pyproject.toml

[build-system]
requires = ['setuptools >= 61.0.0']
build-backend = 'setuptools.build_meta'

[project]
name = 'fastsurfer'
version = '2.5.0-dev'
description = 'A fast and accurate deep-learning based neuroimaging pipeline'
readme = 'README.md'
license = {file = 'LICENSE'}
requires-python = '>=3.10'
authors = [{name = 'Martin Reuter et al.'}]
maintainers = [{name = 'FastSurfer Developers'}]
keywords = [
    'python',
    'Deep learning',
    'Segmentation',
    'Brain segmentation',
    'Brain analysis',
    'volumetry',
]
classifiers = [
    'Operating System :: Microsoft :: Windows',
    'Operating System :: Unix',
    'Operating System :: MacOS',
    'Programming Language :: Python :: 3 :: Only',
    'Programming Language :: Python :: 3.10',
    'Programming Language :: Python :: 3.11',
    'Programming Language :: Python :: 3.12',
    'Programming Language :: Python :: 3.13',
    'Natural Language :: English',
    'License :: OSI Approved :: Apache Software License',
    'Intended Audience :: Science/Research',
]
dependencies = [
    'h5py>=3.7',
    'lapy>=1.5.0',
    'matplotlib>=3.7.1',
    'meshpy>=2025.1.1', # needed for FastSurfer-CC
    'monai>=1.4.0', # needed for FastSurfer-CC
    'nibabel>=5.1.0',
    'numpy>=1.25',
    'packaging',
    'pandas>=1.5.3',
    'pip>=25.0',
    'pyrr>=0.10.3', # needed for FastSurfer-CC
    'pyyaml>=6.0',
    'requests>=2.31.0',
    'scikit-image>=0.19.3',
    'scikit-learn>=1.2.2',
    'scipy>=1.10.1,!=1.13.0',
    'simpleitk>=2.2.1',
    'tensorboard>=2.12.1',
    'torch==2.7.*', # pinned to 2.7, so compatibility to CUDA 11 is ensured for same torch version
    'torchio>=0.18.83',
    'torchvision>=0.22.1,<0.23',
    'tqdm>=4.65',
    'yacs>=0.1.8',
]

[project.optional-dependencies]
qc  = [
    'whippersnappy>=2.1',
]
doc = [
    'fastsurfer[qc]',
    'furo!=2023.8.17',
    'memory-profiler',
    'myst-parser',
    'numpydoc',
    # sphinx 8 handles importing of files differently in some manner and will cause the
    # build of the doc to fail. This will need to be addressed before we up to sphinx 8.
    'sphinx>=7.3,<8',
    'sphinxcontrib-bibtex',
    'sphinxcontrib-programoutput',
    'sphinx-argparse',
    'sphinx-copybutton',
    'sphinx-design',
    'sphinx-gallery',
    'sphinx-issues',
    'pypandoc',
    'nbsphinx',
    'IPython', # For syntax highlighting in notebooks
    'ipykernel',
]
style = [
    'bibclean',
    'codespell',
    'pydocstyle[toml]',
    'ruff',
]
quicktest = [
    'pytest>=8.2.2',
]
all = [
    'fastsurfer[doc]',
    'fastsurfer[style]',
    'fastsurfer[qc]',
    'fastsurfer[quicktest]',
]
full = [
    'fastsurfer[all]',
]

[project.urls]
homepage = 'https://fastsurfer.org'
documentation = 'https://fastsurfer.org'
source = 'https://github.com/Deep-MI/FastSurfer'
tracker = 'https://github.com/Deep-MI/FastSurfer/issues'

[tool.freesurfer]
version = "7.4.1"
# The following URLs use the {version} placeholder, which should be replaced
# with the actual version string using Python's .format(version=...).
[tool.freesurfer.urls]
linux = "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/{version}/freesurfer-linux-ubuntu22_amd64-{version}.tar.gz"
macOS = "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/{version}/freesurfer-macOS-darwin_x86_64-{version}.tar.gz"

[tool.setuptools]
packages = ['FastSurferCNN','CerebNet','recon_surf','HypVINN']

[tool.pydocstyle]
convention = 'numpy'
ignore-decorators = '(copy_doc|property|.*setter|.*getter|pyqtSlot|Slot)'
match = '^(?!setup|__init__|test_).*\.py'
match-dir = '^FastSurferCNN.*,^CerebNet.*,^recon-surf.*,^HypVINN.*'
add_ignore = 'D100,D104,D107'

[tool.ruff]
line-length = 120
target-version = "py310"
extend-exclude = [
    "build",
    "checkpoints",
    "doc",
    "env",
]

[tool.ruff.lint]
# https://docs.astral.sh/ruff/linter/#rule-selection
select = [
    "E",   # pycodestyle
    "F",   # Pyflakes
    "UP",  # pyupgrade
    "B",   # flake8-bugbear
    "I",   # isort
    # "SIM", # flake8-simplify
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"Tutorial/*.ipynb" = ["E501"]  # exclude "Line too long"
"FastSurferCNN/utils/logging.py" = ["F401"]  # exclude "Imported but unused"
"FastSurferCNN/utils/parser_defaults.py" = ["F401"]  # exclude "Imported but unused"

[tool.pytest.ini_options]
minversion = '6.0'
addopts = '--durations 20 --junit-xml=junit-results.xml --verbose'
filterwarnings = []

[tool.coverage.run]
branch = true
cover_pylib = false
omit = [
    '**/__init__.py',
]

[tool.coverage.report]
exclude_lines = [
    'pragma: no cover',
    'if __name__ == .__main__.:',
]
precision = 2