pyproject.toml

[build-system]
requires = ["setuptools>=77", "wheel", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "konfai"
dynamic = ["version"]
description = "A declarative execution engine for reproducible medical-imaging workflows"
readme = "README.md"
license = "Apache-2.0"
license-files = ["LICENSE"]
requires-python = ">=3.11"

authors = [
  { name = "Valentin Boussot", email = "boussot.v@gmail.com" }
]

keywords = ["deep learning", "medical imaging", "workflow", "streaming", "YAML", "PyTorch", "reproducibility"]

classifiers = [
  "Development Status :: 4 - Beta",
  "Intended Audience :: Science/Research",
  "Operating System :: OS Independent",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
  "Topic :: Scientific/Engineering :: Medical Science Apps.",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
]

dependencies = [
  # 2.3 is the first torch with the unsigned dtypes: a uint16 store (what microscopy writes) reaches
  # torch.from_numpy on the read route, and torch.uint16 is named where a label map's sign is read.
  # 2.5 is the first with torch.serialization.safe_globals, which konfai_apps.bundle loads a run's checkpoint under.
  "torch>=2.5",
  "tqdm",
  # 2.0: np._core and np.dtypes, the numpy types konfai_apps.bundle lets through for a checkpoint's numpy scalars.
  "numpy>=2",
  "ruamel.yaml",
  "psutil",
  # Published weights (apps) are .safetensors: read and written without pickle.
  "safetensors"
]

[project.urls]
Homepage = "https://github.com/fideus-labs/KonfAI"
Repository = "https://github.com/fideus-labs/KonfAI"
Issues = "https://github.com/fideus-labs/KonfAI/issues"
License = "https://www.apache.org/licenses/LICENSE-2.0"

[project.scripts]
konfai = "konfai.main:main"
konfai-cluster = "konfai.main:cluster"

[project.optional-dependencies]
itk = ["SimpleITK>=2.0"]
hdf5 = ["h5py"]
monitoring = ["nvidia-ml-py"]
tensorboard = ["tensorboard"]
imaging = ["SimpleITK>=2.0", "h5py", "pydicom", "zarr>=3", "ngff-zarr>=0.49", "dask"]
vtk = ["vtk"]
lpips = ["lpips"]
smp = ["segmentation-models-pytorch"]
cluster = ["submitit"]
dicom = ["pydicom"]
omezarr = ["zarr>=3", "ngff-zarr>=0.49", "dask"]
# Reading a dataset root from S3: s3fs is the fsspec implementation, aiohttp the transport
# aiobotocore drives it over. fsspec itself already comes with the OME-Zarr extra, through dask.
s3 = ["s3fs", "aiohttp"]
export = ["onnx", "onnxruntime", "onnxscript"]
# `konfai <WORKFLOW> --check`: a config against its JSON Schema (konfai.config_schema.config_errors).
check = ["jsonschema"]
# MONAI Bundles (konfai.bundle) and the MONAI networks the docs wrap (monai.networks.nets:UNet).
monai = ["monai"]
all = [
  "konfai[itk]",
  "konfai[hdf5]",
  "konfai[monitoring]",
  "konfai[tensorboard]",
  "konfai[vtk]",
  "konfai[lpips]",
  "konfai[cluster]",
  "konfai[dicom]",
  "konfai[omezarr]",
  "konfai[s3]",
  "konfai[export]",
  "konfai[check]",
  "konfai[smp]",
  # The IMPACT criteria download their feature extractors from the Hub; imported lazily,
  # and their refusal names this extra.
  "huggingface_hub"
]
dev = [
  "SimpleITK>=2.0",
  "h5py",
  "pydicom",
  "zarr>=3",
  "ngff-zarr[validate]>=0.49",
  "dask",
  "scikit-image",
  "onnx",
  "onnxruntime",
  "onnxscript",
  "jsonschema",
  "nvidia-ml-py",
  "tensorboard",
  "pytest",
  "pytest-cov",
  "pytest-xdist",
  "jsonschema",
  "pre-commit",
  "ruff==0.15.2",
  "mypy",
  "build",
  "types-requests",
  # The docs toolchain: keep in sync with docs/requirements.txt (the RTD list).
  "sphinx>=7.0",
  "shibuya",
  "myst-parser",
  "sphinx-autodoc-typehints",
  "sphinx-copybutton",
  "sphinx-togglebutton",
  "sphinx-tabs",
  "sphinxcontrib-mermaid"
]

[tool.setuptools_scm]
tag_regex = "^v(?P<version>.*)$"
local_scheme = "no-local-version"

[tool.setuptools.packages.find]
# "konfai.*" (with the dot) keeps namespace subpackages such as konfai.models.* while NOT matching
# the sibling "konfai-apps" directory (hyphen), which the old "konfai*" glob wrongly bundled into the
# published wheel. Keep the default namespaces=true so PEP 420 packages (konfai/models) ship.
include = ["konfai", "konfai.*"]
exclude = ["apps*", "konfai-apps*"]

[tool.setuptools.package-data]
# Ship the declarative model catalog (konfai/models/yaml/*.yml) and the PEP 561 marker in the wheel.
"konfai" = ["py.typed"]
"konfai.models.yaml" = ["*.yml"]

[tool.pixi.workspace]
channels = ["conda-forge"]
platforms = ["linux-64", "osx-arm64", "win-64"]

[tool.pixi.pypi-dependencies]
# The dev extra IS the dev environment: one list, so `pixi run check` and CI (`pip install -e
# ".[dev]"`) exercise the same dependencies. Only twine and submitit are pixi-only additions.
konfai = { path = ".", editable = true, extras = ["dev"] }

[tool.pixi.dependencies]
python = ">=3.11,<3.14"
pip = "*"

[tool.pixi.environments]
default = { solve-group = "default" }
dev = { features = ["dev"], solve-group = "default" }
lint = { features = ["lint"], no-default-feature = true, solve-group = "default" }
docs = { features = ["default", "docs"], solve-group = "default" }

# ---------------------------------------------------------------------------
# Feature: dev
# ---------------------------------------------------------------------------
[tool.pixi.feature.dev.pypi-dependencies]
twine = "*"
submitit = "*"

[tool.pixi.feature.dev.tasks]
test = { cmd = "pytest -n auto --dist loadfile tests/", env = { OMP_NUM_THREADS = "1" }, description = "Run the test suite (one torch thread per worker: 8x faster on a 24-core box)" }
test-fast = { cmd = 'pytest -n auto --dist loadfile -m "not slow and not integration" tests/', env = { OMP_NUM_THREADS = "1" }, description = "Run the test suite without slow oracle and integration tests" }
test-apps = { cmd = "pytest konfai-apps/tests", env = { OMP_NUM_THREADS = "1" }, description = "Run the konfai-apps test suite" }
test-cov = { cmd = "pytest -n auto --dist loadfile --cov=konfai --cov-report=term-missing tests/", env = { OMP_NUM_THREADS = "1" }, description = "Run tests with coverage" }
lint = { cmd = "ruff check konfai konfai-apps/konfai_apps konfai-mcp/konfai_mcp konfai-studio/konfai_studio apps tests examples benchmarks docs", description = "Lint source code" }
format = { cmd = "ruff format konfai konfai-apps/konfai_apps konfai-mcp/konfai_mcp konfai-studio/konfai_studio apps tests examples benchmarks docs", description = "Format source code" }
format-check = { cmd = "ruff format --check konfai konfai-apps/konfai_apps konfai-mcp/konfai_mcp konfai-studio/konfai_studio apps tests examples benchmarks docs", description = "Check formatting without modifying files" }
typecheck = { cmd = "python -m mypy konfai konfai-apps/konfai_apps konfai-mcp/konfai_mcp konfai-studio/konfai_studio", description = "Type-check all packages ([tool.mypy] governs; real stubs in use)" }
build = { cmd = "python -m build", description = "Build sdist and wheel" }
perf-check = { cmd = "python benchmarks/perf/perf_check.py", description = "Run the perf series on a quiet machine and compare it to this host's committed baseline (benchmarks/perf/baselines)" }
check = { depends-on = ["lint", "format-check", "test", "test-apps"], description = "Run all quality checks" }

# ---------------------------------------------------------------------------
# Feature: lint
# ---------------------------------------------------------------------------
[tool.pixi.feature.lint.dependencies]
python = ">=3.11,<3.14"

[tool.pixi.feature.lint.pypi-dependencies]
ruff = "==0.15.2"
pre-commit = "*"

[tool.pixi.feature.lint.tasks]
pre-commit-install = { cmd = "pre-commit install --hook-type pre-commit --hook-type commit-msg", description = "Install pre-commit and commit-msg hooks" }
pre-commit-run = { cmd = "pre-commit run --all-files", description = "Run pre-commit hooks on all repository files" }

# ---------------------------------------------------------------------------
# Feature: docs
# ---------------------------------------------------------------------------
[tool.pixi.feature.docs.dependencies]
python = ">=3.11,<3.14"

[tool.pixi.feature.docs.pypi-dependencies]
sphinx = ">=7.0"
shibuya = "*"
myst-parser = "*"
sphinx-autodoc-typehints = "*"
sphinx-copybutton = "*"
sphinx-togglebutton = "*"
sphinx-tabs = "*"
sphinxcontrib-mermaid = "*"

[tool.pixi.feature.docs.tasks]
build-docs = { cmd = "make html", cwd = "docs", description = "Build Sphinx documentation" }
dev-docs = { cmd = "sphinx-autobuild docs/source docs/_build/html", description = "Live-reload docs during development" }

# ---------------------------------------------------------------------------
# Ruff (replaces black + flake8 + isort)
# ---------------------------------------------------------------------------
[tool.ruff]
line-length = 120
src = ["konfai", "konfai-apps/konfai_apps"]
# The demo notebooks are left out: formatting would rewrite the cell layout they were written with.
extend-exclude = ["*.ipynb"]

[tool.ruff.lint]
select = ["E", "F", "W", "B", "I", "UP", "C4", "RUF"]
extend-ignore = ["E501", "B006", "B008"]

# ---------------------------------------------------------------------------
# Pytest
# ---------------------------------------------------------------------------
[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-q"
markers = [
    "slow: marks tests as slow (deselect with -m 'not slow')",
    "integration: marks integration tests",
]
filterwarnings = [
    # SimpleITK's GetImageFromArray/GetArrayViewFromImage assigns array.shape in place
    # (SimpleITK/extra.py), which NumPy 2.5 deprecated: ~1000 copies per heavy file run bury every
    # other warning. Drop this once the SimpleITK floor ships a reshape-based fix.
    "ignore:Setting the shape on a NumPy array has been deprecated:DeprecationWarning:SimpleITK",
]

# ---------------------------------------------------------------------------
# Mypy
# ---------------------------------------------------------------------------
[tool.mypy]
ignore_missing_imports = true
check_untyped_defs = true
# No `python_version`: mypy analyses as the interpreter it runs on, which is the only version whose
# stubs are installed. Pinning it to the floor of `requires-python` makes mypy refuse to parse
# NumPy's stubs (they use `type` statements) and a parse error inside a dependency stops the whole
# analysis. Syntax newer than 3.11 is caught by ruff instead, which infers its target from
# `requires-python` (rule set `UP`).

# ---------------------------------------------------------------------------
# Commitizen
# ---------------------------------------------------------------------------
[tool.commitizen]
name = "cz_conventional_commits"
# The git tag is the only place a version exists -- setuptools_scm derives the package version from
# it, and `scm` makes Commitizen read it from there too. No version string is committed anywhere, so
# none can drift from the tag that built the wheel.
version_provider = "scm"
tag_format = "v$version"
annotated_tag = true
changelog_file = "CHANGELOG.md"
# The changelog IS the release notes: the publish workflow renders one version's section and posts it
# as the GitHub Release body, so a released version is never described in two places that disagree.
update_changelog_on_bump = true

# Conventional Commits' own changelog set: feat, fix, refactor, perf and breaking changes -- what a
# reader of this package gets that they did not have. `docs`, `test`, `ci` and `chore` are out. They
# could be let in, but only by shipping a Commitizen plugin to widen `commit_parser` (a class
# attribute, not a setting), and a package to maintain is a steep price for two more bullet points.
change_type_order = [
    "💥 Breaking changes",
    "✨ Features",
    "🐛 Bug Fixes",
    "⚡ Performance",
    "♻️ Refactoring",
]

[tool.commitizen.change_type_map]
"BREAKING CHANGE" = "💥 Breaking changes"
feat = "✨ Features"
fix = "🐛 Bug Fixes"
perf = "⚡ Performance"
refactor = "♻️ Refactoring"