pyproject.toml

[project]
name = "dipy"
description = "Diffusion MRI Imaging in Python"
license = {file = "LICENSE"}
readme = "README.rst"
requires-python = ">=3.9"
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 :: 3.9',
    'Programming Language :: Python :: 3.10',
    'Programming Language :: Python :: 3.11',
    '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',
]
dynamic = ['version']
dependencies = [
    "numpy>=1.22.4",
    "scipy>=1.8",
    "nibabel>=3.0.0",
    "h5py>=3.1.0",
    "packaging>=21",
    "tqdm>=4.30.0",
    "trx-python>=0.2.9",
]

[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_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_dti = "dipy.workflows.cli:run"
dipy_fit_dsi = "dipy.workflows.cli:run"
dipy_fit_ivim = "dipy.workflows.cli:run"
dipy_fit_mapmri = "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_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"

[project.optional-dependencies]
all = ["dipy[dev,doc,style,test, viz, ml, extra]"]
style = ["ruff", "pre-commit"]
viz = ["fury>=0.10.0", "matplotlib"]
test = ["pytest", "coverage", "coveralls", "codecov", "asv"]
ml = ["scikit_learn", "pandas", "statsmodels>=0.14.0", "tables", "tensorflow", "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<=1.4.4",
         "scikit-image",
         "boto3"
        ]

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"
]


[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>='3.9' and platform_python_implementation!='PyPy'",
    "numpy; python_version>='3.9' 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",
]