adjust set_probe tests

src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py

@@ -225,7 +225,7 @@ def set_aligned_segment_starting_times(self, aligned_segment_starting_times: Lis
             ]
             self.set_aligned_segment_timestamps(aligned_segment_timestamps=aligned_segment_timestamps)
 
-    def set_probe(self, probe, *, group_mode: Literal["by_shank", "by_probe"]):
+    def set_probe(self, probe, group_mode: Literal["by_shank", "by_probe"]):
         """
         Set the probe information via a ProbeInterface object.
 

src/neuroconv/tools/testing/data_interface_mixins.py

@@ -19,9 +19,6 @@
 from neuroconv.datainterfaces.ecephys.basesortingextractorinterface import (
     BaseSortingExtractorInterface,
 )
-from neuroconv.datainterfaces.ecephys.intan.intandatainterface import (
-    IntanRecordingInterface,
-)
 from neuroconv.datainterfaces.ophys.baseimagingextractorinterface import (
     BaseImagingExtractorInterface,
 )
@@ -30,7 +27,7 @@
 )
 from neuroconv.utils import NWBMetaDataEncoder
 
-interfaces_for_testing_probe = [IntanRecordingInterface]
+from .mock_probes import generate_mock_probe
 
 
 class DataInterfaceTestMixin:
@@ -114,10 +111,11 @@ def test_conversion_as_lone_interface(self):
                 self.case = num
                 self.test_kwargs = kwargs
                 self.interface = self.data_interface_cls(**self.test_kwargs)
-                do_set_probe = self.data_interface_cls in interfaces_for_testing_probe
+                do_set_probe = isinstance(self.interface, BaseRecordingExtractorInterface)
                 if do_set_probe:
+                    assert isinstance(self.interface, BaseRecordingExtractorInterface)
                     self.interface.set_probe(
-                        _create_mock_probe(num_channels=self.interface.recording_extractor.get_num_channels()),
+                        generate_mock_probe(num_channels=self.interface.recording_extractor.get_num_channels()),
                         group_mode="by_shank",
                     )
                 self.check_metadata_schema_valid()
@@ -131,33 +129,6 @@ def test_conversion_as_lone_interface(self):
                 self.run_custom_checks()
 
 
-def _create_mock_probe(*, num_channels: int):
-    import probeinterface as pi
-
-    # The shank ids will be 0, 0, 0, ..., 1, 1, 1, ..., 2, 2, 2, ...
-    shank_ids: List[int] = []
-    positions = np.zeros((num_channels, 2))
-    num_shanks = 3
-    # ceil division
-    channels_per_shank = (num_channels + num_shanks - 1) // num_shanks
-    for i in range(num_shanks):
-        # x0, y0 is the position of the first electrode in the shank
-        x0 = 0
-        y0 = i * 200
-        for j in range(channels_per_shank):
-            if len(shank_ids) == num_channels:
-                break
-            shank_ids.append(i)
-            x = x0 + j * 10
-            y = y0 + (j % 2) * 10
-            positions[len(shank_ids) - 1] = x, y
-    probe = pi.Probe(ndim=2, si_units="um")
-    probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
-    probe.set_device_channel_indices(np.arange(num_channels))
-    probe.set_shank_ids(shank_ids)
-    return probe
-
-
 class TemporalAlignmentMixin:
     """
     Generic class for testing temporal alignment methods.

src/neuroconv/tools/testing/mock_probes.py

@@ -0,0 +1,28 @@
+from typing import List
+import numpy as np
+
+
+def generate_mock_probe(num_channels: int, num_shanks: int = 3):
+    import probeinterface as pi
+
+    # The shank ids will be 0, 0, 0, ..., 1, 1, 1, ..., 2, 2, 2, ...
+    shank_ids: List[int] = []
+    positions = np.zeros((num_channels, 2))
+    # ceil division
+    channels_per_shank = (num_channels + num_shanks - 1) // num_shanks
+    for i in range(num_shanks):
+        # x0, y0 is the position of the first electrode in the shank
+        x0 = 0
+        y0 = i * 200
+        for j in range(channels_per_shank):
+            if len(shank_ids) == num_channels:
+                break
+            shank_ids.append(i)
+            x = x0 + j * 10
+            y = y0 + (j % 2) * 10
+            positions[len(shank_ids) - 1] = x, y
+    probe = pi.Probe(ndim=2, si_units="um")
+    probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
+    probe.set_device_channel_indices(np.arange(num_channels))
+    probe.set_shank_ids(shank_ids)
+    return probe

tests/test_on_data/test_recording_interfaces.py

@@ -211,7 +211,7 @@ def check_extracted_metadata(self, metadata: dict):
         assert len(metadata["Ecephys"]["Device"]) == 1
         assert metadata["Ecephys"]["Device"][0]["name"] == "Neuronexus-32"
         assert metadata["Ecephys"]["Device"][0]["description"] == "The ecephys device for the MEArec recording."
-        assert len(metadata["Ecephys"]["ElectrodeGroup"]) == 1
+        # assert len(metadata["Ecephys"]["ElectrodeGroup"]) == 1 # do not test this condition because in the test we are setting a mock probe
         assert metadata["Ecephys"]["ElectrodeGroup"][0]["device"] == "Neuronexus-32"
         assert metadata["Ecephys"]["ElectricalSeries"]["description"] == (
             '{"angle_tol": 15, "bursting": false, "chunk_duration": 0, "color_noise_floor": 1, '