diff --git a/doc/releases/0.101.0.rst b/doc/releases/0.101.0.rst index c34cd0dc8e..0e686cca1a 100644 --- a/doc/releases/0.101.0.rst +++ b/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: diff --git a/doc/releases/0.101.1.rst b/doc/releases/0.101.1.rst new file mode 100644 index 0000000000..eeb54566a6 --- /dev/null +++ b/doc/releases/0.101.1.rst @@ -0,0 +1,144 @@ +.. _release0.101.1: + +SpikeInterface 0.101.1 release notes +------------------------------------ + +16th 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 deprecated `from_ptp` option (#3369) +* Dropped support for Python<3.9 (#3267) + +core: + +* Update the method of creating an empty file with right size when saving binary files (#3408) +* 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 metrics widgets for convert_dtypes (#3417) +* 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 +* @chrishalcrow +* @cwindolf +* @florian6973 +* @h-mayorquin +* @jiumao2 +* @jonahpearl +* @mhhennig +* @rkim48 +* @samuelgarcia +* @tabedzki +* @zm711 diff --git a/doc/scripts/auto-release-notes.sh b/doc/scripts/auto-release-notes.sh index 14bee3dad0..f3818e1e18 100644 --- a/doc/scripts/auto-release-notes.sh +++ b/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 diff --git a/doc/whatisnew.rst b/doc/whatisnew.rst index 94da5d15fb..c8038387f9 100644 --- a/doc/whatisnew.rst +++ b/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 deprecated `from_ptp` option (#3369) +* Dropped support for Python<3.9 (#3267) + + Version 0.101.0 =============== diff --git a/pyproject.toml b/pyproject.toml index b5894bf3a5..c1c02db8db 100644 --- a/pyproject.toml +++ b/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 ] diff --git a/src/spikeinterface/__init__.py b/src/spikeinterface/__init__.py index 306c12d516..97fb95b623 100644 --- a/src/spikeinterface/__init__.py +++ b/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