Prepare release 0.101.1

doc/releases/0.101.0.rst

@@ -3,7 +3,7 @@
 SpikeInterface 0.101.0 release notes
 ------------------------------------
 
-Estimated: 19th July 2024
+19th July 2024
 
 Main changes:
 

doc/releases/0.101.1.rst

@@ -0,0 +1,143 @@
+.. _release0.101.1:
+
+SpikeInterface 0.101.1 release notes
+------------------------------------
+
+13th September 2024
+
+Main changes:
+
+* Enabled support for consolidated Zarr-backend for `SortingAnalyzer`, including cloud support (#3314, #3318, #3349, #3351)
+* Improved support for Kilosort4 **ONLY VERSIONS >= 4.0.16** (#3339, #3276)
+* Skip recomputation of quality and template metrics if already computed (#3292)
+* Improved `estimate_sparsity` with new `amplitude` method and and deprecated `from_ptp` option (#3369)
+* Dropped support for Python<3.9 (#3267)
+
+core:
+
+* Refactor pandas save load and convert dtypes (#3412)
+* Check run info completed only if it exists (back-compatibility) (#3407)
+* Fix argument spelling in check for binary compatibility (#3409)
+* Fix proposal for channel location when probegroup (#3392)
+* Fix time handling test memory (#3379)
+* Add `BaseRecording.reset_times()` function (#3363, #3380, #3391)
+* Extend `estimate_sparsity` methods and update `from_ptp`` (#3369)
+* Add `load_sorting_analyzer_or_waveforms` function (#3352)
+* Fix zarr folder suffix handling (#3349)
+* Analyzer extension exit status (#3347)
+* Lazy loading of zarr timestamps (#3318)
+* Enable cloud-loading for analyzer Zarr (#3314, #3351, #3378)
+* Refactor `set_property` in base (#3287)
+* Job kwargs fix (#3259)
+* Add `is_filtered` to annotations in `binary.json` (#3245)
+* Add check for None in `NoiseGeneratorRecordingSegment`` get_traces() (#3230)
+
+extractors:
+
+* Load phy channel_group as group (#3368)
+* "quality" property to be read as string instead of object in `BasePhyKilosortSortingExtractor` (#3365)
+
+preprocessing:
+
+* Auto-cast recording to float prior to interpolation (#3415)
+* Update doc handle drift  + better preset (#3232)
+* Add causal filtering to filter.py (#3172)
+
+sorters:
+
+* Updates to kilosort 4: version >= 4.0.16, `bad_channels`, `clear_cache`, `use_binary_file` (#3339)
+* Download apptainer images without docker client (#3335)
+* Expose save preprocessing in ks4 (#3276)
+* Fix KS2/2.5/3 skip_kilosort_preprocessing (#3265)
+* HS: Added lowpass parameter, fixed verbose option (#3262)
+* Now exclusive support for HS v0.4 (Lightning) (#3210)
+
+postprocessing:
+
+* Add extra protection for template metrics (#3364)
+* Protect median against nans in get_prototype_spike (#3270)
+* Fix docstring and error for spike_amplitudes (#3269)
+
+qualitymetrics:
+
+* Do not delete quality and template metrics on recompute (#3292)
+* Refactor quality metrics tests to use fixture (#3249)
+
+
+curation:
+
+* Clean-up identity merges in `get_potential_auto_merges` (#3346)
+* Fix sortingview curation no merge case  (#3309)
+* Start apply_curation() (#3208)
+
+widgets:
+
+* Fix plot motion for multi-segment (#3414)
+* Sortingview: only round float properties (#3406)
+* Fix widgets tests and add test on unit_table_properties (#3354)
+* Allow quality and template metrics in sortingview's unit table (#3299)
+* Add subwidget parameters for UnitSummaryWidget (#3242)
+* Fix `ipympl`/`widget` backend check (#3238)
+
+generators:
+
+* Handle case where channel count changes from probeA to probeB (#3237)
+
+sortingcomponents:
+
+* Update doc handle drift  + better preset (#3232)
+* Make `InterpolateMotionRecording`` not JSON-serializable (#3341)
+
+documentation:
+
+* Clarify meaning of `delta_time` in  `compare_sorter_to_ground_truth` (#3360)
+* Added sphinxcontrib-jquery (#3307)
+* Adding return type annotations (#3304)
+* More docstring updates for multiple modules (#3298)
+* Fix sampling frequency repr (#3294)
+* Proposal for adding Examples to docstrings (#3279)
+* More numpydoc fixes (#3275)
+* Fix docstring and error for spike_amplitudes (#3269)
+* Fix postprocessing docs (#3268)
+* Fix name of principal_components ext in qm docs (take 2) (#3261)
+* Update doc handle drift  + better preset (#3232)
+* Add `int` type to `num_samples` on `InjectTemplatesRecording`. (#3229)
+
+continuous integration:
+
+* Fix streaming extractor condition in the CI (#3362)
+
+packaging:
+
+* Minor typing fixes (#3374)
+* Drop python 3.8 in pyproject.toml (#3267)
+
+testing:
+
+* Fix time handling test memory (#3379)
+* Fix streaming extractor condition in the CI (#3362)
+* Test IBL skip when the setting up the one client fails (#3289)
+* Refactor `set_property` in base (#3287)
+* Refactor quality metrics tests to use fixture (#3249)
+* Add kilosort4 wrapper tests (#3085)
+* Test IBL skip when the setting up the one client fails (#3289)
+* Add kilosort4 wrapper tests (#3085)
+
+Contributors:
+
+* @Djoels
+* @JoeZiminski
+* @JuanPimientoCaicedo
+* @alejoe91
+* @app/pre-commit-ci
+* @chrishalcrow
+* @cwindolf
+* @florian6973
+* @h-mayorquin
+* @jiumao2
+* @jonahpearl
+* @mhhennig
+* @rkim48
+* @samuelgarcia
+* @tabedzki
+* @zm711

doc/scripts/auto-release-notes.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 if [ $# -eq 0 ]; then
-    echo "Usage: $0 START_DATE END_DATE [LABEL] [BRANCH1,BRANCH2] [LIMIT]"
+    echo "Usage: $0 START_DATE (format: YEAR-MM-DD) END_DATE [LABEL] [BRANCH1,BRANCH2] [LIMIT]"
     exit 1
 fi
 

doc/whatisnew.rst

@@ -8,6 +8,7 @@ Release notes
 .. toctree::
   :maxdepth: 1
 
+  releases/0.101.1.rst
   releases/0.101.0.rst
   releases/0.100.8.rst
   releases/0.100.7.rst
@@ -43,6 +44,16 @@ Release notes
   releases/0.9.1.rst
 
 
+Version 0.101.1
+===============
+
+* Enabled support for consolidated Zarr-backend for `SortingAnalyzer`, including cloud support (#3314, #3318, #3349, #3351)
+* Improved support for Kilosort4 **ONLY VERSIONS >= 4.0.16** (#3339, #3276)
+* Skip recomputation of quality and template metrics if already computed (#3292)
+* Improved `estimate_sparsity` with new `amplitude` method and and deprecated `from_ptp` option (#3369)
+* Dropped support for Python<3.9 (#3267)
+
+
 Version 0.101.0
 ===============
 

pyproject.toml

@@ -124,16 +124,16 @@ test_core = [
 
     # for github test : probeinterface and neo from master
     # for release we need pypi, so this need to be commented
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 test_extractors = [
     # Functions to download data in neo test suite
     "pooch>=1.8.2",
     "datalad>=1.0.2",
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 test_preprocessing = [
@@ -173,8 +173,8 @@ test = [
 
     # for github test : probeinterface and neo from master
     # for release we need pypi, so this need to be commented
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 docs = [
@@ -197,8 +197,8 @@ docs = [
     "datalad>=1.0.2",
 
     # for release we need pypi, so this needs to be commented
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",  # We always build from the latest version
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",  # We always build from the latest version
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",  # We always build from the latest version
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",  # We always build from the latest version
 
 ]
 

src/spikeinterface/__init__.py

@@ -30,5 +30,5 @@
 # This flag must be set to False for release
 # This avoids using versioning that contains ".dev0" (and this is a better choice)
 # This is mainly useful when using run_sorter in a container and spikeinterface install
-DEV_MODE = True
-# DEV_MODE = False
+# DEV_MODE = True
+DEV_MODE = False

src/spikeinterface/widgets/metrics.py

@@ -235,6 +235,9 @@ def plot_sortingview(self, data_plot, **backend_kwargs):
             values = check_json(metrics.loc[unit_id].to_dict())
             values_skip_nans = {}
             for k, v in values.items():
+                # convert_dypes returns NaN as None or np.nan (for float)
+                if v is None:
+                    continue
                 if np.isnan(v):
                     continue
                 values_skip_nans[k] = v

src/spikeinterface/widgets/tests/test_widgets.py

@@ -73,7 +73,7 @@ def setUpClass(cls):
             spike_amplitudes=dict(),
             unit_locations=dict(),
             spike_locations=dict(),
-            quality_metrics=dict(metric_names=["snr", "isi_violation", "num_spikes"]),
+            quality_metrics=dict(metric_names=["snr", "isi_violation", "num_spikes", "amplitude_cutoff"]),
             template_metrics=dict(),
             correlograms=dict(),
             template_similarity=dict(),

src/spikeinterface/widgets/utils_sortingview.py

@@ -106,9 +106,9 @@ def generate_unit_table_view(
             if prop_name in sorting_props:
                 property_values = sorting.get_property(prop_name)
             elif prop_name in qm_props:
-                property_values = qm_data[prop_name].values
+                property_values = qm_data[prop_name].to_numpy()
             elif prop_name in tm_props:
-                property_values = tm_data[prop_name].values
+                property_values = tm_data[prop_name].to_numpy()
             else:
                 warn(f"Property '{prop_name}' not found in sorting, quality_metrics, or template_metrics")
                 continue
@@ -137,9 +137,9 @@ def generate_unit_table_view(
                 if prop_name in sorting_props:
                     property_values = sorting.get_property(prop_name)
                 elif prop_name in qm_props:
-                    property_values = qm_data[prop_name].values
+                    property_values = qm_data[prop_name].to_numpy()
                 elif prop_name in tm_props:
-                    property_values = tm_data[prop_name].values
+                    property_values = tm_data[prop_name].to_numpy()
 
                 # Check for NaN values and round floats
                 val0 = np.array(property_values[0])