Merge branch 'main' into fix-pca-multiprocessing

Author: alejoe91

.github/scripts/determine_testing_environment.py

@@ -31,6 +31,7 @@
 sortingcomponents_changed = False
 generation_changed = False
 stream_extractors_changed = False
+github_actions_changed = False
 
 
 for changed_file in changed_files_in_the_pull_request_paths:
@@ -78,9 +79,12 @@
             sorters_internal_changed = True
         else:
             sorters_changed = True
+    elif ".github" in changed_file.parts:
+        if "workflows" in changed_file.parts:
+            github_actions_changed = True
 
 
-run_everything = core_changed or pyproject_toml_changed or neobaseextractor_changed
+run_everything = core_changed or pyproject_toml_changed or neobaseextractor_changed or github_actions_changed
 run_generation_tests = run_everything or generation_changed
 run_extractor_tests = run_everything or extractors_changed or plexon2_changed
 run_preprocessing_tests = run_everything or preprocessing_changed
@@ -96,7 +100,7 @@
 run_sorters_test = run_everything or sorters_changed
 run_internal_sorters_test = run_everything or run_sortingcomponents_tests or sorters_internal_changed
 
-run_streaming_extractors_test = stream_extractors_changed
+run_streaming_extractors_test = stream_extractors_changed or github_actions_changed
 
 install_plexon_dependencies = plexon2_changed
 

.github/workflows/all-tests.yml

@@ -26,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.12"]  # Lower and higher versions we support
-        os: [macos-13, windows-latest, ubuntu-latest]
+        os: [macos-latest, windows-latest, ubuntu-latest]
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python ${{ matrix.python-version }}

src/spikeinterface/core/baserecording.py

@@ -746,6 +746,30 @@ def _select_segments(self, segment_indices):
 
         return SelectSegmentRecording(self, segment_indices=segment_indices)
 
+    def get_channel_locations(
+        self,
+        channel_ids: list | np.ndarray | tuple | None = None,
+        axes: "xy" | "yz" | "xz" | "xyz" = "xy",
+    ) -> np.ndarray:
+        """
+        Get the physical locations of specified channels.
+
+        Parameters
+        ----------
+        channel_ids : array-like, optional
+            The IDs of the channels for which to retrieve locations. If None, retrieves locations
+            for all available channels. Default is None.
+        axes : "xy" | "yz" | "xz" | "xyz", default: "xy"
+            The spatial axes to return, specified as a string (e.g., "xy", "xyz"). Default is "xy".
+
+        Returns
+        -------
+        np.ndarray
+            A 2D or 3D array of shape (n_channels, n_dimensions) containing the locations of the channels.
+            The number of dimensions depends on the `axes` argument (e.g., 2 for "xy", 3 for "xyz").
+        """
+        return super().get_channel_locations(channel_ids=channel_ids, axes=axes)
+
     def is_binary_compatible(self) -> bool:
         """
         Checks if the recording is "binary" compatible.

src/spikeinterface/core/baserecordingsnippets.py

@@ -349,7 +349,7 @@ def set_channel_locations(self, locations, channel_ids=None):
             raise ValueError("set_channel_locations(..) destroys the probe description, prefer _set_probes(..)")
         self.set_property("location", locations, ids=channel_ids)
 
-    def get_channel_locations(self, channel_ids=None, axes: str = "xy"):
+    def get_channel_locations(self, channel_ids=None, axes: str = "xy") -> np.ndarray:
         if channel_ids is None:
             channel_ids = self.get_channel_ids()
         channel_indices = self.ids_to_indices(channel_ids)

src/spikeinterface/core/job_tools.py

@@ -136,11 +136,8 @@ def divide_segment_into_chunks(num_frames, chunk_size):
     else:
         n = num_frames // chunk_size
 
-        frame_starts = np.arange(n) * chunk_size
-        frame_stops = frame_starts + chunk_size
-
-        frame_starts = frame_starts.tolist()
-        frame_stops = frame_stops.tolist()
+        frame_starts = [i * chunk_size for i in range(n)]
+        frame_stops = [frame_start + chunk_size for frame_start in frame_starts]
 
         if (num_frames % chunk_size) > 0:
             frame_starts.append(n * chunk_size)

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -234,7 +234,7 @@ class BlackrockSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ExtractorClass = BlackrockSortingExtractor
     downloads = ["blackrock"]
     entities = [
-        "blackrock/FileSpec2.3001.nev",
+        dict(file_path=local_folder / "blackrock/FileSpec2.3001.nev", sampling_frequency=30_000.0),
         dict(file_path=local_folder / "blackrock/blackrock_2_1/l101210-001.nev", sampling_frequency=30_000.0),
     ]
 
@@ -278,8 +278,8 @@ class Spike2RecordingTest(RecordingCommonTestSuite, unittest.TestCase):
 
 
 @pytest.mark.skipif(
-    version.parse(platform.python_version()) >= version.parse("3.10"),
-    reason="Sonpy only testing with Python < 3.10!",
+    version.parse(platform.python_version()) >= version.parse("3.10") or platform.system() == "Darwin",
+    reason="Sonpy only testing with Python < 3.10 and not supported on macOS!",
 )
 class CedRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = CedRecordingExtractor
@@ -293,6 +293,7 @@ class CedRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ]
 
 
+@pytest.mark.skipif(platform.system() == "Darwin", reason="Maxwell plugin not supported on macOS")
 class MaxwellRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = MaxwellRecordingExtractor
     downloads = ["maxwell"]