Merge branch 'main' into ruff-test

Author: zm711

pyproject.toml

@@ -72,15 +72,15 @@ extractors = [
     "sonpy;python_version<'3.10'",
     "lxml", # lxml for neuroscope
     "scipy",
-    "ONE-api>=2.7.0", # alf sorter and streaming IBL
-    "ibllib>=2.36.0", # streaming IBL
+    "ONE-api>=2.7.0,<3.0.0", # alf sorter and streaming IBL
+    "ibllib>=2.36.0,<3.0.0", # 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,<2.10.0", # alf sorter and streaming IBL
-    "ibllib>=2.36.0", # streaming IBL
+    "ONE-api>=2.7.0,<3.0.0", # alf sorter and streaming IBL
+    "ibllib>=2.36.0,<3.0.0", # streaming IBL
     # Following dependencies are for streaming with nwb files
     "pynwb>=2.6.0",
     "fsspec",

src/spikeinterface/extractors/iblextractors.py

@@ -294,15 +294,16 @@ class IblSortingExtractor(BaseSorting):
         >>> one = ONE(base_url="https://openalyx.internationalbrainlab.org", password="international", silent=True)
         >>> pids, _ = one.eid2pid("session_eid")
         >>> pid = pids[0]
+    one: One | dict, required
+        Instance of ONE.api or dict to use for data loading.
+        For multi-processing applications, this can also be a dictionary of ONE.api arguments
+        For example: one=dict(base_url='https://alyx.internationalbrainlab.org', mode='remote')
     good_clusters_only: bool, default: False
         If True, only load the good clusters
     load_unit_properties: bool, default: True
         If True, load the unit properties from the IBL database
-    one: One | dict, default: None
-        Instance of ONE.api or dict to use for data loading.
-        For multi-processing applications, this can also be a dictionary of ONE.api arguments
-        For example: one={} or one=dict(base_url='https://alyx.internationalbrainlab.org', mode='remote')
-
+    kwargs: dict, optional
+        Additional keyword arguments to pass to the IBL SpikeSortingLoader constructor, such as `revision`.
     Returns
     -------
     extractor : IBLSortingExtractor
@@ -311,13 +312,14 @@ class IblSortingExtractor(BaseSorting):
 
     installation_mesg = "IBL extractors require ibllib as a dependency." " To install, run: \n\n pip install ibllib\n\n"
 
-    def __init__(self, pid: str, good_clusters_only: bool = False, load_unit_properties: bool = True, one=None):
+    def __init__(
+        self, pid: str, good_clusters_only: bool = False, load_unit_properties: bool = True, one=None, **kwargs
+    ):
         try:
             from one.api import ONE
             from brainbox.io.one import SpikeSortingLoader
 
-            if one is None:
-                one = {}
+            assert one is not None, "one is a required parameter."
             if isinstance(one, dict):
                 one = ONE(**one)
             else:
@@ -327,12 +329,11 @@ def __init__(self, pid: str, good_clusters_only: bool = False, load_unit_propert
         self.ssl = SpikeSortingLoader(one=one, pid=pid)
         sr = self.ssl.raw_electrophysiology(band="ap", stream=True)
         self._folder_path = self.ssl.session_path
-        spikes, clusters, channels = self.ssl.load_spike_sorting(dataset_types=["spikes.samples"])
+        spikes, clusters, channels = self.ssl.load_spike_sorting(dataset_types=["spikes.samples"], **kwargs)
         clusters = self.ssl.merge_clusters(spikes, clusters, channels)
 
         if good_clusters_only:
             good_cluster_slice = clusters["cluster_id"][clusters["label"] == 1]
-            unit_ids = clusters["cluster_id"][good_cluster_slice]
         else:
             good_cluster_slice = slice(None)
         unit_ids = clusters["cluster_id"][good_cluster_slice]

src/spikeinterface/extractors/tests/test_iblextractors.py

@@ -12,6 +12,7 @@
 
 
 @pytest.mark.streaming_extractors
+@pytest.mark.xfail(reason="We need to fix ibllib/one-api dependency")
 class TestDefaultIblRecordingExtractorApBand(TestCase):
     @classmethod
     def setUpClass(cls):
@@ -106,6 +107,7 @@ 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):
@@ -180,6 +182,7 @@ 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):
         """
@@ -197,9 +200,9 @@ def test_ibl_sorting_extractor(self):
             )
         except:
             pytest.skip("Skipping test due to server being down.")
-        sorting = read_ibl_sorting(pid=PID, one=one)
+        sorting = read_ibl_sorting(pid=PID, one=one, revision="2023-12-05")
         assert len(sorting.unit_ids) == 733
-        sorting_good = read_ibl_sorting(pid=PID, good_clusters_only=True)
+        sorting_good = read_ibl_sorting(pid=PID, good_clusters_only=True, one=one, revision="2023-12-05")
         assert len(sorting_good.unit_ids) == 108
 
         # check properties
@@ -208,14 +211,14 @@ def test_ibl_sorting_extractor(self):
         assert "brain_area" in sorting_good.get_property_keys()
 
         # load without properties
-        sorting_no_properties = read_ibl_sorting(pid=PID, load_unit_properties=False)
+        sorting_no_properties = read_ibl_sorting(pid=PID, one=one, load_unit_properties=False, revision="2023-12-05")
         # check properties
         assert "firing_rate" not in sorting_no_properties.get_property_keys()
 
 
 if __name__ == "__main__":
-    TestDefaultIblStreamingRecordingExtractorApBand.setUpClass()
-    test1 = TestDefaultIblStreamingExtractorApBand()
+    TestDefaultIblRecordingExtractorApBand.setUpClass()
+    test1 = TestDefaultIblRecordingExtractorApBand()
     test1.setUp()
     test1.test_get_stream_names()
     test1.test_dtype()
@@ -230,7 +233,7 @@ def test_ibl_sorting_extractor(self):
     test1.test_unscaled_trace_dtype()
 
     TestIblStreamingRecordingExtractorApBandWithLoadSyncChannel.setUpClass()
-    test2 = TestIblStreamingExtractorApBandWithLoadSyncChannel()
+    test2 = TestIblStreamingRecordingExtractorApBandWithLoadSyncChannel()
     test2.setUp()
     test2.test_get_stream_names()
     test2.test_get_stream_names()