pyproject.toml

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

[project]
name = 'fastsurfer'
version = '2.7.0.dev0'
description = 'A fast and accurate deep-learning based neuroimaging pipeline'
readme = 'README.md'
license = { file = 'LICENSE' }
requires-python = '>=3.12'
authors = [{ name = 'FastSurfer Developers' }]
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 :: 3.12',
    'Programming Language :: Python :: 3.13',
    'Programming Language :: Python :: 3.14',
    'Natural Language :: English',
    'License :: OSI Approved :: Apache Software License',
    'Intended Audience :: Science/Research',
]
dependencies = [
    'h5py>=3.7',
    'lapy>=1.5.0',
    'libigl>=2.6.0', # needed for the cortical ribbon
    'matplotlib>=3.7.1',
    'meshpy>=2025.1.1', # needed for FastSurfer-CC
    'monai>=1.4.0', # needed for FastSurfer-CC
    'neuroreg>=0.6.2', # needed for registration / etiv
    'nibabel>=5.4.0', # needed to fix a bug in nibabel
    '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==2.14.*', # pinned to 2.14
    'torchio>=0.18.83',
    'torchvision>=0.29.0,<0.30.0',
    'tqdm>=4.65',
    'yacs>=0.1.8',
]

[project.optional-dependencies]
qc = [
    'whippersnappy>=2.1',
]
lit = [
    'neurolit>=0.7.0',
]
container = [
    'fastsurfer[qc]',
    'fastsurfer[lit]',
]
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',
    # 0.6.0 breaks parallel builds; 0.6.1 emits warnings for unrelated MyST links.
    'sphinx-argparse<0.6',
    'sphinx-copybutton',
    'sphinx-design',
    'sphinx-gallery',
    'sphinx-issues',
    'pypandoc',
    'nbsphinx',
    'IPython', # For syntax highlighting in notebooks
    'ipykernel',
]
style = [
    'bibclean',
    'codespell',
    'pydocstyle[toml]',
    'ruff',
    'ty',
]
pipelinetest = [
    'pytest>=8.2.2',
]
all = [
    'fastsurfer[doc]',
    'fastsurfer[style]',
    'fastsurfer[qc]',
    'fastsurfer[lit]',
    'fastsurfer[pipelinetest]',
]
full = [
    'fastsurfer[all]',
]

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

[tool.python]
# The single exact python version FastSurfer is built and shipped with.
#
# Who uses it today:
#   - tools/Docker/Dockerfile reads this key from the pyproject.toml in the build context, with
#     tools/read_toml.py run by uv.
#   - tools/macos_build/build_release_package.sh reads it to fetch the relocatable standalone
#     CPython it bundles into the installer, and substitutes it into the paths that name the
#     version: python/bin/python<version>, python/lib/python<version>/site-packages.
#   - tools/update_requirements.sh reads it to resolve requirements.txt for this version.
#   - .github/workflows/deploy.yml reads it for the key of the uv cache of the macOS package build.
#   - One place keeps a hardcoded copy because it cannot read this file: the python-version in
#     .github/workflows/pipelinetest.yaml (that step provides the interpreter which then reads
#     this file). test/lint/test_python_version.py asserts it against this key.
#   - doc/conf.py reads this key for {{ PYTHON_VERSION }} in the documentation, from the release
#     the documentation refers to.
#   - NOT .github/workflows/unittest.yaml, which pins the requires-python floor on purpose.
#
# This key is deliberately separate from project.requires-python, which answers a different
# question: requires-python is the support *floor*, a range, and is what pip enforces for anyone
# doing `pip install fastsurfer`. This key is the one *exact* version we build against, which a
# range cannot express -- wheels are cp3XX-tagged, so anything shipping a pre-resolved
# environment needs an exact version.
#
# Raising this version also requires updating the following:
#   - requirements.txt, regenerated for the new interpreter (tools/update_requirements.sh)
#   - the hardcoded copy listed above (CI will fail if you miss it)
version = "3.14"

[tool.freesurfer]
version = "8.2.0"
# The following URLs use the {version} placeholder, which should be replaced
# with the actual version string using Python's .format(version=...).
# tools/Docker/Dockerfile reads version and urls.linux from this file.
# FreeSurfer 8 ships packages, not tarballs. On linux the Rocky 8 rpm: its binaries are
# self-contained, while the Ubuntu debs link the system ITK, VTK and Qt and leave out the talairach
# (4dfp) tools. On macOS the arm64 pkg, the only architecture the FastSurfer package is built for.
[tool.freesurfer.urls]
linux = "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/{version}/freesurfer-Rocky8-{version}-1.x86_64.rpm"
macOS = "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/{version}/freesurfer-macOS-darwin_arm64-{version}.pkg"

[tool.cuda]
# The default CUDA version of the docker images, which the `latest` image is built for. The PyTorch
# backend is cu<version without dots> (13.2 -> cu132), and the --device alias cuda of
# tools/Docker/build.py resolves to it.
#
# Who uses it today:
#   - tools/Docker/build.py, for --device cuda and the tag fastsurfer:dev.
#   - tools/update_requirements.sh, for the install example in the header of requirements.txt.
#   - doc/conf.py reads this key for {{ CUDA_VERSION }} and {{ CUDA_STRING }} in the documentation,
#     from the release the documentation refers to.
#
# Raising this version (or tool.rocm.version) also requires that the torch pinned in
# project.dependencies ships wheels for the backend, and that DeviceType and AllDeviceType in
# tools/Docker/build.py list it.
version = "13.2"

[tool.rocm]
# The default ROCm version of the docker images. The PyTorch backend is rocm<version> (7.2 ->
# rocm7.2), and the --device alias rocm of tools/Docker/build.py resolves to it. PyTorch also
# publishes builds for newer ROCm versions than uv's --torch-backend accepts (rocm7.14 for torch
# 2.14), so this is the newest one uv can install.
version = "7.2"

[tool.docker]
# The default base images of the docker images that tools/Docker/build.py builds: build_base for the
# stages that build the python environment and FreeSurfer, runtime_base for the runtime image.
#
# Who uses it today:
#   - tools/Docker/build.py, as the defaults of --build_base_image and --runtime_base_image.
#   - doc/conf.py reads runtime_base for {{ UBUNTU_VERSION }} in the documentation, from the release
#     the documentation refers to, so it has to be an ubuntu image.
#   - tools/Docker/Dockerfile keeps copies as the defaults of ARG BUILD_BASE_IMAGE and
#     ARG RUNTIME_BASE_IMAGE, for a direct `docker build`.
build_base = "ubuntu:24.04"
runtime_base = "ubuntu:24.04"

[tool.setuptools.packages.find]
# an explicit `packages = [...]` list is not recursive, so it silently dropped every subpackage
# (FastSurferCNN.utils, CerebNet.models, ...) and, since it was added, CorpusCallosum as well
include = ['FastSurferCNN*', 'CerebNet*', 'CorpusCallosum*', 'HypVINN*', 'recon_surf*']
# PyPI: tools/Docker/fastsurfer_startup.{py,pth,start} are not packaged (build_venv copies them); a
# wheel has to put them at the site-packages root via a build_py override in setup.py. The hook then
# runs in every non-editable install, and the .pth, needed below python 3.15, must go before 3.20.

[tool.setuptools.package-data]
# without this, only .py files are installed, and the package cannot find its own configs at
# runtime (checkpoint_paths.yaml, the network configs, the color lookup tables, ...).
# The shell scripts are needed because Python code reads them, e.g.
# recon_surf/long_compat_segmentHA.py parses recon-surf.sh for the supported FreeSurfer version
# while building its argument parser.
'*' = ['*.yaml', '*.tsv', '*.txt', '*.json', '*.csv', '*.sh']

[tool.pydocstyle]
convention = 'numpy'
ignore-decorators = '(copy_doc|property|.*setter|.*getter|pyqtSlot|Slot)'
match = '^(?!setup|__init__|test_).*\.py'
# match-dir is a single regex matched against each directory name while walking (not a list): an
# allow-list of the package roots would also prune their subdirectories (utils, models, config,
# ...), so exclude the non-package directories instead
match-dir = '^(?!\.|__pycache__$|build$|checkpoints$|doc$|Documentation$|env$|test$|tools$|Tutorial$).*'
add_ignore = 'D100,D104,D107'

[tool.ruff]
line-length = 120
target-version = "py312"
# recon_surf/fs_time is python, but carries no .py suffix because the pipeline invokes it as a
# command; without this ruff would skip it
extend-include = ["recon_surf/fs_time"]
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
    "NPY201", # numpy 2
]

[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 --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