Merge pull request #3234 from SpikeInterface/prepare_release

Prepare release 0.101.0

Author: alejoe91

doc/api.rst

@@ -336,6 +336,7 @@ spikeinterface.curation
 Deprecated
 ~~~~~~~~~~
 .. automodule:: spikeinterface.curation
+    :noindex:
 
     .. autofunction:: apply_sortingview_curation
     .. autoclass:: CurationSorting

doc/how_to/drift_with_lfp.rst

@@ -64,6 +64,7 @@ Preprocessing
 Contrary to the **dredge_ap** approach, which needs detected peaks and peak locations, the **dredge_lfp**
 method is estimating the motion directly on traces.
 Importantly, the method requires some additional pre-processing steps:
+
   * ``bandpass_filter``: to "focus" the signal on a particular band
   * ``phase_shift``: to compensate for the sampling misalignement
   * ``resample``: to further reduce the sampling fequency of the signal and speed up the computation. The sampling frequency of the estimated motion will be the same as the resampling frequency. Here we choose 250Hz, which corresponds to a sampling interval of 4ms.

doc/index.rst

@@ -14,12 +14,12 @@ state-of-the-art spike sorters, post-process and curate the output, compute qual
 
 .. warning::
 
-    Version 0.101.0 introduces a major API improvement: the :code:`SortingAnalyzer`.`
+    Version 0.101.0 introduces a major API improvement: the :code:`SortingAnalyzer`.
     To read more about the motivations, checkout the
     `enhancement proposal <https://github.com/SpikeInterface/spikeinterface/issues/2282>`_.
     Learn how to :ref:`update your code here <tutorials/waveform_extractor_to_sorting_analyzer:From WaveformExtractor to SortingAnalyzer>`
     and read more about the :code:`SortingAnalyzer`, please refer to the
-    :ref:`core <modules/core:SortingAnalyzer>` and :ref:`postprocessing <modules/postprocessing>` module
+    :ref:`core <modules/core:SortingAnalyzer>` and :ref:`postprocessing <modules/postprocessing:Postprocessing module>` module
     documentation.
 
 

doc/modules/postprocessing.rst

@@ -13,12 +13,12 @@ Extensions as AnalyzerExtensions
 --------------------------------
 
 There are several postprocessing tools available, and all of them are implemented as a
-:py:class:`~spikeinterface.core.ResultExtension`. If the :code:`SortingAnalyzer` is saved to disk, all computations on
+:py:class:`~spikeinterface.core.AnalyzerExtension`. If the :code:`SortingAnalyzer` is saved to disk, all computations on
 top of it will be saved alongside the :code:`SortingAnalyzer` itself (sub folder, zarr path or sub dict).
 This workflow is convenient for retrieval of time-consuming computations (such as pca or spike amplitudes) when reloading a
 :code:`SortingAnalyzer`.
 
-:py:class:`~spikeinterface.core.ResultExtension` objects are tightly connected to the
+:py:class:`~spikeinterface.core.AnalyzerExtension` objects are tightly connected to the
 parent :code:`SortingAnalyzer` object, so that operations done on the :code:`SortingAnalyzer`, such as saving,
 loading, or selecting units, will be automatically applied to all extensions.
 

doc/releases/0.101.0.rst

@@ -8,14 +8,15 @@ Estimated: 19th July 2024
 Main changes:
 
 * Implementation of `SortingAnalyzer` (#2398)
-* Improved auto-merging functions and enable `SortingAnalyzer` to merge units and extensions (#3043, #3154, #3203)
+* Improved auto-merging functions and enable `SortingAnalyzer` to merge units and extensions (#3043, #3154, #3203, #3208)
 * Added framework for hybrid recording generation (#2436, #2769, #2857)
 * Refactored motion correction with the `Motion` class and the DREDGE AP and LFP methods (#2915, #3062)
 * Extendeded benchmarking of `sortingcomponents` (#2501, #2518, #2586, #2811, #2959)
 * Added a powerful drift generator module (#2683)
 
 core:
 
+* Implement a simple system to have backward compatibility for Analyzer extension (#3215)
 * Units aggregation preserve unit ids of aggregated sorters (#3180)
 * Better error message for `BaseExtractor.load()` (#3170)
 * Saving provenance with paths relative to folder (#3165)
@@ -98,6 +99,7 @@ core:
 
 preprocessing:
 
+* Update doc handle drift + better preset (#3232)
 * Remove name class attribute in preprocessing module (#3200)
 * Add option to use ref_channel_ids in global common reference (#3139)
 * Adding option to overwrite while doing correct_motion and saving to a folder (#3088)
@@ -150,6 +152,7 @@ extractors:
 
 sorters:
 
+* Patch for SC2 after release AND bugs in auto merge (#3213)
 * Improve error log to json in run_sorter (#3057)
 * Add support for kilosort>=4.0.12 (#3055)
 * Make sure we check `is_filtered()` rather than bound method during run basesorter (#3037)
@@ -179,7 +182,7 @@ sorters:
 
 postprocessing:
 
-* Fix pca transform error (#3178)
+* Fix pca transform error (#3178, #3224)
 * Fix `spike_vector_to_indices()` (#3048)
 * Remove un-used argument (#3021)
 * Optimize numba cross-correlation and extend `correlograms.py` docstrings and tests (#3017)
@@ -199,6 +202,7 @@ qualitymetrics:
 
 curation:
 
+* Add `apply_curation()` (#3208)
 * Port auto-merge changes and refactor (#3203)
 * Implement `apply_merges_to_sorting()` (#3154)
 * Proposal of format to hold the manual curation information (#2933)
@@ -249,6 +253,7 @@ generation:
 
 sortingcomponents:
 
+* Fix estimate_motion when time_vector is set (#3218)
 * Fix select peaks (#3132)
 * Dredge lfp and dredge ap (#3062)
 * Use "available" for memory caching (#3008)
@@ -269,6 +274,7 @@ sortingcomponents:
 
 documentation:
 
+* Analyzer docstring cleanup (#3220)
 * Eradicate sphinx warnings (#3188)
 * Convert doc references from `wf_extractor` -> `sorting_analyzer` (#3185)
 * Add explainer of compute always computing in the analyzer (vs WaveformExtractor behavior) documentation (#3173)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.101.0rc1"
+version = "0.101.0"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
@@ -25,7 +25,7 @@ dependencies = [
     "tqdm",
     "zarr>=2.16,<2.18",
     "neo>=0.13.0",
-    "probeinterface>=0.2.22",
+    "probeinterface>=0.2.23",
     "packaging",
 ]
 

src/spikeinterface/core/generate.py

@@ -1079,8 +1079,8 @@ class NoiseGeneratorRecording(BaseRecording):
     noise_block_size: int
         Size in sample of noise block.
 
-    Note
-    ----
+    Notes
+    -----
     If modifying this function, ensure that only one call to malloc is made per call get_traces to
     maintain the optimized memory profile.
     """

src/spikeinterface/curation/__init__.py

@@ -12,6 +12,6 @@
 from .splitunitsorting import SplitUnitSorting, split_unit_sorting
 
 # curation format
-from .curation_format import validate_curation_dict, curation_label_to_dataframe
+from .curation_format import validate_curation_dict, curation_label_to_dataframe, apply_curation
 
 from .sortingview_curation import apply_sortingview_curation

src/spikeinterface/sortingcomponents/motion/dredge.py

@@ -182,8 +182,8 @@ def dredge_ap(
     matrix (or several, one for each nonrigid window). This matrix is used to solve for a
     motion estimate.
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     recording: BaseRecording
         The recording extractor
     peaks: numpy array
@@ -518,8 +518,8 @@ def dredge_online_lfp(
 ):
     """Online registration of a preprocessed LFP recording
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     {}
 
     Returns
@@ -1065,8 +1065,8 @@ def calc_corr_decent_pair(
     the normxcorrs at the best displacement, and the matrix of the best
     displacements.
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     raster : DxT array
     batch_size : int
         How many raster rows to xcorr against the whole raster

src/spikeinterface/sortingcomponents/motion/motion_cleaner.py

@@ -9,8 +9,8 @@ def clean_motion_vector(motion, temporal_bins, bin_duration_s, speed_threshold=3
     Also can apply a smoothing.
 
 
-    Arguments
-    ---------
+    Parameters
+    ----------
     motion: numpy array 2d
         Motion estimate in um.
     temporal_bins: numpy.array 1d