Merge pull request #602 from catalystneuro/deprecate_ced_name

Deprecate CED Recording

CHANGELOG.md

@@ -1,12 +1,15 @@
 # (Upcoming)
 
+### Back-compatibility break
+* The `CEDRecordingInterface` has now been removed; use the `Spike2RecordingInterface` instead. [PR #602](https://github.com/catalystneuro/neuroconv/pull/602)
+
 ### Features
-Added `session_start_time` extraction to `FicTracDataInterface`. [PR #598](https://github.com/catalystneuro/neuroconv/pull/598)
+* Added `session_start_time` extraction to `FicTracDataInterface`. [PR #598](https://github.com/catalystneuro/neuroconv/pull/598)
 * Added `imaging_plane_name` keyword argument to `add_imaging_plane` function to determine which imaging plane to add from the metadata by name instead of `imaging_plane_index`.
   Added reference for `imaging_plane` to default plane segmentation metadata. [PR #594](https://github.com/catalystneuro/neuroconv/pull/594)
 
 ### Fixes
-Remove `starting_time` reset to default value (0.0) when adding the rate and updating the `photon_series_kwargs` or `roi_response_series_kwargs`, in `add_photon_series` or `add_fluorescence_traces`. [PR #595](https://github.com/catalystneuro/neuroconv/pull/595)
+* Remove `starting_time` reset to default value (0.0) when adding the rate and updating the `photon_series_kwargs` or `roi_response_series_kwargs`, in `add_photon_series` or `add_fluorescence_traces`. [PR #595](https://github.com/catalystneuro/neuroconv/pull/595)
 
 ### Features
 

src/neuroconv/datainterfaces/__init__.py

@@ -52,10 +52,7 @@
     PlexonRecordingInterface,
     PlexonSortingInterface,
 )
-from .ecephys.spike2.spike2datainterface import (
-    CEDRecordingInterface,
-    Spike2RecordingInterface,
-)
+from .ecephys.spike2.spike2datainterface import Spike2RecordingInterface
 from .ecephys.spikegadgets.spikegadgetsdatainterface import (
     SpikeGadgetsRecordingInterface,
 )
@@ -105,7 +102,6 @@
     SpikeGLXNIDQInterface,
     SpikeGadgetsRecordingInterface,
     IntanRecordingInterface,
-    CEDRecordingInterface,
     CellExplorerSortingInterface,
     CellExplorerRecordingInterface,
     CellExplorerLFPInterface,

src/neuroconv/datainterfaces/ecephys/spike2/spike2datainterface.py

@@ -19,9 +19,7 @@ class Spike2RecordingInterface(BaseRecordingExtractorInterface):
     Data interface class for converting Spike2 data from CED (Cambridge Electronic
     Design) using the :py:class:`~spikeinterface.extractors.CedRecordingExtractor`."""
 
-    keywords = BaseRecordingExtractorInterface.keywords + [
-        "CED",
-    ]
+    keywords = BaseRecordingExtractorInterface.keywords + ["CED"]
 
     ExtractorName = "CedRecordingExtractor"
 
@@ -59,22 +57,3 @@ def __init__(self, file_path: FilePathType, verbose: bool = True, es_key: str =
         signal_channels = self.recording_extractor.neo_reader.header["signal_channels"]
         channel_ids_of_raw_data = [channel_info[1] for channel_info in signal_channels if channel_info[4] == "mV"]
         self.recording_extractor = self.recording_extractor.channel_slice(channel_ids=channel_ids_of_raw_data)
-
-
-class CEDRecordingInterface(Spike2RecordingInterface):
-    def __init__(self, file_path: FilePathType, verbose: bool = True, es_key: str = "ElectricalSeries"):
-        """
-        Initialize reading of CED file.
-
-        Parameters
-        ----------
-        file_path : FilePathType
-            Path to .smr or .smrx file.
-        verbose : bool, default: True
-        es_key : str, default: "ElectricalSeries"
-        """
-        warn(
-            message="CEDRecordingInterface will soon be deprecated. Please use Spike2RecordingInterface instead.",
-            category=DeprecationWarning,
-        )
-        super().__init__(file_path=file_path, verbose=verbose, es_key=es_key)

tests/test_ecephys/test_ecephys_interfaces.py

@@ -15,7 +15,7 @@
 from spikeinterface.extractors import NumpySorting
 
 from neuroconv import NWBConverter
-from neuroconv.datainterfaces import CEDRecordingInterface
+from neuroconv.datainterfaces import Spike2RecordingInterface
 from neuroconv.datainterfaces.ecephys.basesortingextractorinterface import (
     BaseSortingExtractorInterface,
 )
@@ -43,32 +43,21 @@ def test_stub_multi_segment(self):
 
 
 class TestAssertions(TestCase):
-    @pytest.mark.skipif(
-        platform != "darwin" or python_version >= Version("3.8"),
-        reason="Only testing on MacOSX with Python 3.7!",
-    )
-    def test_ced_import_assertions_python_3_7(self):
-        with self.assertRaisesWith(
-            exc_type=ModuleNotFoundError,
-            exc_msg="\nThe package 'sonpy' is not available on the darwin platform for Python version 3.7!",
-        ):
-            CEDRecordingInterface.get_all_channels_info(file_path="does_not_matter.smrx")
-
     @pytest.mark.skipif(python_version.minor != 10, reason="Only testing with Python 3.10!")
-    def test_ced_import_assertions_3_10(self):
+    def test_spike2_import_assertions_3_10(self):
         with self.assertRaisesWith(
             exc_type=ModuleNotFoundError,
             exc_msg="\nThe package 'sonpy' is not available for Python version 3.10!",
         ):
-            CEDRecordingInterface.get_all_channels_info(file_path="does_not_matter.smrx")
+            Spike2RecordingInterface.get_all_channels_info(file_path="does_not_matter.smrx")
 
     @pytest.mark.skipif(python_version.minor != 11, reason="Only testing with Python 3.11!")
-    def test_ced_import_assertions_3_11(self):
+    def test_spike2_import_assertions_3_11(self):
         with self.assertRaisesWith(
             exc_type=ModuleNotFoundError,
             exc_msg="\nThe package 'sonpy' is not available for Python version 3.11!",
         ):
-            CEDRecordingInterface.get_all_channels_info(file_path="does_not_matter.smrx")
+            Spike2RecordingInterface.get_all_channels_info(file_path="does_not_matter.smrx")
 
 
 class TestSortingInterface(unittest.TestCase):

tests/test_on_data/test_gin_ecephys/test_raw_recordings.py

@@ -17,7 +17,6 @@
     AxonaRecordingInterface,
     BiocamRecordingInterface,
     BlackrockRecordingInterface,
-    CEDRecordingInterface,
     EDFRecordingInterface,
     IntanRecordingInterface,
     MaxOneRecordingInterface,
@@ -139,15 +138,6 @@ class TestEcephysRawRecordingsNwbConversions(unittest.TestCase):
         ),
     ]
 
-    this_python_version = version.parse(python_version())
-    if system() != "Darwin" and version.parse("3.8") <= this_python_version < version.parse("3.10"):
-        parameterized_recording_list.append(
-            param(
-                data_interface=CEDRecordingInterface,
-                interface_kwargs=dict(file_path=str(DATA_PATH / "spike2" / "m365_1sec.smrx")),
-                case_name="smrx",
-            )
-        )
     if system() == "Linux":
         parameterized_recording_list.append(
             param(
@@ -188,16 +178,6 @@ class TestEcephysRawRecordingsNwbConversions(unittest.TestCase):
         ]
     )
 
-    this_python_version = version.parse(python_version())
-    if system() != "Darwin" and version.parse("3.8") <= this_python_version < version.parse("3.10"):
-        parameterized_recording_list.append(
-            param(
-                data_interface=CEDRecordingInterface,
-                interface_kwargs=dict(file_path=str(DATA_PATH / "spike2" / "m365_1sec.smrx")),
-                case_name="smrx",
-            )
-        )
-
     for suffix in ["rhd", "rhs"]:
         parameterized_recording_list.append(
             param(

tests/test_on_data/test_recording_interfaces.py

@@ -14,7 +14,6 @@
     AxonaRecordingInterface,
     BiocamRecordingInterface,
     BlackrockRecordingInterface,
-    CEDRecordingInterface,
     CellExplorerRecordingInterface,
     EDFRecordingInterface,
     IntanRecordingInterface,
@@ -27,6 +26,7 @@
     OpenEphysLegacyRecordingInterface,
     OpenEphysRecordingInterface,
     PlexonRecordingInterface,
+    Spike2RecordingInterface,
     SpikeGadgetsRecordingInterface,
     SpikeGLXRecordingInterface,
     TdtRecordingInterface,
@@ -81,8 +81,8 @@ class TestBlackrockRecordingInterface(RecordingExtractorInterfaceTestMixin, Test
     platform == "darwin" or this_python_version < version.parse("3.8") or this_python_version > version.parse("3.9"),
     reason="Interface unsupported for OSX. Only runs on Python 3.8 and 3.9",
 )
-class TestCEDRecordingInterface(RecordingExtractorInterfaceTestMixin, TestCase):
-    data_interface_cls = CEDRecordingInterface
+class TestSpike2RecordingInterface(RecordingExtractorInterfaceTestMixin, TestCase):
+    data_interface_cls = Spike2RecordingInterface
     interface_kwargs = dict(file_path=str(DATA_PATH / "spike2" / "m365_1sec.smrx"))
     save_directory = OUTPUT_PATH