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238 lines (201 loc) · 5.7 KB
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[project]
name = "spikeinterface"
version = "0.102.3"
authors = [
{ name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
{ name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
]
description = "Python toolkit for analysis, visualization, and comparison of spike sorting output"
readme = "README.md"
requires-python = ">=3.9,<3.14"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
"License :: OSI Approved :: MIT License",
"Intended Audience :: Science/Research",
"Operating System :: POSIX :: Linux",
"Operating System :: Microsoft :: Windows",
"Operating System :: MacOS",
"Operating System :: OS Independent"
]
dependencies = [
"numpy>=1.20;python_version<'3.13'",
"numpy>=2.0.0;python_version>='3.13'",
"threadpoolctl>=3.0.0",
"tqdm",
"zarr>=2.18,<3",
"neo>=0.14.0",
"probeinterface>=0.2.23",
"packaging",
"numcodecs<0.16.0", # For supporting zarr < 3
]
[build-system]
requires = ["setuptools>=78.0.2"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
include-package-data = true
package-data = {"spikeinterface.sorters" = ["**/*.m", "**/*.prm", "**/*.params", "**/*.yaml"]}
[tool.setuptools.exclude-package-data]
spikeinterface = ["**/tests/test_*"]
[tool.setuptools.packages.find]
where = ["src"]
include = ["spikeinterface*"]
namespaces = false
exclude = ["spikeinterface.*.tests"]
[tool.black]
line-length = 120
[project.urls]
homepage = "https://github.com/SpikeInterface/spikeinterface"
repository = "https://github.com/SpikeInterface/spikeinterface"
documentation = "https://spikeinterface.readthedocs.io/"
changelog = "https://spikeinterface.readthedocs.io/en/latest/whatisnew.html"
[project.optional-dependencies]
extractors = [
"MEArec>=1.8",
"pynwb>=2.6.0",
"hdmf-zarr>=0.11.0",
"pyedflib>=0.1.30,<0.1.39",
"sonpy;python_version<'3.10'",
"lxml", # lxml for neuroscope
"scipy",
"ibllib", # streaming IBL
"pymatreader>=0.0.32", # For cell explorer matlab files
"zugbruecke>=0.2; sys_platform!='win32'", # For plexon2
]
streaming_extractors = [
"ibllib", # streaming IBL
# Following dependencies are for streaming with nwb files
"pynwb>=2.6.0",
"fsspec",
"aiohttp",
"requests",
"hdmf-zarr>=0.11.0",
"remfile",
"s3fs"
]
preprocessing = [
"scipy",
]
full = [
"h5py",
"pandas",
"scipy",
"scikit-learn",
"networkx",
"distinctipy",
"matplotlib>=3.6", # matplotlib.colormaps
"cuda-python; platform_system != 'Darwin'",
"numba",
"skops",
"huggingface_hub"
]
widgets = [
"matplotlib",
"ipympl",
"ipywidgets",
"sortingview>=0.12.0",
]
qualitymetrics = [
"scikit-learn",
"scipy",
"pandas",
"numba",
]
test_core = [
"pytest",
"pytest-dependency",
"psutil",
# 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",
]
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", # for IBL
"torch",
]
test = [
"pytest",
"pytest-dependency",
"pytest-cov",
"psutil",
"huggingface_hub",
# preprocessing
"ibllib", # for IBL
# streaming templates
"s3fs",
# tridesclous
"numba<0.61.0;python_version<'3.13'",
"numba>=0.61.0;python_version>='3.13'",
"hdbscan>=0.8.33", # Previous version had a broken wheel
# for sortingview backend
"sortingview>=0.12.0",
# for motion and sortingcomponents
"torch",
# curation
"skops",
"huggingface_hub",
# 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",
]
docs = [
"Sphinx",
"sphinx_rtd_theme>=1.2",
"sphinx-gallery",
"sphinx-design",
"numpydoc",
"ipython",
"sphinxcontrib-jquery",
# for notebooks in the gallery
"MEArec", # Use as an example
"pandas", # in the modules gallery comparison tutorial
"hdbscan>=0.8.33", # For sorters spykingcircus2 + tridesclous
"numba", # For many postprocessing functions
"networkx",
"skops", # For auotmated curation
"scikit-learn", # For auotmated curation
# Download data
"pooch>=1.8.2",
"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
]
dev = [
"spikeinterface[test]",
"spikeinterface[test_core]",
"spikeinterface[docs]",
"black",
"pre-commit",
]
[tool.pytest.ini_options]
markers = [
"core",
"generation",
"extractors",
"preprocessing",
"postprocessing",
"qualitymetrics",
"sorters",
"sorters_external",
"sorters_internal",
"comparison",
"curation",
"exporters",
"widgets",
"sortingcomponents",
"streaming_extractors: extractors that require streaming such as ross and fsspec",
]
filterwarnings =[
'ignore:.*distutils Version classes are deprecated.*:DeprecationWarning',
'ignore:.*the imp module is deprecated in favour of importlib.*:DeprecationWarning',
]