Merge branch 'main' into curation-pot-merges

Author: zm711

.github/workflows/all-tests.yml

@@ -139,7 +139,7 @@ jobs:
 
       - name: Test streaming extractors
         shell: bash
-        if: env.RUN_STREAMING_EXTRACTORS_TESTS
+        if: env.RUN_STREAMING_EXTRACTORS_TESTS == 'true'
         run: |
           pip install -e .[streaming_extractors,test_extractors]
           ./.github/run_tests.sh "streaming_extractors" --no-virtual-env
@@ -202,7 +202,7 @@ jobs:
         shell: bash
         if: env.RUN_WIDGETS_TESTS == 'true'
         run: |
-          pip install -e .[full]
+          pip install -e .[full,widgets]
           ./.github/run_tests.sh widgets --no-virtual-env
 
       - name: Test exporters

doc/api.rst

@@ -73,6 +73,19 @@ Low-level
 
     .. autoclass:: ChunkRecordingExecutor
 
+
+Back-compatibility with ``WaveformExtractor`` (version < 0.101.0)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: spikeinterface.core
+    :noindex:
+
+    .. autofunction:: extract_waveforms
+    .. autofunction:: load_waveforms
+    .. autofunction:: load_sorting_analyzer_or_waveforms
+
+
+
 spikeinterface.extractors
 -------------------------
 

src/spikeinterface/core/__init__.py

@@ -166,4 +166,8 @@
 
 # Important not for compatibility!!
 # This wil be uncommented after 0.100
-from .waveforms_extractor_backwards_compatibility import extract_waveforms, load_waveforms
+from .waveforms_extractor_backwards_compatibility import (
+    extract_waveforms,
+    load_waveforms,
+    load_sorting_analyzer_or_waveforms,
+)

src/spikeinterface/core/sortinganalyzer.py

@@ -145,7 +145,7 @@ def create_sorting_analyzer(
     return sorting_analyzer
 
 
-def load_sorting_analyzer(folder, load_extensions=True, format="auto"):
+def load_sorting_analyzer(folder, load_extensions=True, format="auto", storage_options=None):
     """
     Load a SortingAnalyzer object from disk.
 
@@ -157,16 +157,17 @@ def load_sorting_analyzer(folder, load_extensions=True, format="auto"):
         Load all extensions or not.
     format : "auto" | "binary_folder" | "zarr"
         The format of the folder.
+    storage_options : dict | None, default: None
+        The storage options to specify credentials to remote zarr bucket.
+        For open buckets, it doesn't need to be specified.
 
     Returns
     -------
     sorting_analyzer : SortingAnalyzer
         The loaded SortingAnalyzer
 
     """
-    if format == "zarr":
-        folder = clean_zarr_folder_name(folder)
-    return SortingAnalyzer.load(folder, load_extensions=load_extensions, format=format)
+    return SortingAnalyzer.load(folder, load_extensions=load_extensions, format=format, storage_options=storage_options)
 
 
 class SortingAnalyzer:

src/spikeinterface/core/waveforms_extractor_backwards_compatibility.py

@@ -343,6 +343,31 @@ def get_template(
         return templates[0]
 
 
+def load_sorting_analyzer_or_waveforms(folder, sorting=None):
+    """
+    Load a SortingAnalyzer from either a newly saved SortingAnalyzer folder or an old WaveformExtractor folder.
+
+    Parameters
+    ----------
+    folder: str | Path
+        The folder to the sorting analyzer or waveform extractor
+    sorting: BaseSorting | None, default: None
+        The sorting object to instantiate with the SortingAnalyzer (only used for old WaveformExtractor)
+
+    Returns
+    -------
+    sorting_analyzer: SortingAnalyzer
+        The returned SortingAnalyzer.
+    """
+    folder = Path(folder)
+    if folder.suffix == ".zarr":
+        return load_sorting_analyzer(folder)
+    elif (folder / "spikeinterface_info.json").exists():
+        return load_sorting_analyzer(folder)
+    else:
+        return load_waveforms(folder, sorting=sorting, output="SortingAnalyzer")
+
+
 def load_waveforms(
     folder,
     with_recording: bool = True,

src/spikeinterface/widgets/tests/test_widgets.py

@@ -539,6 +539,21 @@ def test_plot_sorting_summary(self):
                     backend=backend,
                     **self.backend_kwargs[backend],
                 )
+                # add unit_properties
+                sw.plot_sorting_summary(
+                    self.sorting_analyzer_sparse,
+                    unit_table_properties=["firing_rate", "snr"],
+                    backend=backend,
+                    **self.backend_kwargs[backend],
+                )
+                # adding a missing property should raise a warning
+                with self.assertWarns(UserWarning):
+                    sw.plot_sorting_summary(
+                        self.sorting_analyzer_sparse,
+                        unit_table_properties=["missing_property"],
+                        backend=backend,
+                        **self.backend_kwargs[backend],
+                    )
 
     def test_plot_agreement_matrix(self):
         possible_backends = list(sw.AgreementMatrixWidget.get_possible_backends())

src/spikeinterface/widgets/utils_sortingview.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 
+from ..core import SortingAnalyzer, BaseSorting
 from ..core.core_tools import check_json
 from warnings import warn
 
@@ -46,26 +47,42 @@ def handle_display_and_url(widget, view, **backend_kwargs):
     return url
 
 
-def generate_unit_table_view(analyzer, unit_properties=None, similarity_scores=None):
+def generate_unit_table_view(
+    sorting_or_sorting_analyzer: SortingAnalyzer | BaseSorting,
+    unit_properties: list[str] | None = None,
+    similarity_scores: npndarray | None = None,
+):
     import sortingview.views as vv
 
-    sorting = analyzer.sorting
+    if isinstance(sorting_or_sorting_analyzer, SortingAnalyzer):
+        analyzer = sorting_or_sorting_analyzer
+        sorting = analyzer.sorting
+    else:
+        sorting = sorting_or_sorting_analyzer
+        analyzer = None
 
     # Find available unit properties from all sources
     sorting_props = list(sorting.get_property_keys())
-    if analyzer.get_extension("quality_metrics") is not None:
-        qm_props = list(analyzer.get_extension("quality_metrics").get_data().columns)
-        qm_data = analyzer.get_extension("quality_metrics").get_data()
+    if analyzer is not None:
+        if analyzer.get_extension("quality_metrics") is not None:
+            qm_props = list(analyzer.get_extension("quality_metrics").get_data().columns)
+            qm_data = analyzer.get_extension("quality_metrics").get_data()
+        else:
+            qm_props = []
+        if analyzer.get_extension("template_metrics") is not None:
+            tm_props = list(analyzer.get_extension("template_metrics").get_data().columns)
+            tm_data = analyzer.get_extension("template_metrics").get_data()
+        else:
+            tm_props = []
+        # Check for any overlaps and warn user if any
+        all_props = sorting_props + qm_props + tm_props
     else:
+        all_props = sorting_props
         qm_props = []
-    if analyzer.get_extension("template_metrics") is not None:
-        tm_props = list(analyzer.get_extension("template_metrics").get_data().columns)
-        tm_data = analyzer.get_extension("template_metrics").get_data()
-    else:
         tm_props = []
+        qm_data = None
+        tm_data = None
 
-    # Check for any overlaps and warn user if any
-    all_props = sorting_props + qm_props + tm_props
     overlap_props = [prop for prop in all_props if all_props.count(prop) > 1]
     if len(overlap_props) > 0:
         warn(
@@ -93,7 +110,8 @@ def generate_unit_table_view(analyzer, unit_properties=None, similarity_scores=N
             elif prop_name in tm_props:
                 property_values = tm_data[prop_name].values
             else:
-                raise ValueError(f"Property '{prop_name}' not found in sorting, quality_metrics, or template_metrics")
+                warn(f"Property '{prop_name}' not found in sorting, quality_metrics, or template_metrics")
+                continue
 
             # make dtype available
             val0 = np.array(property_values[0])
@@ -106,7 +124,7 @@ def generate_unit_table_view(analyzer, unit_properties=None, similarity_scores=N
             elif val0.dtype.kind == "b":
                 dtype = "bool"
             else:
-                print(f"Unsupported dtype {val0.dtype} for property {prop_name}. Skipping")
+                warn(f"Unsupported dtype {val0.dtype} for property {prop_name}. Skipping")
                 continue
             ut_columns.append(vv.UnitsTableColumn(key=prop_name, label=prop_name, dtype=dtype))
             valid_unit_properties.append(prop_name)
@@ -122,10 +140,6 @@ def generate_unit_table_view(analyzer, unit_properties=None, similarity_scores=N
                     property_values = qm_data[prop_name].values
                 elif prop_name in tm_props:
                     property_values = tm_data[prop_name].values
-                else:
-                    raise ValueError(
-                        f"Property '{prop_name}' not found in sorting, quality_metrics, or template_metrics"
-                    )
 
                 # Check for NaN values
                 val0 = np.array(property_values[0])