pyproject.toml

[build-system]
requires = [
  "setuptools",
  "wheel",
  "versioneer[toml]",
  "more-itertools>=8.0",
  "ninja",
  "packaging",
  "torch>=2.8.0",
  "numpy>=1.24,<3.0",
  "backports.tarfile"  # see https://github.com/Project-MONAI/MONAI/issues/8791
]
build-backend = "setuptools.build_meta"

[project]
name = "monai"
description = "AI Toolkit for Healthcare Imaging"
readme = { file = "README.md", content-type = "text/markdown" }
requires-python = ">=3.10"
license = { text = "Apache License 2.0" }
authors = [{ name = "MONAI Consortium", email = "monai.contact@gmail.com" }]
classifiers = [
  "Intended Audience :: Developers",
  "Intended Audience :: Education",
  "Intended Audience :: Science/Research",
  "Intended Audience :: Healthcare Industry",
  "Programming Language :: C++",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Topic :: Scientific/Engineering",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
  "Topic :: Scientific/Engineering :: Medical Science Apps.",
  "Topic :: Scientific/Engineering :: Information Analysis",
  "Topic :: Software Development",
  "Topic :: Software Development :: Libraries",
  "Typing :: Typed",
]
dependencies = [
  "torch>=2.8.0",
  "numpy>=1.24,<3.0"
]
dynamic = ["version"]

[project.urls]
Homepage = "https://project-monai.github.io/"
Documentation = "https://monai.readthedocs.io/"
"Bug Tracker" = "https://github.com/Project-MONAI/MONAI/issues"
"Source Code" = "https://github.com/Project-MONAI/MONAI"

[project.optional-dependencies]
# All dependencies are included here except some omitted for compatibility. Testing dependencies are typically not
# needed and so present only in "testing". Ensure requirement changes in other lists are reflected here as well.
all = [
  "clearml>=1.10.0rc0",
  "cucim-cu12; platform_system == 'Linux' and python_version <= '3.10'",
  "cucim-cu13; platform_system == 'Linux' and python_version >= '3.11'",
  "einops",
  "filelock<3.12.0",
  "fire",
  "gdown>=4.7.3",
  "h5py",
  "huggingface_hub",
  "imagecodecs; platform_system == 'Linux' or platform_system == 'Darwin'",
  "itk>=5.2",
  "jsonschema",
  "lmdb",
  "lpips==0.1.4",
  "matplotlib>=3.6.3",
  "MetricsReloaded @ git+https://github.com/Project-MONAI/MetricsReloaded@monai-support",
  "mlflow>=2.12.2,<3.13",
  "nibabel",
  "ninja",
  "nni; platform_system == 'Linux' and 'arm' not in platform_machine and 'aarch' not in platform_machine",
  "nvidia-ml-py",
  "onnx_graphsurgeon",
  "onnx>=1.13.0",
  "onnxruntime; python_version <= '3.10'",
  "onnxscript",
  "openslide-bin",
  "openslide-python",
  "optuna",
  "pandas",
  "pillow!=8.3.0",
  "polygraphy",
  "psutil",
  "pyamg>=5.0.0,<5.3.0",
  "pybind11",
  "pydicom",
  "pynrrd",
  "pytorch-ignite",
  "pyyaml",
  "requests",
  "segment_anything @ git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588",
  "scikit-image>=0.19.0",
  "scipy>=1.12.0",
  "tensorboard>=2.12.0",
  "tensorboardX",
  "tifffile; platform_system == 'Linux' or platform_system == 'Darwin'",
  "torchio",
  "torchvision",
  "tqdm>=4.47.0",
  "transformers>=4.53.0, <5.0",
  "zarr"
]
clearml = ["clearml>=1.10.0rc0"]
cucim = [
  "cucim-cu12; platform_system == 'Linux' and python_version <= '3.10'",
  "cucim-cu13; platform_system == 'Linux' and python_version >= '3.11'"
]
cupy = ["cupy-cuda13x!=14.1.0"]  # not in all, the choice between cuda12x and cuda13x that can't be resolved here
einops = ["einops"]
fire = ["fire"]
gdown = ["gdown>=4.7.3"]
h5py = ["h5py"]
huggingface_hub = ["huggingface_hub"]
hyena = ["nvsubquadratic>=0.1.1", "omegaconf", "einops"]  # omitted from all for compatibility
ignite = ["pytorch-ignite"]
imagecodecs = ["imagecodecs; platform_system == 'Linux' or platform_system == 'Darwin'"]
itk = ["itk>=5.2"]
jsonschema = ["jsonschema"]
lmdb = ["lmdb"]
lpips = ["lpips==0.1.4"]
matplotlib = ["matplotlib>=3.6.3"]
metrics_reloaded = ["MetricsReloaded @ git+https://github.com/Project-MONAI/MetricsReloaded@monai-support"]
mlflow = ["mlflow>=2.12.2,<3.13"]
nibabel = ["nibabel"]
nni = [
  "nni; platform_system == 'Linux' and 'arm' not in platform_machine and 'aarch' not in platform_machine",
  "filelock<3.12.0"  # https://github.com/microsoft/nni/issues/5523
]
onnx = ["onnx>=1.13.0", "onnxruntime; python_version <= '3.10'", "onnx_graphsurgeon", "onnxscript"]
openslide = ["openslide-python", "openslide-bin"]
optuna = ["optuna"]
pandas = ["pandas"]
pillow = ["pillow!=8.3.0"]  # https://github.com/python-pillow/Pillow/issues/5571
polygraphy = ["polygraphy"]
psutil = ["psutil"]
pyamg = ["pyamg>=5.0.0,<5.3.0"]
pybind11 = ["pybind11"]
pydicom = ["pydicom"]
pynrrd = ["pynrrd"]
pynvml = ["nvidia-ml-py"]
pyyaml = ["pyyaml"]
requests = ["requests"]
segment_anything = ["segment_anything @ git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588"]
scipy = ["scipy>=1.12.0"]
skimage = ["scikit-image>=0.19.0"]
tensorboard = ["tensorboard>=2.12.0"]  # https://github.com/Project-MONAI/MONAI/issues/7434
tensorboardX = ["tensorboardX"]
tifffile = ["tifffile; platform_system == 'Linux' or platform_system == 'Darwin'"]
torchio = ["torchio"]
torchvision = ["torchvision"]
tqdm = ["tqdm>=4.47.0"]
transformers = ["transformers>=4.53.0, <5.0"]  # 5.x references torch.float8_e8m0fnu absent in older PyTorch builds
zarr = ["zarr"]
# these dependencies are for testing/building only, they aren't needed for regular use so don't appear in "all"
testing = [
  "black>=26.3.1",
  "coverage>=5.5",
  "isort>=5.1,<6,!=6.0.0",
  "mccabe",
  "packaging",
  "parameterized",
  "pep8-naming",
  "pre-commit",
  "pycodestyle",
  "pyflakes",
  "pyrefly>=1.0.0",
  "ruff>=0.14.11,<0.15",
  "tomli",  # used in print_dependencies.py for Python<3.11
  "typeguard<3",  # https://github.com/microsoft/nni/issues/5457
  "types-PyYAML",
  "types-setuptools"
]

[tool.setuptools]
license-files = ["LICENSE"]

[tool.setuptools.dynamic]
version = {attr = "monai.__version__"}

[tool.versioneer]
VCS = "git"
style = "pep440"
versionfile_source = "monai/_version.py"
versionfile_build = "monai/_version.py"
tag_prefix = ""
parentdir_prefix = ""

[tool.isort]
known_first_party = ["monai"]
profile = "black"
line_length = 120
skip = [".git", ".eggs", "venv", ".venv", "versioneer.py", "_version.py", "conf.py", "monai/__init__.py"]
skip_glob = ["*.pyi"]
add_imports = ["from __future__ import annotations"]
append_only = true

[tool.mypy]
ignore_missing_imports = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = false
warn_return_any = true
strict_equality = true
show_column_numbers = true
show_error_codes = true
pretty = false
warn_unused_configs = true
extra_checks = true
exclude = ["venv/"]

[[tool.mypy.overrides]]
module = ["versioneer", "monai._version", "monai.eggs"]
ignore_errors = true

[[tool.mypy.overrides]]
module = ["monai.*"]
check_untyped_defs = true
disallow_untyped_decorators = true

[[tool.mypy.overrides]]
module = [
  "monai._extensions.*",
  "monai.apps.*",
  "monai.auto3dseg.*",
  "monai.bundle.*",
  "monai.config.*",
  "monai.engines.*",
  "monai.fl.*",
  "monai.handlers.*",
  "monai.inferers.*",
  "monai.losses.*",
  "monai.metrics.*",
  "monai.optimizers.*",
  "monai.utils.*",
  "monai.visualize.*"
]
disallow_incomplete_defs = true

[tool.coverage.run]
concurrency = ["multiprocessing"]
source = ["."]
data_file = ".coverage/.coverage"
omit = ["setup.py"]

[tool.coverage.report]
exclude_lines = [
  "pragma: no cover",
  "if TYPE_CHECKING:",
  "raise NotImplementedError",
  "if __name__ == .__main__.:",
]
show_missing = true
skip_covered = true

[tool.coverage.xml]
output = "coverage.xml"

[tool.black]
line-length = 120
target-version = ['py310']
skip-magic-trailing-comma = true
include = '\.pyi?$'
exclude = '''
(
  /(
    # exclude a few common directories in the root of the project
      \.eggs
    | \.git
    | \.hg
    | \.tox
    | \.venv
    | \.mypy_cache
    | \.pytype
    | venv
    | _build
    | buck-out
    | build
    | dist
  )/
  # also separately exclude a file named versioneer.py
  | versioneer.py
  | monai/_version.py
)
'''

[tool.pycln]
all = true
exclude = "monai/bundle/__main__.py"

[tool.ruff]
line-length = 120
target-version = "py310"

[tool.ruff.lint]
select = [
  "B",  # flake8-bugbear - https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
  "C90",  # mccabe (complexity) - https://docs.astral.sh/ruff/rules/#mccabe-c90
  "E",  # pycodestyle errors - https://docs.astral.sh/ruff/rules/#error-e
  "F",  # pyflakes - https://docs.astral.sh/ruff/rules/#pyflakes-f
  "N",  # pep8-naming - https://docs.astral.sh/ruff/rules/#pep8-naming-n
  "PIE",  # flake8-pie - https://docs.astral.sh/ruff/rules/#flake8-pie-pie
  "TID", # flake8-tidy-imports - https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
  "W",  # pycodestyle warnings - https://docs.astral.sh/ruff/rules/#warning-w
  "NPY",         # NumPy specific rules
  "UP",          # pyupgrade
  "RUF100",      # aka yesqa
]
extend-ignore = [
  "E741", # ambiguous variable name
  "F401", # unused import
  "NPY002", # numpy-legacy-random
  "E203", # whitespace before ':' (pycodestyle)
  "E501", # line too long (pycodestyle)
  "C408", # unnecessary collection call (flake8-comprehensions)
  "N812", # lowercase imported as non lowercase (pep8-naming)
  "B023", # function uses loop variable (flake8-bugbear)
  "B905", # zip() without an explicit strict= parameter (flake8-bugbear)
  "B028", # no explicit stacklevel keyword argument found (flake8-bugbear)
]

[tool.ruff.lint.per-file-ignores]
"tests/**" = [
  "B018",
  "C901",
  "N999",
  "N801"
]
"monai/apps/detection/utils/ATSS_matcher.py" = [
  "N999"
]

[tool.ruff.lint.mccabe]
max-complexity = 50  # todo lower this treshold when yesqa id replaced with Ruff's RUF100

[tool.pytype]
# Space-separated list of files or directories to exclude.
exclude = ["versioneer.py", "_version.py"]
# Space-separated list of files or directories to process.
inputs = ["monai"]
# Keep going past errors to analyze as many files as possible.
keep_going = true
# Run N jobs in parallel.
jobs = 8
# All pytype output goes here.
output = ".pytype"
# Paths to source code directories, separated by ':'.
pythonpath = "."
# Check attribute values against their annotations.
check_attribute_types = true
# Check container mutations against their annotations.
check_container_types = true
# Check parameter defaults and assignments against their annotations.
check_parameter_types = true
# Check variable values against their annotations.
check_variable_types = true
# Comma or space separated list of error names to ignore.
disable = ["pyi-error"]
# Report errors.
report_errors = true
# Experimental: Infer precise return types even for invalid function calls.
precise_return = true
# Experimental: solve unknown types to label with structural types.
protocols = true
# Experimental: Only load submodules that are explicitly imported.
strict_import = false

[tool.pyrefly]
# Check only the monai package
project-includes = ["monai/"]

# Exclude auto-generated and vendored files
project-excludes = [
    "**/venv/**",
    "**/.venv/**",
    "versioneer.py",
    "monai/_version.py",
]

# Match CI environment
python-version = "3.10"
python-platform = "linux"

# "legacy" preset provides a smooth migration from previous type checkers
preset = "legacy"

# Check unannotated defs (previously enforced in mypy config)
check-unannotated-defs = true

[tool.pyrefly.errors]
# Ignore missing imports
missing-import = "ignore"

# Suppress unused-ignore warnings
unused-ignore = "ignore"

# Suppress implicit-import globally (MONAI style uses lazy imports)
implicit-import = "ignore"

# Downgrade errors in unannotated/dynamic code to warnings
# (pre-existing issues, not new — will fix incrementally)
bad-assignment = "warn"
bad-return = "warn"
bad-argument-type = "warn"
invalid-annotation = "ignore"
not-iterable = "warn"
not-callable = "warn"
bad-index = "warn"

# Pre-existing errors not flagged by previous type checkers
# Suppress for a smooth migration; fix incrementally
missing-attribute = "ignore"
bad-override = "ignore"
no-matching-overload = "ignore"
unsupported-operation = "ignore"
unnecessary-type-conversion = "ignore"
missing-module-attribute = "ignore"
not-a-type = "ignore"
invalid-yield = "ignore"
deprecated = "ignore"