Merge branch 'main' into add_del_method_to_binary

Author: h-mayorquin

.github/scripts/determine_testing_environment.py

@@ -48,7 +48,7 @@
     elif changed_file.name == "nwbextractors.py":
         extractors_changed = True  # There are NWB tests that are not streaming
         stream_extractors_changed = True
-    elif changed_file.name == "iblextractors.py":
+    elif changed_file.name == "iblextractors.py" or changed_file.name == "test_iblextractors.py":
         stream_extractors_changed = True
     elif "core" in changed_file.parts:
         core_changed = True

doc/api.rst

@@ -143,7 +143,9 @@ Non-NEO-based
     .. autofunction:: read_mcsh5
     .. autofunction:: read_mda_recording
     .. autofunction:: read_mda_sorting
-    .. autofunction:: read_nwb
+    .. autofunction:: read_nwb_sorting
+    .. autofunction:: read_nwb_recording
+    .. autofunction:: read_nwb_timeseries
     .. autofunction:: read_phy
     .. autofunction:: read_shybrid_recording
     .. autofunction:: read_shybrid_sorting

doc/releases/0.102.2.rst

@@ -0,0 +1,120 @@
+.. _release0.102.2:
+
+SpikeInterface 0.102.2 release notes
+------------------------------------
+
+2nd April 2025
+
+Minor release with bug fixes
+
+core:
+
+* Add check that `remove_channel_ids` are in parent recording (#3822)
+* Print zarr exception if `super_zarr_open` fails (#3803)
+* Add `_precomputable_kwarg_names` to `BaseExtractor` (#3781)
+* Fix dict representation in aggregation (numpy 2.0) (#3744)
+* Explicit sparsity mask for SparseWaveform (#3742)
+* Renaming: `from_time_labels` -> `from_samples_and_labels` (#3724)
+* New sparsity (to add Ks clustering in components) (#3717)
+
+extractors:
+
+* Add nwb extractors to API docs (#3810)
+* Make sure to use the latest ibllib version - ONE will come along (#3802)
+* Better naming for SI units  (#3788)
+* Add Intan port groups by default (#3753)
+* Fix stream names and ids representation in numpy 2.0 (#3751)
+* Add warning message for streams with mixed units (#3739)
+* Fix: get_streams call in OpenEphysBinaryRecordingExtractor completed (#3738)
+* Fix gain inference for "Volts" unit in Plexon2 files (#3728)
+* Fix IBL streaming tests (#3718)
+* Set max_channel property of MdaSortingExtractor (#3701)
+
+preprocessing:
+
+* Allow preprocessing on dicts of recordings (again) (#3773)
+* Update `load_motion_info` to load legacy motion folders (#3772)
+* Allow `aggregate_channels` to accept a dict of recordings (#3767)
+
+sorters:
+
+* Add job kwargs to KS4 (#3786)
+* Fix KS4 tests (#3768)
+* Patch for merging (#3749)
+
+postprocessing:
+
+* Warn instead of print in solve_monopolar (#3736)
+
+curation:
+
+* Support new sortingview and kachery (#3762)
+* Improve merging and iterative merging (#3487)
+
+widgets:
+
+* In sorting_summary: `rp_violation` -> `rp_violations` (#3770)
+* Support new sortingview and kachery (#3762)
+* Pin sortingview version (#3757)
+* Fitting scaling factors in waveform/template plots for irregular probe layouts (#3748)
+* Fix `extra_properties` propagation in sorting summary and SV string properties (#3716)
+* Enhance the CC plots (#3713)
+* Add `BaseRasterWidget` (#3661)
+* Add LocationsWidget and plot_locations (#3649)
+* Adding colorbar support to peak activity widget (#3646)
+
+sortingcomponents:
+
+* Prevent error of trying to delete non-existent variable in sorting components (#3820)
+* Ks clustering (#3712)
+* Peak SVD motion extraction (#3693)
+* Implement motion_aware option in tdc-peeler (#3682)
+* Improve peak detection benchmark (#3662)
+* improve tdc clustering options (#3658)
+* Improve merging and iterative merging (#3487)
+
+motion correction:
+
+* Wrap medicine motion estimation (#3552)
+
+documentation:
+
+* Switch `print` to `warnings.warn` (#3811)
+* Add nwb extractors to API docs (#3810)
+* Fixed typo in import statement (#3791)
+* Clean up all docs warnings (#3746)
+* Remove commented-out study classes from comparison (#3743)
+
+continuous integration:
+
+* Update tj-actions changes-files for security (#3787)
+* Add torch to test installation (#3706)
+
+packaging:
+
+* Update floor of `setuptools` for metadata (#3800)
+* Switch `numba` check to `importlib.util.find_spec` (#3797)
+* Cleanup imports and use `importlib.util.find_spec` rather than try-except (#3795)
+* Replace deep relative imports with absolute imports (#3766)
+* Add psutil to [test] (#3759)
+
+testing:
+
+* Fix KS4 tests (#3768)
+
+Contributors:
+
+* @FrancescoNegri
+* @OleBialas
+* @abhinavsns
+* @alejoe91
+* @chrishalcrow
+* @guptadivyansh
+* @h-mayorquin
+* @oliche
+* @remi-pr
+* @rly
+* @samuelgarcia
+* @yger
+* @zm711
+* @zzhmark

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.102.2"
+version = "0.102.3"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
@@ -31,7 +31,7 @@ dependencies = [
 ]
 
 [build-system]
-requires = ["setuptools>=62.0"]
+requires = ["setuptools>=78.0.2"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
@@ -67,15 +67,13 @@ extractors = [
     "sonpy;python_version<'3.10'",
     "lxml", # lxml for neuroscope
     "scipy",
-    "ONE-api>=2.7.0,<3.0.0", # alf sorter and streaming IBL
-    "ibllib>=2.36.0,<3.0.0", # streaming IBL
+    "ibllib", # streaming IBL
     "pymatreader>=0.0.32", # For cell explorer matlab files
     "zugbruecke>=0.2; sys_platform!='win32'", # For plexon2
 ]
 
 streaming_extractors = [
-    "ONE-api>=2.7.0,<3.0.0", # alf sorter and streaming IBL
-    "ibllib>=2.36.0,<3.0.0", # streaming IBL
+    "ibllib", # streaming IBL
     # Following dependencies are for streaming with nwb files
     "pynwb>=2.6.0",
     "fsspec",
@@ -135,12 +133,13 @@ test_extractors = [
     # Functions to download data in neo test suite
     "pooch>=1.8.2",
     "datalad>=1.0.2",
+    # Commenting out for release
     "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
     "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 test_preprocessing = [
-    "ibllib>=2.36.0", # for IBL
+    "ibllib", # for IBL
     "torch",
 ]
 
@@ -154,7 +153,7 @@ test = [
     "huggingface_hub",
 
     # preprocessing
-    "ibllib>=2.36.0", # for IBL
+    "ibllib", # for IBL
 
     # streaming templates
     "s3fs",
@@ -204,7 +203,6 @@ docs = [
     # 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
-
 ]
 
 dev = [