Merge branch 'sc2_recording_slices' of github.com:yger/spikeinterface…

… into sc2_recording_slices

.github/actions/build-test-environment/action.yml

@@ -1,41 +1,20 @@
 name: Install packages
 description: This action installs the package and its dependencies for testing
 
-inputs:
-  python-version:
-    description: 'Python version to set up'
-    required: false
-  os:
-    description: 'Operating system to set up'
-    required: false
-
 runs:
   using: "composite"
   steps:
     - name: Install dependencies
       run: |
-        sudo apt install git
         git config --global user.email "[email protected]"
         git config --global user.name "CI Almighty"
-        python -m venv ${{ github.workspace }}/test_env # Environment used in the caching step
-        python -m pip install -U pip  # Official recommended way
-        source ${{ github.workspace }}/test_env/bin/activate
         pip install tabulate  # This produces summaries at the end
         pip install -e .[test,extractors,streaming_extractors,test_extractors,full]
       shell: bash
-    - name: Force installation of latest dev from key-packages when running dev (not release)
-      run: |
-        source ${{ github.workspace }}/test_env/bin/activate
-        spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)")
-        if [ $spikeinterface_is_dev_version = "True" ]; then
-          echo "Running spikeinterface dev version"
-          pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo
-          pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface
-        fi
-          echo "Running tests for release, using pyproject.toml versions of neo and probeinterface"
+    - name: Install git-annex
       shell: bash
-    - name: git-annex install
       run: |
+        pip install datalad-installer
         wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
         mkdir /home/runner/work/installation
         mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/
@@ -44,4 +23,14 @@ runs:
         tar xvzf git-annex-standalone-amd64.tar.gz
         echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
         cd $workdir
+        git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
+    - name: Force installation of latest dev from key-packages when running dev (not release)
+      run: |
+        spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)")
+        if [ $spikeinterface_is_dev_version = "True" ]; then
+          echo "Running spikeinterface dev version"
+          pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo
+          pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface
+        fi
+          echo "Running tests for release, using pyproject.toml versions of neo and probeinterface"
       shell: bash

.github/workflows/all-tests.yml

@@ -47,7 +47,7 @@ jobs:
             echo "$file was changed"
           done
 
-      - name: Set testing environment  # This decides which tests are run and whether to install especial dependencies
+      - name: Set testing environment  # This decides which tests are run and whether to install special dependencies
         shell: bash
         run: |
           changed_files="${{ steps.changed-files.outputs.all_changed_files }}"

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

@@ -45,7 +45,6 @@ jobs:
         env:
           HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell
         run: |
-          source ${{ github.workspace }}/test_env/bin/activate
           pytest -m "not sorters_external" --cov=./ --cov-report xml:./coverage.xml -vv -ra --durations=0 | tee report_full.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1
           echo "# Timing profile of full tests" >> $GITHUB_STEP_SUMMARY
           python ./.github/scripts/build_job_summary.py report_full.txt >> $GITHUB_STEP_SUMMARY

pyproject.toml

@@ -73,7 +73,7 @@ extractors = [
 ]
 
 streaming_extractors = [
-    "ONE-api>=2.7.0", # alf sorter and streaming IBL
+    "ONE-api>=2.7.0,<2.10.0", # alf sorter and streaming IBL
     "ibllib>=2.36.0", # streaming IBL
     # Following dependencies are for streaming with nwb files
     "pynwb>=2.6.0",

src/spikeinterface/extractors/nwbextractors.py

@@ -599,6 +599,8 @@ def __init__(
         else:
             gains, offsets, locations, groups = self._fetch_main_properties_backend()
             self.extra_requirements.append("h5py")
+        if stream_mode is not None:
+            self.extra_requirements.append(stream_mode)
         self.set_channel_gains(gains)
         self.set_channel_offsets(offsets)
         if locations is not None:
@@ -1100,6 +1102,8 @@ def __init__(
             for property_name, property_values in properties.items():
                 values = [x.decode("utf-8") if isinstance(x, bytes) else x for x in property_values]
                 self.set_property(property_name, values)
+        if stream_mode is not None:
+            self.extra_requirements.append(stream_mode)
 
         if stream_mode is None and file_path is not None:
             file_path = str(Path(file_path).resolve())

src/spikeinterface/postprocessing/unit_locations.py

@@ -26,7 +26,7 @@ class ComputeUnitLocations(AnalyzerExtension):
     ----------
     sorting_analyzer : SortingAnalyzer
         A SortingAnalyzer object
-    method : "center_of_mass" | "monopolar_triangulation" | "grid_convolution", default: "center_of_mass"
+    method : "monopolar_triangulation" |  "center_of_mass" | "grid_convolution", default: "monopolar_triangulation"
         The method to use for localization
     **method_kwargs : dict, default: {}
         Kwargs which are passed to the method function. These can be found in the docstrings of `compute_center_of_mass`, `compute_grid_convolution` and `compute_monopolar_triangulation`.

src/spikeinterface/preprocessing/silence_periods.py

@@ -97,7 +97,8 @@ def __init__(self, recording, list_periods, mode="zeros", noise_levels=None, see
             rec_segment = SilencedPeriodsRecordingSegment(parent_segment, periods, mode, noise_generator, seg_index)
             self.add_recording_segment(rec_segment)
 
-        self._kwargs = dict(recording=recording, list_periods=list_periods, mode=mode, noise_generator=noise_generator)
+        self._kwargs = dict(recording=recording, list_periods=list_periods, mode=mode, seed=seed)
+        self._kwargs.update(random_chunk_kwargs)
 
 
 class SilencedPeriodsRecordingSegment(BasePreprocessorSegment):

src/spikeinterface/widgets/unit_waveforms.py

@@ -565,7 +565,7 @@ def _update_plot(self, change):
             channel_locations = self.sorting_analyzer.get_channel_locations()
         else:
             unit_indices = [list(self.templates.unit_ids).index(unit_id) for unit_id in unit_ids]
-            templates = self.templates.templates_array[unit_indices]
+            templates = self.templates.get_dense_templates()[unit_indices]
             templates_shadings = None
             channel_locations = self.templates.get_channel_locations()