cd6d45bfd73e"
 
+if sys.version_info < (3, 10):
+    pytest.skip("IBL support requires Python 3.10 or higher", allow_module_level=True)
+
 
 @pytest.mark.streaming_extractors
-@pytest.mark.xfail(reason="We need to fix ibllib/one-api dependency")
 class TestDefaultIblRecordingExtractorApBand(TestCase):
     @classmethod
     def setUpClass(cls):
@@ -107,7 +110,6 @@ def test_unscaled_trace_dtype(self):
 
 
 @pytest.mark.streaming_extractors
-@pytest.mark.xfail(reason="We need to fix ibllib/one-api dependency")
 class TestIblStreamingRecordingExtractorApBandWithLoadSyncChannel(TestCase):
     @classmethod
     def setUpClass(cls):
@@ -182,7 +184,6 @@ def test_unscaled_trace_dtype(self):
 
 
 @pytest.mark.streaming_extractors
-@pytest.mark.xfail(reason="We need to fix ibllib/one-api dependency")
 class TestIblSortingExtractor(TestCase):
     def test_ibl_sorting_extractor(self):
         """

src/spikeinterface/preprocessing/whiten.py

@@ -57,6 +57,8 @@ class WhitenRecording(BasePreprocessor):
         The whitened recording extractor
     """
 
+    _precomputable_kwarg_names = ["W", "M"]
+
     def __init__(
         self,
         recording,