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Merge pull request #2473 from SpikeInterface/prepare_release
Prepare release 0.100.0
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| Original file line number | Diff line number | Diff line change |
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| .. _release0.100.0: | ||
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| SpikeInterface 0.100.0 release notes | ||
| ------------------------------------ | ||
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| 6th February 2024 | ||
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| Main changes: | ||
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| * Several improvements and bug fixes for Windows users | ||
| * Important refactoring of NWB extractors: | ||
| * implemented direct backend implementation (to avoid using `pynwb`) | ||
| * sped up streaming using `remfile` | ||
| * added support for `zarr` backend | ||
| * Removed `joblib` dependency in favor of `ParallelProcessExecutor` | ||
| * Improved flexibility when running sorters in containers by adding several options for installing `spikeinterface` | ||
| * Add `Templates` class to core, which handles unit templates and sparsity (#1982) | ||
| * Added Zarr-backend to `Sorting` objects (`sorting.save(folder="...", format="zarr")`) (#2403) | ||
| * Added `SharedmemRecording` for shared memory recordings (#2365) | ||
| * Added machinery for moving/interpolating templates for generating hybrid recordings with drift (#2291) | ||
| * Added new fast method for unit/spike/peak localization: `grid_convolution` (#2172) | ||
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| core: | ||
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| * Add `Templates` class (#1982) | ||
| * Use python methods instead of parsing and eleminate try-except in to_dict | ||
| (#2157) | ||
| * `WaveformExtractor.is_extension` --> `has_extension` (#2158) | ||
| * Speed improvement to `get_empty_units()` (#2173) | ||
| * Allow precomputing spike trains (#2175) | ||
| * Add 'percentile' to template modes and `plot_unit_templates` (#2179) | ||
| * Add `rename_units` method in sorting (#2207) | ||
| * Add an option for count_num_spikes_per_unit (#2209) | ||
| * Remove joblib in favor of `ParallelProcessExecutor` (#2218) | ||
| * Fixed a bug when caching recording noise levels (#2220) | ||
| * Various fixes for Windows (#2221) | ||
| * Fix num_samples in concatenation (#2223) | ||
| * Disable writing templates modes npy in read-only mode (#2251) | ||
| * Assert renamed_channels/unit_ids is unique (#2252) | ||
| * Implement save_to_zarr for BaseSorting (#2254) | ||
| * Improve the BaseExtractor.to_dict() relative_to machanism to make it safer on Windows (#2279) | ||
| * Make sure sampling frequency is always float (#2283) | ||
| * `NumpySorting.from_peaks`: make `unit_ids` mandatory (#2315) | ||
| * Make chunksize in `get_random_data_chunks` throw warning and clip if under limit (#2321) | ||
| * ids can be a tuple in `ids_to_indices` (#2324) | ||
| * `get_num_frames` to return a python int (#2326) | ||
| * Add an auto adjustment if n_jobs too high on Windows (#2329) | ||
| * Cache spike_vector from parent (#2353) | ||
| * Refactor recording tools (#2363) | ||
| * Add rename_channels method to recording extractors (#2364) | ||
| * Create `SharedmemRecording` (#2365) | ||
| * `WaveformExtractor.select_units` also functional if `we.has_recording()=False` (#2368) | ||
| * Add zarrrecordingextractor.py for backward compatibility (#2377, #2395, #2451) | ||
| * Improve `ZarrSortingExtractor` (#2403) | ||
| * Improvement to compute sparsity without `WaveformsExtractor` (#2410) | ||
| * Zarr backcompatibility: map `root_path` to `folder_path` (#2451) | ||
| * Fix spikes generation on borders (#2453) | ||
| * Zarr IO for `Templates` object (#2423) | ||
| * Avoid double parsing in Plexon (#2459) | ||
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| extractors: | ||
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| * Add .stream.cbin compatibility to `CompressedBinaryIblExtractor` (#2297) | ||
| * Add stream_folders path to `OpenEphysBinaryRecordingExtractor` (#2369) | ||
| * Deprecate `ignore_timestamps_errors` in `OpenEphysLegacyRecordingExtractor` (#2450) | ||
| * Better auto-guess of open-ephys format (#2465) | ||
| * Several improvements to NWB extractors: | ||
| * Add option for no caching option to the NWB extractor when streaming (#2246, #2248, #2268) | ||
| * Fix `NwbSortingExtractor` reading of ragged arrays (#2255) | ||
| * Add nwb sorting `remfile` support (#2275) | ||
| * Avoid loading `channel_name` property in `NwbRecordingExtractor` (#2285) | ||
| * Add hdf5 backend support for Nwb extractors (#2294, #2297, #2341) | ||
| * Refactor `NwbSortingSegment` (#2313) | ||
| * Add `t_start` argument to NwbSortingExtractor (#2333) | ||
| * Add support for NWB-Zarr enhancement and zarr streaming (#2441, #2464) | ||
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| preprocessing: | ||
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| * Fix filtering rounding error (#2189) | ||
| * Fix: save a copy of group ids in `CommonReferenceRecording` (#2215) | ||
| * Add `outside_channels_location` option in `detect_bad_channels` (#2250) | ||
| * Fix overflow problems with CAR (#2362) | ||
| * Fix for Silence periods (saving noise levels) (#2375) | ||
| * Add `DecimateRecording` (#2385) | ||
| * Add `margin_sd` argument to gaussian filtering (#2389) | ||
| * Faster Gaussian filter implementation preprocessing (#2420) | ||
| * Faster unpickling of ZScoreRecording (#2431) | ||
| * Add bit depth compensation to unsigned_to_signed (#2438) | ||
| * Renaming: `GaussianBandpassFilter` -> `GaussianFilter` (and option for low/high pass filter) (#2397, #2466) | ||
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| sorters: | ||
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| * Several updates to SpykingCircus2 (#2205, #2236, #2244, #2276) | ||
| * Handling segments in SpykingCircus2 and Tridesclous2 (#2208) | ||
| * A couple updates to `mountainsort5` sorter (#2225) | ||
| * `run_sorter` in containers: dump to json or pickle (#2271) | ||
| * `run_sorter` in containers: add several options for installing spikeinterface (#2273) | ||
| * Close `ShellScript` and pipes process at deletion (#2292, #2338) | ||
| * Remove deprecated direct function to `run_sorter` (e.g., `run_kilosort2` -> `run_sorter('kilosort2')` (#2355) | ||
| * Expose `lam` and `momentum` params in the appropriate kilosorts (#2358) | ||
| * Tridesclous2 update (#2267) | ||
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| postprocessing: | ||
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| * Use sampling_frequency instead of get_sampling_frequency in _make_bins (#2284) | ||
| * Multi-channel template metrics fix (#2323) | ||
| * Fix bug in get_repolarization_slope with wrong index type (#2432) | ||
| * Estimation of depth for `grid_convolution` localization (#2172) | ||
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| qualitymetrics: | ||
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| * Implemented sd_ratio as quality metric (#2146, #2402) | ||
| * Avoid duplicated template and quality metric names (#2210) | ||
| * Fix rp_violations when specifying unit_ids (#2247) | ||
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| curation: | ||
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| * Fix bug in `mergeunits` (#2443) | ||
| * Fix sortingview curation and merge units with array properties (#2427) | ||
| * Move computation away from __init__ in duplicated spikes (#2446) | ||
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| widgets: | ||
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| * Sorting summary updates in sortingview (#2318) | ||
| * Add a more robust `delta_x` to unit_waveforms (#2287) | ||
| * Prevent users from providing a `time_range` after the ending of the segment in `plot_traces` (#2286) | ||
| * Fix sortingview checks for NaN if strings (#2243) | ||
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| generation: | ||
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| * Creation of a TransformSorting object to track modifications and bencharmk (#1999) | ||
| * Add a minimum distance in generate_unit_locations (#2147) | ||
| * Add Poisson statistics to generate_sorting and optimize memory profile (#2226) | ||
| * Fix add_shift_shuffle section in synthesize_random_firings (#2334) | ||
| * Machinery for moving templates and generating hybrid recordings with drift (#2291) | ||
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| sortingcomponents: | ||
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| * Strict inegality for sparsity with radius_um (#2277) by yger was merged on Dec 1, 2023 | ||
| * Fix memory leak in lsmr solver and optimize correct_motion (#2263) | ||
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| docs: | ||
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| * Various improvements to docs (#2168, #2229, #2407) | ||
| * Improve `ids_to_indices` docstring (#2301) | ||
| * Fix for docstring of `get_traces` (#2320) | ||
| * Fix RTD warnings (#2348) | ||
| * Improve CMR docstring (#2354) | ||
| * Correct warning format in neo base extractors (#2357) | ||
| * Typo fix for verbose setting in `Multicomparison` (#2399) | ||
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| ci / packaging / tests: | ||
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| * Add tests for unique names in channel slice and unit selection (#2258) | ||
| * Add from `__future__` import annotations to all files for Python3.8 (#2340, #2468) | ||
| * Add pickling test to streamers (#2170) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| [project] | ||
| name = "spikeinterface" | ||
| version = "0.100.0.dev0" | ||
| version = "0.100.0" | ||
| authors = [ | ||
| { name="Alessio Buccino", email="[email protected]" }, | ||
| { name="Samuel Garcia", email="[email protected]" }, | ||
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@@ -23,9 +23,9 @@ dependencies = [ | |
| "numpy", | ||
| "threadpoolctl>=3.0.0", | ||
| "tqdm", | ||
| "zarr>=2.15", | ||
| "neo>=0.12.0", | ||
| "probeinterface>=0.2.19", | ||
| "zarr>=0.2.16", | ||
| "neo>=0.13.0", | ||
| "probeinterface>=0.2.21", | ||
| ] | ||
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| [build-system] | ||
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@@ -119,8 +119,8 @@ test_core = [ | |
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| # 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", | ||
| ] | ||
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| test = [ | ||
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@@ -152,8 +152,8 @@ test = [ | |
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| # 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", | ||
| ] | ||
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| docs = [ | ||
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@@ -170,8 +170,8 @@ docs = [ | |
| "hdbscan>=0.8.33", # For sorters spykingcircus2 + tridesclous | ||
| "numba", # For many postprocessing functions | ||
| # 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 | ||
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| ] | ||
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