pyproject.toml

[project]
name = "fl4health"
version = "0.4.2"
description = "Federated Learning for Health"
authors = [
    {name = "Vector AI Engineering", email = "fl4health@vectorinstitute.ai"}
]
license = {text = "Apache-2.0"}
readme = "README.md"
requires-python = ">=3.10.0,<3.11"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
]

dependencies = [
    "numpy>=1.24,<2.0",
    "pandas>=2.0,<3.0",
    "flwr>=1.18.0,<1.19.0",
    "opacus>=1.3.0,<2.0.0",
    "torch==2.6.0",
    "pyarrow>=17.0.0,<18.0.0",  # Pin as there is potential ACE with v0.14.2 that is resolved in v17.0
    "dp-accounting>=0.4.3,<0.5.0",
    "torchmetrics>=1.3.0,<2.0.0",
    "aiohttp>=3.13.3,<4.0.0",
    "ecos>=2.0.7.post1,<3.0.0",
    "qpth>=0.0.16,<0.1.0",
    "urllib3>=2.6.3,<3.0.0",
    "grpcio>=1.60.0,<2.0.0,!=1.64.2,!=1.65.1,!=1.65.2,!=1.65.4",
    "monai>=1.5.1,<2.0.0",
    "nnunetv2>=2.3.1,<3.0.0",
    "wandb>=0.18.0,<1.0.0",
    "acvl_utils==0.2",  # Pin as it was causing an issue with nnunet (ModuleNotFoundError: No module named 'blosc2')
    "scikit-learn==1.5.0",  # Pin as it was causing issues with nnunet
    "peft>=0.14.0,<1.0.0",
    "starlette>=0.49.1,<1.0.0",
    "jupyter-core>=5.8.1,<6.0.0",
    "fastapi>=0.121.0,<1.0.0",
    "tornado>=6.5,<7.0",
    "pympler>=1.1,<2.0",
    "flwr-datasets>=0.5.0,<1.0.0",
    "dm-tree>=0.1.9,<0.2.0",
    "cmake>=3.31.6,<4.0.0",
    "matplotlib>=3.10.1,<4.0.0",
    "pyasn1>=0.6.2",
]

[dependency-groups]
dev = [
    # locked the 2.15 version because of restrictions with tensorflow-io
    # (see https://pypi.org/project/tensorflow-io/ section "TensorFlow Version Compatibility")
    # Note: tensorflow 2.15 requires keras<2.16
    # SECURITY NOTE: keras 2.15.0 has known CVEs (CVE-2024-55459, CVE-2025-9906, CVE-2025-12058, CVE-2025-12060)
    # that require keras>=3.12.0 to fix. However, upgrading requires tensorflow>=2.16 which breaks tensorflow-io
    # compatibility. These CVEs are accepted risk until tensorflow-io supports newer tensorflow versions.
    "tensorflow>=2.15,<2.16",
    "keras>=2.15.0,<2.16",
    "nltk>=3.8.0,<4.0.0",
    "torchvision==0.21.0",
    "torchinfo>=1.8.0,<2.0.0",
    "ipykernel>=6.25.1,<7.0.0",
    "pytest-test-groups>=1.2.1,<2.0.0",
    "torchtext>=0.14.1,<1.0.0",
    "torchdata>=0.7.0,<1.0.0",
    "torcheval>=0.0.6,<1.0.0",
    "transformers>=4.37.2,<5.0.0",
    "datasets>=2.17.1,<3.0.0",
]

test = [
    "pytest>=8.3.4,<9.0.0",
    "mock>=5.1.0,<6.0.0",
    "pytest-cov>=4.1.0,<5.0.0",
    "freezegun>=1.4.0,<2.0.0",
    "pytest-asyncio>=0.25.2,<1.0.0",
    "py-cpuinfo>=9.0.0,<10.0.0",
]

codestyle = [
    "ruff>=0.12.1,<1.0.0",
    "pre-commit>=3.0.1,<4.0.0",
    "toml>=0.10.2,<1.0.0",
    "types-requests>=2.28.11.8",
    "types-setuptools>=65.7.0.3",
    "types-protobuf>=4.24.0.4",
    "types-pyyaml>=6.0.12.12",
    "types-six>=1.16.21.9",
    "types-tabulate>=0.9.0.3",
    "types-tqdm>=4.66.0,<5.0.0",
    "pandas-stubs>=2.0.0,<3.0.0",
    "types-mock>=5.1.0,<6.0.0",
    "pip-audit>=2.4,<3.0",
    "cyclonedx-python-lib<6",  # fix to make pip-audit 2.4 work
    "mypy>=1.9.0,<2.0.0",
]

picai = [
    "simpleitk>=2.3.1,<3.0.0",
    "openpyxl>=3.1.2,<4.0.0",
    "picai_eval>=1.4.6,<2.0.0",
    "mlflow>=2.12.2,<4.0.0",
    "fire>=0.6.0,<1.0.0",
    "einops==0.8.0",
]

llm = [
    "trl>=0.14.0,<1.0.0",
    "tiktoken>=0.8.0,<1.0.0",
    "blobfile>=3.0.0,<4.0.0",
    "sentencepiece>=0.2.0,<1.0.0",
    "evaluate>=0.4.3,<1.0.0",
    "py7zr>=0.22.0,<1.0.0",
    "rouge-score>=0.1.2,<1.0.0",
    "deepspeed==0.15.1",
]

docs = [
    "mkdocs>=1.6.0,<2.0.0",
    "mkdocs-material>=9.5.15,<10.0.0",
    "mkdocstrings[python]>=0.24.0,<1.0.0",
    "mkdocs-autorefs>=1.0.1,<2.0.0",
]

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.uv]
default-groups = ["dev", "test", "codestyle"]

[tool.ruff]
include = ["*.py", "pyproject.toml"]
exclude = ["mypy_disallow_legacy_types.py", "*.ipynb", "conf.py"]
line-length = 119

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
docstring-code-format = true

[tool.ruff.lint]
select = [
    "A", # flake8-builtins
    "B", # flake8-bugbear
    "COM", # flake8-commas
    "C4", # flake8-comprehensions
    "RET", # flake8-return
    "SIM", # flake8-simplify
    "ICN", # flake8-import-conventions
    "Q", # flake8-quotes
    "RSE", # flake8-raise
    "D", # pydocstyle
    "E", # pycodestyle
    "F", # pyflakes
    "I", # isort
    "W", # pycodestyle
    "N", # pep8-naming
    "ERA", # eradicate
    "PL", # pylint
    "D213", # Multiline Docstrings start on newline
]
fixable = ["A", "B", "COM", "C4", "RET", "SIM", "ICN", "Q", "RSE", "D", "E", "F", "I", "W", "N", "ERA", "PL", "D213"]
ignore = [
    "B905", # `zip()` without an explicit `strict=` parameter
    "D203", # 1 blank line required before class docstring
    "D205", # 1 blank line required between summary line and description
    "ERA001", # Found commented-out code (too many false positives with math comments)
    "PLR0913", # Too many arguments
    "COM812", # Missing trailing comma
    "A001", # Ignore variable `input` is shadowing a Python builtin
    "A002", # Ignore variable `input` is shadowing a Python builtin in function
    "PLR0915", # Too many statements (> 50)
    "PLR0912", # Too many branches (>12)
    "PLW2901", # `for` loop variable `target` overwritten by assignment target
    "D212", # Multi-line docstring summary should start at the first line
    "D301", # r-strings for docstrings with backslashes
    "D101", # Public class requires documentation. Ignoring since we document our inits
    "D100", # TEMPORARY IGNORE: Ignore module level docstrings requirement
    "D104", # TEMPORARY IGNORE: Ignore package level docstrings requirement
    "D103", # TEMPORARY IGNORE WILL FIX: Undocumented public function
    "D102", # TEMPORARY IGNORE WILL FIX: Undocumented public method
]

# Ignore import violations in all `__init__.py` files.
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402", "F401", "F403", "F811"]
# Ignoring undocumented public functions, public init, magic method, and magic numbers
"tests/*" = ["D103", "D105", "D107", "PLR2004"]
# Ignoring undocumented, public init, magic method, and magic numbers
"research/*" = ["PLR2004", "D105", "D107"]
# Ignoring undocumented public init
"examples/*" = ["D107"]

[tool.ruff.lint.pep8-naming]
ignore-names = ["SimpleITK", "F", "NN"]

[tool.ruff.lint.isort]
lines-after-imports = 2

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.pycodestyle]
max-doc-length = 119

[tool.ruff.lint.flake8-builtins]
strict-checking = false

[tool.pytest.ini_options]
markers = [
    "smoketest: marks tests as smoke tests (deselect with '-m \"not smoketest\"')",
]
asyncio_default_fixture_loop_scope = "session"