Merge branch 'main' into move_imports_to_the_correct_place

CHANGELOG.md

@@ -11,6 +11,7 @@
 * Added .csv support to DeepLabCutInterface [PR #1140](https://github.com/catalystneuro/neuroconv/pull/1140)
 
 ## Improvements
+* Use mixing tests for ecephy's mocks [PR #1136](https://github.com/catalystneuro/neuroconv/pull/1136)
 
 # v0.6.5 (November 1, 2024)
 

src/neuroconv/tools/testing/data_interface_mixins.py

@@ -92,7 +92,6 @@ def test_metadata_schema_valid(self, setup_interface):
         Draft7Validator.check_schema(schema=schema)
 
     def test_metadata(self, setup_interface):
-        # Validate metadata now happens on the class itself
         metadata = self.interface.get_metadata()
         self.check_extracted_metadata(metadata)
 

tests/test_ecephys/test_ecephys_interfaces.py

@@ -27,42 +27,61 @@
 
 python_version = Version(get_python_version())
 
+from neuroconv.tools.testing.data_interface_mixins import (
+    RecordingExtractorInterfaceTestMixin,
+    SortingExtractorInterfaceTestMixin,
+)
 
-class TestRecordingInterface(TestCase):
-    @classmethod
-    def setUpClass(cls):
-        cls.single_segment_recording_interface = MockRecordingInterface(durations=[0.100])
-        cls.multi_segment_recording_interface = MockRecordingInterface(durations=[0.100, 0.100])
 
-    def test_stub_single_segment(self):
-        interface = self.single_segment_recording_interface
+class TestSortingInterface(SortingExtractorInterfaceTestMixin):
+
+    data_interface_cls = MockSortingInterface
+    interface_kwargs = dict(num_units=4, durations=[0.100])
+
+    def test_propagate_conversion_options(self, setup_interface):
+        interface = self.interface
         metadata = interface.get_metadata()
-        interface.create_nwbfile(stub_test=True, metadata=metadata)
+        nwbfile = interface.create_nwbfile(
+            stub_test=True,
+            metadata=metadata,
+            write_as="processing",
+            units_name="processed_units",
+            units_description="The processed units.",
+        )
 
-    def test_stub_multi_segment(self):
-        interface = self.multi_segment_recording_interface
+        ecephys = get_module(nwbfile, "ecephys")
+
+        assert nwbfile.units is None
+        assert "processed_units" in ecephys.data_interfaces
+
+
+class TestRecordingInterface(RecordingExtractorInterfaceTestMixin):
+    data_interface_cls = MockRecordingInterface
+    interface_kwargs = dict(durations=[0.100])
+
+    def test_stub(self, setup_interface):
+        interface = self.interface
         metadata = interface.get_metadata()
         interface.create_nwbfile(stub_test=True, metadata=metadata)
 
-    def test_no_slash_in_name(self):
-        interface = self.single_segment_recording_interface
+    def test_no_slash_in_name(self, setup_interface):
+        interface = self.interface
         metadata = interface.get_metadata()
         metadata["Ecephys"]["ElectricalSeries"]["name"] = "test/slash"
-        with self.assertRaises(jsonschema.exceptions.ValidationError):
+        with pytest.raises(jsonschema.exceptions.ValidationError):
             interface.validate_metadata(metadata)
 
+    def test_stub_multi_segment(self):
 
-class TestAlwaysWriteTimestamps:
+        interface = MockRecordingInterface(durations=[0.100, 0.100])
+        metadata = interface.get_metadata()
+        interface.create_nwbfile(stub_test=True, metadata=metadata)
 
-    def test_always_write_timestamps(self):
-        # By default the MockRecordingInterface has a uniform sampling rate
-        interface = MockRecordingInterface(durations=[1.0], sampling_frequency=30_000.0)
+    def test_always_write_timestamps(self, setup_interface):
 
-        nwbfile = interface.create_nwbfile(always_write_timestamps=True)
+        nwbfile = self.interface.create_nwbfile(always_write_timestamps=True)
         electrical_series = nwbfile.acquisition["ElectricalSeries"]
-
-        expected_timestamps = interface.recording_extractor.get_times()
-
+        expected_timestamps = self.interface.recording_extractor.get_times()
         np.testing.assert_array_equal(electrical_series.timestamps[:], expected_timestamps)
 
 
@@ -84,33 +103,9 @@ def test_spike2_import_assertions_3_11(self):
             Spike2RecordingInterface.get_all_channels_info(file_path="does_not_matter.smrx")
 
 
-class TestSortingInterface:
-
-    def test_run_conversion(self, tmp_path):
-
-        nwbfile_path = Path(tmp_path) / "test_sorting.nwb"
-        num_units = 4
-        interface = MockSortingInterface(num_units=num_units, durations=(1.0,))
-        interface.sorting_extractor = interface.sorting_extractor.rename_units(new_unit_ids=["a", "b", "c", "d"])
-
-        interface.run_conversion(nwbfile_path=nwbfile_path)
-        with NWBHDF5IO(nwbfile_path, "r") as io:
-            nwbfile = io.read()
-
-            units = nwbfile.units
-            assert len(units) == num_units
-            units_df = units.to_dataframe()
-            # Get index in units table
-            for unit_id in interface.sorting_extractor.unit_ids:
-                # In pynwb we write unit name as unit_id
-                row = units_df.query(f"unit_name == '{unit_id}'")
-                spike_times = interface.sorting_extractor.get_unit_spike_train(unit_id=unit_id, return_times=True)
-                written_spike_times = row["spike_times"].iloc[0]
-
-                np.testing.assert_array_equal(spike_times, written_spike_times)
-
-
 class TestSortingInterfaceOld(unittest.TestCase):
+    """Old-style tests for the SortingInterface. Remove once we we are sure all the behaviors are covered by the mock."""
+
     @classmethod
     def setUpClass(cls) -> None:
         cls.test_dir = Path(mkdtemp())
@@ -194,28 +189,3 @@ def test_sorting_full(self):
             nwbfile = io.read()
             for i, start_times in enumerate(self.sorting_start_frames):
                 assert len(nwbfile.units["spike_times"][i]) == self.num_frames - start_times
-
-    def test_sorting_propagate_conversion_options(self):
-        minimal_nwbfile = self.test_dir / "temp2.nwb"
-        metadata = self.test_sorting_interface.get_metadata()
-        metadata["NWBFile"]["session_start_time"] = datetime.now().astimezone()
-        units_description = "The processed units."
-        conversion_options = dict(
-            TestSortingInterface=dict(
-                write_as="processing",
-                units_name="processed_units",
-                units_description=units_description,
-            )
-        )
-        self.test_sorting_interface.run_conversion(
-            nwbfile_path=minimal_nwbfile,
-            metadata=metadata,
-            conversion_options=conversion_options,
-        )
-
-        with NWBHDF5IO(minimal_nwbfile, "r") as io:
-            nwbfile = io.read()
-            ecephys = get_module(nwbfile, "ecephys")
-            self.assertIsNone(nwbfile.units)
-            self.assertIn("processed_units", ecephys.data_interfaces)
-            self.assertEqual(ecephys["processed_units"].description, units_description)