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Merge pull request #3370 from SpikeInterface/prepare_release
Prepare release 0.101.1
2 parents 55c7de1 + 086e8c7 commit 4ab6223

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‎doc/releases/0.101.0.rst‎

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SpikeInterface 0.101.0 release notes
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------------------------------------
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Estimated: 19th July 2024
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19th July 2024
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Main changes:
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‎doc/releases/0.101.1.rst‎

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.. _release0.101.1:
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SpikeInterface 0.101.1 release notes
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------------------------------------
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16th September 2024
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Main changes:
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* Enabled support for consolidated Zarr-backend for `SortingAnalyzer`, including cloud support (#3314, #3318, #3349, #3351)
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* Improved support for Kilosort4 **ONLY VERSIONS >= 4.0.16** (#3339, #3276)
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* Skip recomputation of quality and template metrics if already computed (#3292)
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* Improved `estimate_sparsity` with new `amplitude` method and deprecated `from_ptp` option (#3369)
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* Dropped support for Python<3.9 (#3267)
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core:
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* Update the method of creating an empty file with right size when saving binary files (#3408)
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* Refactor pandas save load and convert dtypes (#3412)
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* Check run info completed only if it exists (back-compatibility) (#3407)
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* Fix argument spelling in check for binary compatibility (#3409)
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* Fix proposal for channel location when probegroup (#3392)
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* Fix time handling test memory (#3379)
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* Add `BaseRecording.reset_times()` function (#3363, #3380, #3391)
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* Extend `estimate_sparsity` methods and update `from_ptp`` (#3369)
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* Add `load_sorting_analyzer_or_waveforms` function (#3352)
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* Fix zarr folder suffix handling (#3349)
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* Analyzer extension exit status (#3347)
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* Lazy loading of zarr timestamps (#3318)
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* Enable cloud-loading for analyzer Zarr (#3314, #3351, #3378)
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* Refactor `set_property` in base (#3287)
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* Job kwargs fix (#3259)
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* Add `is_filtered` to annotations in `binary.json` (#3245)
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* Add check for None in `NoiseGeneratorRecordingSegment`` get_traces() (#3230)
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extractors:
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* Load phy channel_group as group (#3368)
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* "quality" property to be read as string instead of object in `BasePhyKilosortSortingExtractor` (#3365)
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preprocessing:
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* Auto-cast recording to float prior to interpolation (#3415)
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* Update doc handle drift + better preset (#3232)
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* Add causal filtering to filter.py (#3172)
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sorters:
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* Updates to kilosort 4: version >= 4.0.16, `bad_channels`, `clear_cache`, `use_binary_file` (#3339)
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* Download apptainer images without docker client (#3335)
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* Expose save preprocessing in ks4 (#3276)
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* Fix KS2/2.5/3 skip_kilosort_preprocessing (#3265)
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* HS: Added lowpass parameter, fixed verbose option (#3262)
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* Now exclusive support for HS v0.4 (Lightning) (#3210)
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postprocessing:
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* Add extra protection for template metrics (#3364)
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* Protect median against nans in get_prototype_spike (#3270)
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* Fix docstring and error for spike_amplitudes (#3269)
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qualitymetrics:
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* Do not delete quality and template metrics on recompute (#3292)
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* Refactor quality metrics tests to use fixture (#3249)
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curation:
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* Clean-up identity merges in `get_potential_auto_merges` (#3346)
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* Fix sortingview curation no merge case (#3309)
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* Start apply_curation() (#3208)
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widgets:
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* Fix metrics widgets for convert_dtypes (#3417)
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* Fix plot motion for multi-segment (#3414)
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* Sortingview: only round float properties (#3406)
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* Fix widgets tests and add test on unit_table_properties (#3354)
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* Allow quality and template metrics in sortingview's unit table (#3299)
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* Add subwidget parameters for UnitSummaryWidget (#3242)
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* Fix `ipympl`/`widget` backend check (#3238)
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generators:
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* Handle case where channel count changes from probeA to probeB (#3237)
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sortingcomponents:
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* Update doc handle drift + better preset (#3232)
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* Make `InterpolateMotionRecording`` not JSON-serializable (#3341)
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documentation:
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* Clarify meaning of `delta_time` in `compare_sorter_to_ground_truth` (#3360)
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* Added sphinxcontrib-jquery (#3307)
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* Adding return type annotations (#3304)
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* More docstring updates for multiple modules (#3298)
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* Fix sampling frequency repr (#3294)
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* Proposal for adding Examples to docstrings (#3279)
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* More numpydoc fixes (#3275)
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* Fix docstring and error for spike_amplitudes (#3269)
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* Fix postprocessing docs (#3268)
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* Fix name of principal_components ext in qm docs (take 2) (#3261)
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* Update doc handle drift + better preset (#3232)
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* Add `int` type to `num_samples` on `InjectTemplatesRecording`. (#3229)
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continuous integration:
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* Fix streaming extractor condition in the CI (#3362)
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packaging:
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* Minor typing fixes (#3374)
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* Drop python 3.8 in pyproject.toml (#3267)
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testing:
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* Fix time handling test memory (#3379)
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* Fix streaming extractor condition in the CI (#3362)
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* Test IBL skip when the setting up the one client fails (#3289)
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* Refactor `set_property` in base (#3287)
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* Refactor quality metrics tests to use fixture (#3249)
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* Add kilosort4 wrapper tests (#3085)
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* Test IBL skip when the setting up the one client fails (#3289)
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* Add kilosort4 wrapper tests (#3085)
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Contributors:
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* @Djoels
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* @JoeZiminski
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* @JuanPimientoCaicedo
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* @alejoe91
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* @chrishalcrow
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* @cwindolf
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* @florian6973
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* @h-mayorquin
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* @jiumao2
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* @jonahpearl
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* @mhhennig
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* @rkim48
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* @samuelgarcia
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* @tabedzki
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* @zm711

‎doc/scripts/auto-release-notes.sh‎

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

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

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

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

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