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[project]
name = "dipy"
description = "Diffusion MRI Imaging in Python"
license = {file = "LICENSE"}
readme = "README.rst"
requires-python = ">=3.10"
authors = [{ name = "DIPY developers", email = "dipy@python.org" }]
maintainers = [
{name = "Eleftherios Garyfallidis", email="neuroimaging@python.org"},
{name = "Ariel Rokem", email="neuroimaging@python.org"},
{name = "Serge Koudoro", email="neuroimaging@python.org"},
]
keywords = ["dipy", "diffusionimaging", "dti", "tracking", "tractography",
"diffusionmri", "mri", "tractometry", "connectomics", "brain",
"dipymri", "microstructure", "deeplearning", "registration",
"segmentations", "simulation", "medical", "imaging", "brain",
"machinelearning", "signalprocessing"]
classifiers = [
'Development Status :: 4 - Beta',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Programming Language :: Python',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
'Programming Language :: Python :: 3.12',
'Programming Language :: Python :: 3 :: Only',
"Topic :: Software Development :: Libraries",
'Topic :: Scientific/Engineering',
"Operating System :: OS Independent",
'Operating System :: Microsoft :: Windows',
'Operating System :: POSIX',
'Operating System :: Unix',
'Operating System :: MacOS',
]
version = "1.11.0"
dependencies = [
"numpy>=1.22.4",
"scipy>=1.8",
"nibabel>=3.0.0",
"h5py>=3.1.0",
"packaging>=21",
"tqdm>=4.30.0",
"trx-python>=0.3.0",
]
[project.scripts]
dipy_align_syn = "dipy.workflows.cli:run"
dipy_align_affine = "dipy.workflows.cli:run"
dipy_apply_transform = "dipy.workflows.cli:run"
dipy_buan_shapes = "dipy.workflows.cli:run"
dipy_buan_profiles = "dipy.workflows.cli:run"
dipy_buan_lmm = "dipy.workflows.cli:run"
dipy_bundlewarp = "dipy.workflows.cli:run"
dipy_classify_tissue = "dipy.workflows.cli:run"
dipy_correct_biasfield = "dipy.workflows.cli:run"
dipy_correct_motion = "dipy.workflows.cli:run"
dipy_denoise_nlmeans = "dipy.workflows.cli:run"
dipy_denoise_lpca = "dipy.workflows.cli:run"
dipy_denoise_mppca = "dipy.workflows.cli:run"
dipy_denoise_patch2self = "dipy.workflows.cli:run"
dipy_evac_plus = "dipy.workflows.cli:run"
dipy_fetch = "dipy.workflows.cli:run"
dipy_fit_csa = "dipy.workflows.cli:run"
dipy_fit_csd = "dipy.workflows.cli:run"
dipy_fit_dki = "dipy.workflows.cli:run"
dipy_fit_dsi = "dipy.workflows.cli:run"
dipy_fit_dsid = "dipy.workflows.cli:run"
dipy_fit_dti = "dipy.workflows.cli:run"
dipy_fit_forecast = "dipy.workflows.cli:run"
dipy_fit_gqi = "dipy.workflows.cli:run"
dipy_fit_ivim = "dipy.workflows.cli:run"
dipy_fit_mapmri = "dipy.workflows.cli:run"
dipy_fit_opdt = "dipy.workflows.cli:run"
dipy_fit_qball = "dipy.workflows.cli:run"
dipy_fit_sdt = "dipy.workflows.cli:run"
dipy_fit_sfm = "dipy.workflows.cli:run"
dipy_math = "dipy.workflows.cli:run"
dipy_mask = "dipy.workflows.cli:run"
dipy_gibbs_ringing = "dipy.workflows.cli:run"
dipy_horizon = "dipy.workflows.cli:run"
dipy_info = "dipy.workflows.cli:run"
dipy_extract_b0 = "dipy.workflows.cli:run"
dipy_extract_shell = "dipy.workflows.cli:run"
dipy_extract_volume = "dipy.workflows.cli:run"
dipy_labelsbundles = "dipy.workflows.cli:run"
dipy_median_otsu = "dipy.workflows.cli:run"
dipy_recobundles = "dipy.workflows.cli:run"
dipy_reslice = "dipy.workflows.cli:run"
dipy_sh_convert_mrtrix = "dipy.workflows.cli:run"
dipy_snr_in_cc = "dipy.workflows.cli:run"
dipy_split = "dipy.workflows.cli:run"
dipy_track = "dipy.workflows.cli:run"
dipy_track_pft = "dipy.workflows.cli:run"
dipy_slr = "dipy.workflows.cli:run"
dipy_concatenate_tractograms = "dipy.workflows.cli:run"
dipy_convert_tractogram = "dipy.workflows.cli:run"
dipy_convert_tensors = "dipy.workflows.cli:run"
dipy_convert_sh = "dipy.workflows.cli:run"
dipy_nifti2pam = "dipy.workflows.cli:run"
dipy_pam2nifti = "dipy.workflows.cli:run"
dipy_tensor2pam = "dipy.workflows.cli:run"
[project.optional-dependencies]
all = ["dipy[dev,doc,style,test, viz, ml, extra, benchmark]"]
style = ["ruff", "pre-commit"]
viz = ["fury>=0.10.0", "matplotlib"]
test = ["pytest", "coverage", "coveralls", "codecov"]
ml = ["scikit_learn", "pandas", "statsmodels>=0.14.0", "tables", "tensorflow>=2.18.0", "torch"]
dev = [
# Also update [build-system] -> requires
'meson-python>=0.13',
'wheel',
'setuptools~=69.5',
'packaging>=21',
'ninja',
'Cython>=0.29.35',
'numpy>=1.22.4',
# Developer UI
'spin>=0.5',
'build',
]
extra = ["dipy[viz, ml]",
"cvxpy",
"scikit-image",
"boto3",
"numexpr"
]
doc = [
"numpydoc",
"sphinx>=7.2.6",
"texext",
"tomli; python_version < \"3.11\"",
"sphinxcontrib-bibtex",
"sphinx_design",
"sphinx-gallery>=0.10.0",
"tomli>=2.0.1",
"grg-sphinx-theme>=0.4.0",
"Jinja2"
]
benchmark = [
"asv",
"pyperf",
"virtualenv",
]
[project.urls]
homepage = "https://dipy.org"
documentation = "https://docs.dipy.org/stable/"
source = "https://github.com/dipy/dipy"
download = "https://pypi.org/project/dipy/#files"
tracker = "https://github.com/dipy/dipy/issues"
[build-system]
build-backend = "mesonpy"
requires = [
"meson-python>=0.13.1",
"Cython>=3.0.4",
"packaging>21.0",
"wheel",
# numpy requirement for wheel builds for distribution on PyPI - building
# against 2.x yields wheels that are also compatible with numpy 1.x at
# runtime.
# Note that building against numpy 1.x works fine too - users and
# redistributors can do this by installing the numpy version they like and
# disabling build isolation.
"numpy>=2.0.0rc1; python_version>='3.10' and platform_python_implementation!='PyPy'",
"numpy; python_version>='3.10' and platform_python_implementation=='PyPy'",
]
[tool.spin]
package = 'dipy'
[tool.spin.commands]
Build = [
"spin.cmds.meson.build",
"spin.cmds.meson.test",
"spin.cmds.build.sdist",
".spin/cmds.py:clean"
]
Environments = [
"spin.cmds.meson.run",
"spin.shell",
"spin.ipython",
"spin.python"
]
"Documentation" = [
"spin.cmds.meson.docs",
# ".spin/cmds.py:docs"
]
Metrics = [
".spin/cmds.py:bench",
# ".spin/cmds.py:coverage
]
# TODO: Add custom commands
[tool.pytest.ini_options]
addopts = "--ignore=dipy/testing/decorators.py --ignore-glob='bench*.py' --ignore-glob=**/benchmarks/*"
filterwarnings = [
# FURY
"ignore:.*You do not have FURY installed.*:UserWarning",
# pkg_resources (via Ray)
"ignore:Implementing implicit namespace packages.*:DeprecationWarning",
"ignore:Deprecated call to `pkg_resources.*:DeprecationWarning",
"ignore:pkg_resources is deprecated as an API.*:DeprecationWarning",
]
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