Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …

…refactor_GTStudy

.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

@@ -12,6 +12,7 @@ on:
 env:
   KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }}
   KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }}
+  KACHERY_ZONE: ${{ secrets.KACHERY_ZONE }}
 
 concurrency:  # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -25,7 +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 }}

.github/workflows/full-test-with-codecov.yml

@@ -8,6 +8,7 @@ on:
 env:
   KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }}
   KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }}
+  KACHERY_ZONE: ${{ secrets.KACHERY_ZONE }}
 
 jobs:
   full-tests-with-codecov:

doc/development/development.rst

@@ -192,6 +192,7 @@ Miscelleaneous Stylistic Conventions
 #. Avoid using abbreviations in variable names (e.g. use :code:`recording` instead of :code:`rec`). It is especially important to avoid single letter variables.
 #. Use index as singular and indices for plural following the NumPy convention. Avoid idx or indexes. Plus, id and ids are reserved for identifiers (i.e. channel_ids)
 #. We use file_path and folder_path (instead of file_name and folder_name) for clarity.
+#. For the titles of documentation pages, only capitalize the first letter of the first word and classes or software packages. For example, "How to use a SortingAnalyzer in SpikeInterface".
 #. For creating headers to divide sections of code we use the following convention (see issue `#3019 <https://github.com/SpikeInterface/spikeinterface/issues/3019>`_):
 
 

doc/how_to/combine_recordings.rst

@@ -1,4 +1,4 @@
-Combine Recordings in SpikeInterface
+Combine recordings in SpikeInterface
 ====================================
 
 In this tutorial we will walk through combining multiple recording objects. Sometimes this occurs due to hardware

doc/how_to/load_matlab_data.rst

@@ -1,4 +1,4 @@
-Export MATLAB Data to Binary & Load in SpikeInterface
+Export MATLAB data to binary & load in SpikeInterface
 ========================================================
 
 In this tutorial, we will walk through the process of exporting data from MATLAB in a binary format and subsequently loading it using SpikeInterface in Python.

doc/how_to/load_your_data_into_sorting.rst

@@ -1,5 +1,5 @@
-Load Your Own Data into a Sorting
-=================================
+Load your own data into a Sorting object
+========================================
 
 Why make a :code:`Sorting`?
 

doc/how_to/process_by_channel_group.rst

@@ -1,4 +1,4 @@
-Process a Recording by Channel Group
+Process a recording by channel group
 ====================================
 
 In this tutorial, we will walk through how to preprocess and sort a recording

doc/how_to/viewers.rst

@@ -1,4 +1,4 @@
-Visualize Data
+Visualize data
 ==============
 
 There are several ways to plot signals (raw, preprocessed) and spikes.

doc/releases/0.101.2.rst

@@ -0,0 +1,66 @@
+.. _release0.101.2:
+
+SpikeInterface 0.101.2 release notes
+------------------------------------
+
+4th October 2024
+
+Minor release with bug fixes
+
+core:
+
+* Fix `random_spikes_selection()` (#3456)
+* Expose `backend_options` at the analyzer level to set `storage_options` and `saving_options` (#3446)
+* Avoid warnings in `SortingAnalyzer` (#3455)
+* Fix `reset_global_job_kwargs` (#3452)
+* Allow to save recordingless analyzer as (#3443)
+* Fix compute analyzer pipeline with tmp recording (#3433)
+* Fix bug in saving zarr recordings (#3432)
+* Set `run_info` to `None` for `load_waveforms` (#3430)
+* Fix integer overflow in parallel computing (#3426)
+* Refactor `pandas` save load and `convert_dtypes` (#3412)
+* Add spike-train based lazy `SortingGenerator` (#2227)
+
+
+extractors:
+
+* Improve IBL recording extractors by PID (#3449)
+
+sorters:
+
+* Get default encoding for `Popen` (#3439)
+
+postprocessing:
+
+* Add `max_threads_per_process` and `mp_context` to pca by channel computation and PCA metrics (#3434)
+
+widgets:
+
+* Fix metrics widgets for convert_dtypes (#3417)
+* Fix plot motion for multi-segment (#3414)
+
+motion correction:
+
+* Auto-cast recording to float prior to interpolation (#3415)
+
+documentation:
+
+* Add docstring for `generate_unit_locations`  (#3418)
+* Add `get_channel_locations` to the base recording API (#3403)
+
+continuous integration:
+
+* Enable testing arm64 Mac architecture in the CI (#3422)
+* Add kachery_zone secret (#3416)
+
+testing:
+
+* Relax causal filter tests (#3445)
+
+Contributors:
+
+* @alejoe91
+* @h-mayorquin
+* @jiumao2
+* @samuelgarcia
+* @zm711

doc/whatisnew.rst

@@ -8,6 +8,7 @@ Release notes
 .. toctree::
   :maxdepth: 1
 
+  releases/0.101.2.rst
   releases/0.101.1.rst
   releases/0.101.0.rst
   releases/0.100.8.rst
@@ -44,6 +45,11 @@ Release notes
   releases/0.9.1.rst
 
 
+Version 0.101.2
+===============
+
+* Minor release with bug fixes
+
 Version 0.101.1
 ===============
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.101.1"
+version = "0.101.2"
 authors = [
   { name="Alessio Buccino", email="[email protected]" },
   { name="Samuel Garcia", email="[email protected]" },

src/spikeinterface/core/baserecording.py

@@ -608,11 +608,11 @@ def _save(self, format="binary", verbose: bool = False, **save_kwargs):
             probegroup = self.get_probegroup()
             cached.set_probegroup(probegroup)
 
-        time_vectors = self._get_time_vectors()
-        if time_vectors is not None:
-            for segment_index, time_vector in enumerate(time_vectors):
-                if time_vector is not None:
-                    cached.set_times(time_vector, segment_index=segment_index)
+        for segment_index in range(self.get_num_segments()):
+            if self.has_time_vector(segment_index):
+                # the use of get_times is preferred since timestamps are converted to array
+                time_vector = self.get_times(segment_index=segment_index)
+                cached.set_times(time_vector, segment_index=segment_index)
 
         return cached
 
@@ -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)